def beforeAddingToNetwork(self, net):
MacroNode.beforeAddingToNetwork(self, net)
from WebServices.VisionInterface.WSNodes import wslib
net.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
def beforeAddingToNetwork(self, net):
MacroNode.beforeAddingToNetwork(self, net)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
net.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
def beforeAddingToNetwork(self, net):
MacroNode.beforeAddingToNetwork(self, net)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
net.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory(
"http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
VirtualScreeningCSF_120 = self
from traceback import print_exc
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_121 = self.macroNetwork.ipNode
apply(input_Ports_121.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_121=None
try:
## saving node output Ports ##
output_Ports_122 = self.macroNetwork.opNode
apply(output_Ports_122.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_122.move(217, 330)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_122=None
try:
## saving node PrepareReceptor ##
from Adt.Macro.PrepareReceptor import PrepareReceptor
PrepareReceptor_141 = PrepareReceptor(constrkw={}, name='PrepareReceptor', library=Adt)
self.macroNetwork.addNode(PrepareReceptor_141,115,96)
apply(PrepareReceptor_141.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
Pdb2pqrWS_144 = PrepareReceptor_141.macroNetwork.nodes[2]
Pdb2pqrOpalService_ws_nbcr_net_148 = Pdb2pqrWS_144.macroNetwork.nodes[3]
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['with_ph'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['apbs_input'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName['assign_only'].widget.set(0, run=False)
GetURLFromList_149 = Pdb2pqrWS_144.macroNetwork.nodes[4]
GetURLFromList_149.inputPortByName['ext'].widget.set(r"pqr", run=False)
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_144.macroNetwork.freeze()
Pdb2pqrWS_144.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_145 = Pdb2pqrWS_144.macroNetwork.ipNode
input_Ports_145.outputPorts[1].configure(name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_146 = Pdb2pqrWS_144.macroNetwork.opNode
output_Ports_146.inputPorts[1].configure(singleConnection='auto')
output_Ports_146.inputPorts[2].configure(singleConnection='auto')
output_Ports_146.inputPorts[1].configure(name='UpdateReceptor_receptor_obj')
output_Ports_146.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_144.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_144.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_144.outputPorts[0].configure(name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_144.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_144.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_144.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_144.shrink()
PrepareReceptorWS_151 = PrepareReceptor_141.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_155 = PrepareReceptorWS_151.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName['o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName['v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName['localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName['execPath'].widget.set(r"", run=False)
GetURLFromList_156 = PrepareReceptorWS_151.macroNetwork.nodes[4]
GetURLFromList_156.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
DownloadToFile_157 = PrepareReceptorWS_151.macroNetwork.nodes[5]
DownloadToFile_157.inputPortByName['overwrite'].widget.set(1, run=False)
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_151.macroNetwork.freeze()
PrepareReceptorWS_151.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_152 = PrepareReceptorWS_151.macroNetwork.ipNode
input_Ports_152.outputPorts[1].configure(name='CheckFileFormat_value')
input_Ports_152.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_153 = PrepareReceptorWS_151.macroNetwork.opNode
output_Ports_153.inputPorts[1].configure(singleConnection='auto')
output_Ports_153.inputPorts[2].configure(singleConnection='auto')
output_Ports_153.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj')
output_Ports_153.inputPorts[2].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_151.inputPorts[0].configure(name='CheckFileFormat_value')
PrepareReceptorWS_151.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_151.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_151.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_151.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_151.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptorWS_151.outputPorts[1].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_151.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_151.shrink()
## saving connections for network PrepareReceptor ##
PrepareReceptor_141.macroNetwork.freeze()
PrepareReceptor_141.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_142 = PrepareReceptor_141.macroNetwork.ipNode
input_Ports_142.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_142.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_143 = PrepareReceptor_141.macroNetwork.opNode
output_Ports_143.inputPorts[1].configure(singleConnection='auto')
output_Ports_143.inputPorts[2].configure(singleConnection='auto')
output_Ports_143.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_143.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_141.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_141.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_141.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_141.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptor_141.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_141.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptor_141.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_141.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptor_141.shrink()
apply(PrepareReceptor_141.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore PrepareReceptor named PrepareReceptor in network self.macroNetwork"
print_exc()
PrepareReceptor_141=None
try:
## saving node ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_159 = ComputeGrids(constrkw={}, name='ComputeGrids', library=Adt)
self.macroNetwork.addNode(ComputeGrids_159,136,207)
apply(ComputeGrids_159.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
prepareGPF_kryptonite_nbcr_net_163 = ComputeGrids_159.macroNetwork.nodes[3]
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['filter_file_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['p'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['o'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['v'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['execPath'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_164 = ComputeGrids_159.macroNetwork.nodes[4]
autogrid_kryptonite_nbcr_net_164.inputPortByName['infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['l'].widget.set(r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['o'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['p'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['execPath'].widget.set(r"", run=False)
GetURLFromList_167 = ComputeGrids_159.macroNetwork.nodes[7]
GetURLFromList_167.inputPortByName['ext'].widget.set(r"gpf", run=False)
## saving connections for network ComputeGrids ##
ComputeGrids_159.macroNetwork.freeze()
ComputeGrids_159.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_160 = ComputeGrids_159.macroNetwork.ipNode
input_Ports_160.outputPorts[1].configure(name='GetComputeGridsInputs_ligands')
input_Ports_160.outputPorts[2].configure(name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_160.outputPorts[3].configure(name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_161 = ComputeGrids_159.macroNetwork.opNode
output_Ports_161.inputPorts[1].configure(singleConnection='auto')
output_Ports_161.inputPorts[2].configure(singleConnection='auto')
output_Ports_161.inputPorts[1].configure(name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_161.inputPorts[2].configure(name='GetMainURLFromList_newurl')
ComputeGrids_159.inputPorts[0].configure(name='GetComputeGridsInputs_ligands')
ComputeGrids_159.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_159.inputPorts[1].configure(name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_159.inputPorts[1].configure(datatype='receptor_prepared')
ComputeGrids_159.inputPorts[2].configure(name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_159.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode input ports
ComputeGrids_159.outputPorts[0].configure(name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_159.outputPorts[0].configure(datatype='autogrid_results')
ComputeGrids_159.outputPorts[1].configure(name='GetMainURLFromList_newurl')
ComputeGrids_159.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
ComputeGrids_159.shrink()
apply(ComputeGrids_159.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore ComputeGrids named ComputeGrids in network self.macroNetwork"
print_exc()
ComputeGrids_159=None
try:
## saving node AutodockVsCSF ##
from Adt.Macro.AutodockVsCSF import AutodockVsCSF
AutodockVsCSF_168 = AutodockVsCSF(constrkw={}, name='AutodockVsCSF', library=Adt)
self.macroNetwork.addNode(AutodockVsCSF_168,234,272)
apply(AutodockVsCSF_168.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
autodock_kryptonite_nbcr_net_172 = AutodockVsCSF_168.macroNetwork.nodes[3]
autodock_kryptonite_nbcr_net_172.inputPortByName['ga_run'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['lib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['sched'].widget.set(r"CSF", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175 = AutodockVsCSF_168.macroNetwork.nodes[6]
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName['execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName['localRun'].widget.set(0, run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName['divisor'].widget.set(r"", run=False)
## saving connections for network AutodockVsCSF ##
AutodockVsCSF_168.macroNetwork.freeze()
AutodockVsCSF_168.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_169 = AutodockVsCSF_168.macroNetwork.ipNode
input_Ports_169.outputPorts[1].configure(name='PrepareADVSInputs_ligands')
input_Ports_169.outputPorts[2].configure(name='PrepareADVSInputs_autogrid_results')
input_Ports_169.outputPorts[3].configure(name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_170 = AutodockVsCSF_168.macroNetwork.opNode
output_Ports_170.inputPorts[1].configure(singleConnection='auto')
output_Ports_170.inputPorts[1].configure(name='GetMainURLFromList_newurl')
AutodockVsCSF_168.inputPorts[0].configure(name='PrepareADVSInputs_ligands')
AutodockVsCSF_168.inputPorts[0].configure(datatype='LigandDB')
AutodockVsCSF_168.inputPorts[1].configure(name='PrepareADVSInputs_autogrid_results')
AutodockVsCSF_168.inputPorts[1].configure(datatype='autogrid_results')
AutodockVsCSF_168.inputPorts[2].configure(name='PrepareADVSInputs_dpf_template_obj')
AutodockVsCSF_168.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode input ports
AutodockVsCSF_168.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AutodockVsCSF_168.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
AutodockVsCSF_168.shrink()
apply(AutodockVsCSF_168.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore AutodockVsCSF named AutodockVsCSF in network self.macroNetwork"
print_exc()
AutodockVsCSF_168=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network VirtualScreeningCSF ##
input_Ports_121 = self.macroNetwork.ipNode
if input_Ports_121 is not None and PrepareReceptor_141 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, PrepareReceptor_141, "new", "Pdb2pqrWS_CheckFileFormat_value", blocking=True
, splitratio=[0.70852617526621731, 0.39749336046566702])
except:
print "WARNING: failed to restore connection between input_Ports_121 and PrepareReceptor_141 in network self.macroNetwork"
if PrepareReceptor_141 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptor_141, ComputeGrids_159, "PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj", "GetComputeGridsInputs_receptor_pdbqt", blocking=True
, splitratio=[0.35807693100671723, 0.50862337251735745])
except:
print "WARNING: failed to restore connection between PrepareReceptor_141 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, ComputeGrids_159, "new", "GetComputeGridsInputs_ligands", blocking=True
, splitratio=[0.40102167589221782, 0.6253111040879471])
except:
print "WARNING: failed to restore connection between input_Ports_121 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, AutodockVsCSF_168, "ComputeGrids_GetComputeGridsInputs_ligands", "PrepareADVSInputs_ligands", blocking=True
, splitratio=[0.65260935115862417, 0.64296744661832661])
except:
print "WARNING: failed to restore connection between input_Ports_121 and AutodockVsCSF_168 in network self.macroNetwork"
if ComputeGrids_159 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
ComputeGrids_159, AutodockVsCSF_168, "MakeAutogridResultObj_autogrid_result_obj", "PrepareADVSInputs_autogrid_results", blocking=True
, splitratio=[0.50054097826587762, 0.55954672420260165])
except:
print "WARNING: failed to restore connection between ComputeGrids_159 and AutodockVsCSF_168 in network self.macroNetwork"
if input_Ports_121 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, ComputeGrids_159, "new", "GetComputeGridsInputs_gpf_obj", blocking=True
, splitratio=[0.73607423731241384, 0.54225043834950515])
except:
print "WARNING: failed to restore connection between input_Ports_121 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, AutodockVsCSF_168, "new", "PrepareADVSInputs_dpf_template_obj", blocking=True
, splitratio=[0.24404719659126095, 0.41822006352735946])
except:
print "WARNING: failed to restore connection between input_Ports_121 and AutodockVsCSF_168 in network self.macroNetwork"
if input_Ports_121 is not None and PrepareReceptor_141 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121, PrepareReceptor_141, "new", "PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True
, splitratio=[0.73098254809437191, 0.23999050334763958])
except:
print "WARNING: failed to restore connection between input_Ports_121 and PrepareReceptor_141 in network self.macroNetwork"
output_Ports_122 = self.macroNetwork.opNode
if AutodockVsCSF_168 is not None and output_Ports_122 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVsCSF_168, output_Ports_122, "GetMainURLFromList_newurl", "new", blocking=True
, splitratio=[0.55528494083678659, 0.33476142488031579])
except:
print "WARNING: failed to restore connection between AutodockVsCSF_168 and output_Ports_122 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_121 = self.macroNetwork.ipNode
input_Ports_121.outputPorts[1].configure(name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
input_Ports_121.outputPorts[2].configure(name='ComputeGrids_GetComputeGridsInputs_ligands')
input_Ports_121.outputPorts[3].configure(name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
input_Ports_121.outputPorts[4].configure(name='AutodockVsCSF_PrepareADVSInputs_dpf_template_obj')
input_Ports_121.outputPorts[5].configure(name='PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_122 = self.macroNetwork.opNode
output_Ports_122.inputPorts[1].configure(singleConnection='auto')
output_Ports_122.inputPorts[1].configure(name='AutodockVsCSF_GetMainURLFromList_newurl')
## configure MacroNode input ports
VirtualScreeningCSF_120.inputPorts[0].configure(name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
VirtualScreeningCSF_120.inputPorts[0].configure(datatype='receptor')
VirtualScreeningCSF_120.inputPorts[1].configure(name='ComputeGrids_GetComputeGridsInputs_ligands')
VirtualScreeningCSF_120.inputPorts[1].configure(datatype='LigandDB')
VirtualScreeningCSF_120.inputPorts[2].configure(name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
VirtualScreeningCSF_120.inputPorts[2].configure(datatype='gpf_template')
VirtualScreeningCSF_120.inputPorts[3].configure(name='AutodockVsCSF_PrepareADVSInputs_dpf_template_obj')
VirtualScreeningCSF_120.inputPorts[3].configure(datatype='dpf_template')
VirtualScreeningCSF_120.inputPorts[4].configure(name='PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
VirtualScreeningCSF_120.inputPorts[4].configure(datatype='boolean')
## configure MacroNode output ports
VirtualScreeningCSF_120.outputPorts[0].configure(name='AutodockVsCSF_GetMainURLFromList_newurl')
VirtualScreeningCSF_120.outputPorts[0].configure(datatype='string')
VirtualScreeningCSF_120.shrink()
## reset modifications ##
VirtualScreeningCSF_120.resetTags()
VirtualScreeningCSF_120.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
PrepareSingleLigand_18 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_19 = self.macroNetwork.ipNode
apply(input_Ports_19.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_19 = None
try:
## saving node output Ports ##
output_Ports_20 = self.macroNetwork.opNode
apply(output_Ports_20.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_20 = None
try:
## saving node PrepareLigandSingle_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
PrepareLigandSingle_kryptonite_nbcr_net_21 = FunctionNode(
functionOrString='PrepareLigandSingle_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'A': '',
'C': False,
'B': '',
'ligand': '',
'g': False,
'F': False,
'I': '',
'M': False,
'p': '',
'R': '',
'U': '',
'v': False,
'Z': False,
'localRun': False,
'execPath': '',
'd': ''
},
constrkw={
'functionOrString':
"'PrepareLigandSingle_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'A': '',
'C': False,
'B': '',
'ligand': '',
'g': False,
'F': False,
'I': '',
'M': False,
'p': '',
'R': '',
'U': '',
'v': False,
'Z': False,
'localRun': False,
'execPath': '',
'd': ''
}
},
name='PrepareLigandSingle_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(
PrepareLigandSingle_kryptonite_nbcr_net_21, 217, 92)
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['A'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['C'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['B'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['ligand'].configure, (), {
'defaultValue': None,
'required': True
})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['g'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['F'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['I'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['M'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['p'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['R'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['U'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['v'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['Z'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['localRun'].configure, (),
{'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['execPath'].configure, (),
{'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['d'].configure, (), {'defaultValue': None})
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['A'].widget.configure, (),
{'choices': ('bonds_hydrogens', 'bonds', 'hydrogens')})
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'A'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'C'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'B'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'ligand'].rebindWidget()
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'ligand'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'ligand'].unbindWidget()
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'g'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'F'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'I'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'M'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'p'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'R'].widget.set(r"", run=False)
apply(
PrepareLigandSingle_kryptonite_nbcr_net_21.
inputPortByName['U'].widget.configure, (),
{'choices': ('nphs_lps', 'nphs', 'lps')})
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'U'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'v'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'Z'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'localRun'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'execPath'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName[
'd'].widget.set(r"", run=False)
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named PrepareLigandSingle_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
PrepareLigandSingle_kryptonite_nbcr_net_21 = None
try:
## saving node GetURLFromList ##
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_22 = GetURLFromListNode(constrkw={},
name='GetURLFromList',
library=wslib)
self.macroNetwork.addNode(GetURLFromList_22, 217, 171)
apply(GetURLFromList_22.inputPortByName['urllist'].configure, (),
{'defaultValue': None})
apply(GetURLFromList_22.inputPortByName['ext'].configure, (),
{'defaultValue': None})
GetURLFromList_22.inputPortByName['ext'].widget.set(r"pdbqt",
run=False)
apply(GetURLFromList_22.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore GetURLFromListNode named GetURLFromList in network self.macroNetwork"
print_exc()
GetURLFromList_22 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network PrepareSingleLigand ##
if PrepareLigandSingle_kryptonite_nbcr_net_21 is not None and GetURLFromList_22 is not None:
try:
self.macroNetwork.connectNodes(
PrepareLigandSingle_kryptonite_nbcr_net_21,
GetURLFromList_22,
"result",
"urllist",
blocking=True,
splitratio=[0.32868238447942777, 0.66102005033481848])
except:
print "WARNING: failed to restore connection between PrepareLigandSingle_kryptonite_nbcr_net_21 and GetURLFromList_22 in network self.macroNetwork"
output_Ports_20 = self.macroNetwork.opNode
if GetURLFromList_22 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
GetURLFromList_22,
output_Ports_20,
"url",
"new",
blocking=True,
splitratio=[0.24357139972148803, 0.60352121442381113])
except:
print "WARNING: failed to restore connection between GetURLFromList_22 and output_Ports_20 in network self.macroNetwork"
input_Ports_19 = self.macroNetwork.ipNode
if input_Ports_19 is not None and PrepareLigandSingle_kryptonite_nbcr_net_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
PrepareLigandSingle_kryptonite_nbcr_net_21,
"new",
"ligand",
blocking=True,
splitratio=[0.58130558930809739, 0.62673128127582967])
except:
print "WARNING: failed to restore connection between input_Ports_19 and PrepareLigandSingle_kryptonite_nbcr_net_21 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_19 = self.macroNetwork.ipNode
input_Ports_19.outputPorts[1].configure(
name='PrepareLigandSingle_kryptonite_nbcr_net_ligand')
## modifying MacroOutputNode dynamic ports
output_Ports_20 = self.macroNetwork.opNode
output_Ports_20.inputPorts[1].configure(singleConnection='auto')
output_Ports_20.inputPorts[1].configure(name='GetURLFromList_url')
## configure MacroNode input ports
PrepareSingleLigand_18.inputPorts[0].configure(
name='PrepareLigandSingle_kryptonite_nbcr_net_ligand')
PrepareSingleLigand_18.inputPorts[0].configure(datatype='string')
## configure MacroNode output ports
PrepareSingleLigand_18.outputPorts[0].configure(
name='GetURLFromList_url')
PrepareSingleLigand_18.outputPorts[0].configure(datatype='string')
PrepareSingleLigand_18.shrink()
## reset modifications ##
PrepareSingleLigand_18.resetTags()
PrepareSingleLigand_18.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
LocalLigandDirectory_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(294, 448)
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_2 = None
try:
## saving node Make Zip File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make Zip File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 136, 158)
Make_Zip_File_3.inputPortByName['input_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_name'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MakeZipFileNE named Make Zip File in network self.macroNetwork"
)
print_exc()
Make_Zip_File_3 = None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_4 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_4, 312, 18)
Entry_4.inputPortByName['entry'].configure(
*(), **{'defaultValue': None})
Entry_4.inputPortByName['entry'].widget.set(r"my_ligands.zip",
run=False)
Entry_4.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
)
print_exc()
Entry_4 = None
try:
## saving node LigandDBUpload_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
LigandDBUpload_kryptonite_nbcr_net_5 = FunctionNode(
functionOrString='LigandDBUpload_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
},
constrkw={
'functionOrString': "'LigandDBUpload_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
}
},
name='LigandDBUpload_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(LigandDBUpload_kryptonite_nbcr_net_5,
136, 216)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].rebindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].unbindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].widget.set(0, run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named LigandDBUpload_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
LigandDBUpload_kryptonite_nbcr_net_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 136, 273)
Index_6.inputPortByName['data'].configure(*(),
**{'defaultValue': None})
Index_6.inputPortByName['index'].configure(
*(), **{'defaultValue': None})
Index_6.outputPortByName['data'].configure(
*(), **{'datatype': 'string'})
Index_6.inputPortByName['index'].widget.configure(
*(), **{
'max': 7,
'min': -8
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
Index_6.configure(*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Index named Index in network self.macroNetwork"
)
print_exc()
Index_6 = None
try:
## saving node ReplaceURL ##
from WebServices.VisionInterface.WSNodes import ReplaceURLNode
ReplaceURL_7 = ReplaceURLNode(constrkw={},
name='ReplaceURL',
library=wslib)
self.macroNetwork.addNode(ReplaceURL_7, 328, 327)
ReplaceURL_7.inputPortByName['url'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['newfilename'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['url'].rebindWidget()
ReplaceURL_7.inputPortByName['url'].widget.set(r"", run=False)
ReplaceURL_7.inputPortByName['url'].unbindWidget()
ReplaceURL_7.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore ReplaceURLNode named ReplaceURL in network self.macroNetwork"
)
print_exc()
ReplaceURL_7 = None
try:
## saving node CreateLigandDBObj ##
from Vision.StandardNodes import Generic
CreateLigandDBObj_8 = Generic(constrkw={},
name='CreateLigandDBObj',
library=stdlib)
self.macroNetwork.addNode(CreateLigandDBObj_8, 217, 385)
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligand_lib_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'log_file',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': False,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addOutputPort(
*(), **{
'name': 'ligand_db_obj',
'datatype': 'LigandDB',
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF'
})
code = """def doit(self, ligand_lib_url, log_file):
if log_file == None:
log_file = "ligand_lib_uploads.log"
log_file = os.path.abspath(log_file)
if log_file != None:
from time import strftime
now = strftime("%Y-%m-%d %H:%M:%S")
log_str = '''On ''' + now + ''', you uploaded a ligand library to: \n'''
log_str = log_str + ligand_lib_url + '''\n\n'''
f = open(log_file, '''a''')
f.write(log_str)
print "This ligand library upload has been recorded in " + log_file
from AutoDockTools.VisionInterface.Adt.LigandDB import LigandDB
ligand_db_obj = LigandDB(url_lib=ligand_lib_url)
pass
## to ouput data on port ligand_db_obj use
self.outputData(ligand_db_obj=ligand_db_obj)
"""
CreateLigandDBObj_8.configure(function=code)
CreateLigandDBObj_8.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named CreateLigandDBObj in network self.macroNetwork"
)
print_exc()
CreateLigandDBObj_8 = None
try:
## saving node get_paths ##
from Vision.StandardNodes import Generic
get_paths_9 = Generic(constrkw={},
name='get_paths',
library=stdlib)
self.macroNetwork.addNode(get_paths_9, 136, 105)
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'directory',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'zip_name',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'input_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_name',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_basedir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, directory, zip_name):
input_directory = os.path.abspath(directory)
if not(os.path.exists(input_directory)):
print "ERROR: ligand input directory " + input_directory + " does not exist"
return '''stop'''
output_directory = os.path.abspath('''.''')
output_name = zip_name
output_basedir = zip_name.rstrip('''.zip''')
pass
self.outputData(input_directory=input_directory, output_directory=output_directory, output_name=zip_name, output_basedir=output_basedir)
## to ouput data on port input_directory use
## self.outputData(input_directory=data)
## to ouput data on port output_directory use
## self.outputData(output_directory=data)
## to ouput data on port output_name use
## self.outputData(output_name=data)
## to ouput data on port output_basedir use
## self.outputData(output_basedir=data)
"""
get_paths_9.configure(function=code)
get_paths_9.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named get_paths in network self.macroNetwork"
)
print_exc()
get_paths_9 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network LocalLigandDirectory ##
if Make_Zip_File_3 is not None and LigandDBUpload_kryptonite_nbcr_net_5 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
LigandDBUpload_kryptonite_nbcr_net_5,
"zipfile",
"userlib",
blocking=True,
splitratio=[0.67700056401206909, 0.41786522052018427])
except:
print(
"WARNING: failed to restore connection between Make_Zip_File_3 and LigandDBUpload_kryptonite_nbcr_net_5 in network self.macroNetwork"
)
if LigandDBUpload_kryptonite_nbcr_net_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
LigandDBUpload_kryptonite_nbcr_net_5,
Index_6,
"result",
"data",
blocking=True,
splitratio=[0.27868065815947218, 0.69101010116597561])
except:
print(
"WARNING: failed to restore connection between LigandDBUpload_kryptonite_nbcr_net_5 and Index_6 in network self.macroNetwork"
)
if Index_6 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
ReplaceURL_7,
"data",
"url",
blocking=True,
splitratio=[0.0, 0.50910496731074983])
except:
print(
"WARNING: failed to restore connection between Index_6 and ReplaceURL_7 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
CreateLigandDBObj_8,
"newurl",
"ligand_lib_url",
blocking=True,
splitratio=[0.7375258387145982, 0.34433018843468416])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and CreateLigandDBObj_8 in network self.macroNetwork"
)
output_Ports_2 = self.macroNetwork.opNode
if CreateLigandDBObj_8 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
CreateLigandDBObj_8,
output_Ports_2,
"ligand_db_obj",
"new",
blocking=True,
splitratio=[0.25450332220506922, 0.49254602433654382])
except:
print(
"WARNING: failed to restore connection between CreateLigandDBObj_8 and output_Ports_2 in network self.macroNetwork"
)
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
get_paths_9,
"new",
"directory",
blocking=True,
splitratio=[0.73592256661833422, 0.40050624233195609])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and get_paths_9 in network self.macroNetwork"
)
if Entry_4 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
Entry_4,
get_paths_9,
"string",
"zip_name",
blocking=True,
splitratio=[0.74641701362897139, 0.56047721560743557])
except:
print(
"WARNING: failed to restore connection between Entry_4 and get_paths_9 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"input_directory",
"input_directory",
blocking=True,
splitratio=[0.24975092021298884, 0.59053364249853169])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_name",
"output_name",
blocking=True,
splitratio=[0.44934886807300634, 0.5145630699734256])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_directory",
"output_directory",
blocking=True,
splitratio=[0.65054191214838031, 0.31030412383438832])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
ReplaceURL_7,
"output_basedir",
"newfilename",
blocking=True,
splitratio=[0.5380996717918376, 0.39023381726820411])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and ReplaceURL_7 in network self.macroNetwork"
)
if input_Ports_1 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
CreateLigandDBObj_8,
"new",
"log_file",
blocking=True,
splitratio=[0.49268182912115838, 0.67412763774649975])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and CreateLigandDBObj_8 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
output_Ports_2,
"newurl",
"new",
blocking=True,
splitratio=[0.67446600768034171, 0.74989471765767979])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and output_Ports_2 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='CreateLigandDBObj_log_file')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='CreateLigandDBObj_ligand_db_obj')
output_Ports_2.inputPorts[2].configure(name='ReplaceURL_newurl')
## configure MacroNode input ports
LocalLigandDirectory_0.inputPorts[0].configure(
name='Make_Zip_File_input_directory')
LocalLigandDirectory_0.inputPorts[0].configure(datatype='string')
LocalLigandDirectory_0.inputPorts[1].configure(
name='CreateLigandDBObj_log_file')
LocalLigandDirectory_0.inputPorts[1].configure(datatype='string')
## configure MacroNode output ports
LocalLigandDirectory_0.outputPorts[0].configure(
name='CreateLigandDBObj_ligand_db_obj')
LocalLigandDirectory_0.outputPorts[0].configure(datatype='LigandDB')
LocalLigandDirectory_0.outputPorts[1].configure(
name='ReplaceURL_newurl')
LocalLigandDirectory_0.outputPorts[1].configure(datatype='string')
LocalLigandDirectory_0.shrink()
## reset modifications ##
LocalLigandDirectory_0.resetTags()
LocalLigandDirectory_0.buildOriginalList()
## loading libraries ##
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
try:
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
## saving node FileWithCommandOrdering ##
from Vision.StandardNodes import FileBrowserNE
FileWithCommandOrdering_0 = FileBrowserNE(constrkw={}, name='FileWithCommandOrdering', library=stdlib)
masterNet.addNode(FileWithCommandOrdering_0,30,10)
FileWithCommandOrdering_0.inputPortByName['filename'].widget.set(r"NAMDTeragridGPU_0.1_input/order.txt", run=False)
apply(FileWithCommandOrdering_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
print_exc()
FileWithCommandOrdering_0=None
try:
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
VirtualScreening_0 = self
from traceback import print_exc
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_2.move(217, 346)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node PrepareReceptor ##
from Adt.Macro.PrepareReceptor import PrepareReceptor
PrepareReceptor_3 = PrepareReceptor(constrkw={}, name='PrepareReceptor', library=Adt)
self.macroNetwork.addNode(PrepareReceptor_3,96,114)
apply(PrepareReceptor_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
Pdb2pqrWS_6 = PrepareReceptor_3.macroNetwork.nodes[2]
Pdb2pqrOpalService_ws_nbcr_net_10 = Pdb2pqrWS_6.macroNetwork.nodes[3]
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['with_ph'].widget.set(r"", run=False)
apply(Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['forcefield'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['apbs_input'].widget.set(0, run=False)
apply(Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['ffout'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['assign_only'].widget.set(0, run=False)
GetURLFromList_11 = Pdb2pqrWS_6.macroNetwork.nodes[4]
GetURLFromList_11.inputPortByName['ext'].widget.set(r"pqr", run=False)
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_6.macroNetwork.freeze()
Pdb2pqrWS_6.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_7 = Pdb2pqrWS_6.macroNetwork.ipNode
input_Ports_7.outputPorts[1].configure(name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_8 = Pdb2pqrWS_6.macroNetwork.opNode
output_Ports_8.inputPorts[1].configure(singleConnection='auto')
output_Ports_8.inputPorts[2].configure(singleConnection='auto')
output_Ports_8.inputPorts[1].configure(name='UpdateReceptor_receptor_obj')
output_Ports_8.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_6.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_6.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_6.outputPorts[0].configure(name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_6.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_6.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_6.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_6.shrink()
PrepareReceptorWS_13 = PrepareReceptor_3.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_17 = PrepareReceptorWS_13.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName['o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName['v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName['localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName['execPath'].widget.set(r"", run=False)
GetURLFromList_18 = PrepareReceptorWS_13.macroNetwork.nodes[4]
GetURLFromList_18.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
DownloadToFile_19 = PrepareReceptorWS_13.macroNetwork.nodes[5]
DownloadToFile_19.inputPortByName['overwrite'].widget.set(1, run=False)
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_13.macroNetwork.freeze()
PrepareReceptorWS_13.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_14 = PrepareReceptorWS_13.macroNetwork.ipNode
input_Ports_14.outputPorts[1].configure(name='CheckFileFormat_value')
input_Ports_14.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_15 = PrepareReceptorWS_13.macroNetwork.opNode
output_Ports_15.inputPorts[1].configure(singleConnection='auto')
output_Ports_15.inputPorts[2].configure(singleConnection='auto')
output_Ports_15.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj')
output_Ports_15.inputPorts[2].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_13.inputPorts[0].configure(name='CheckFileFormat_value')
PrepareReceptorWS_13.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_13.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_13.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_13.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_13.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptorWS_13.outputPorts[1].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_13.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_13.shrink()
## saving connections for network PrepareReceptor ##
PrepareReceptor_3.macroNetwork.freeze()
PrepareReceptor_3.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_4 = PrepareReceptor_3.macroNetwork.ipNode
input_Ports_4.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_4.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_5 = PrepareReceptor_3.macroNetwork.opNode
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[2].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_5.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_3.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_3.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_3.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_3.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptor_3.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_3.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptor_3.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_3.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptor_3.shrink()
apply(PrepareReceptor_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore PrepareReceptor named PrepareReceptor in network self.macroNetwork"
print_exc()
PrepareReceptor_3=None
try:
## saving node ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_21 = ComputeGrids(constrkw={}, name='ComputeGrids', library=Adt)
self.macroNetwork.addNode(ComputeGrids_21,187,205)
apply(ComputeGrids_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
prepareGPF_kryptonite_nbcr_net_25 = ComputeGrids_21.macroNetwork.nodes[3]
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['filter_file_url'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_25.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['p'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['o'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['v'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['execPath'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_26 = ComputeGrids_21.macroNetwork.nodes[4]
autogrid_kryptonite_nbcr_net_26.inputPortByName['infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['l'].widget.set(r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['o'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['p'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['execPath'].widget.set(r"", run=False)
GetURLFromList_29 = ComputeGrids_21.macroNetwork.nodes[7]
GetURLFromList_29.inputPortByName['ext'].widget.set(r"gpf", run=False)
## saving connections for network ComputeGrids ##
ComputeGrids_21.macroNetwork.freeze()
ComputeGrids_21.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_22 = ComputeGrids_21.macroNetwork.ipNode
input_Ports_22.outputPorts[1].configure(name='GetComputeGridsInputs_ligands')
input_Ports_22.outputPorts[2].configure(name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_22.outputPorts[3].configure(name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_23 = ComputeGrids_21.macroNetwork.opNode
output_Ports_23.inputPorts[1].configure(singleConnection='auto')
output_Ports_23.inputPorts[2].configure(singleConnection='auto')
output_Ports_23.inputPorts[1].configure(name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_23.inputPorts[2].configure(name='GetMainURLFromList_newurl')
ComputeGrids_21.inputPorts[0].configure(name='GetComputeGridsInputs_ligands')
ComputeGrids_21.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_21.inputPorts[1].configure(name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_21.inputPorts[1].configure(datatype='receptor_prepared')
ComputeGrids_21.inputPorts[2].configure(name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_21.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode input ports
ComputeGrids_21.outputPorts[0].configure(name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_21.outputPorts[0].configure(datatype='autogrid_results')
ComputeGrids_21.outputPorts[1].configure(name='GetMainURLFromList_newurl')
ComputeGrids_21.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
ComputeGrids_21.shrink()
apply(ComputeGrids_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore ComputeGrids named ComputeGrids in network self.macroNetwork"
print_exc()
ComputeGrids_21=None
try:
## saving node AutodockVS ##
from Adt.Macro.AutodockVS import AutodockVS
AutodockVS_30 = AutodockVS(constrkw={}, name='AutodockVS', library=Adt)
self.macroNetwork.addNode(AutodockVS_30,234,289)
apply(AutodockVS_30.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
autodock_kryptonite_nbcr_net_34 = AutodockVS_30.macroNetwork.nodes[3]
autodock_kryptonite_nbcr_net_34.inputPortByName['ga_run'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_34.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
autodock_kryptonite_nbcr_net_34.inputPortByName['lib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['ga_num_evals'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_34.inputPortByName['sched'].widget.configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_34.inputPortByName['sched'].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName['execPath'].widget.set(r"", run=False)
## saving connections for network AutodockVS ##
AutodockVS_30.macroNetwork.freeze()
AutodockVS_30.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_31 = AutodockVS_30.macroNetwork.ipNode
input_Ports_31.outputPorts[1].configure(name='PrepareADVSInputs_ligands')
input_Ports_31.outputPorts[2].configure(name='PrepareADVSInputs_autogrid_results')
input_Ports_31.outputPorts[3].configure(name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_32 = AutodockVS_30.macroNetwork.opNode
output_Ports_32.inputPorts[1].configure(singleConnection='auto')
output_Ports_32.inputPorts[1].configure(name='GetMainURLFromList_newurl')
AutodockVS_30.inputPorts[0].configure(name='PrepareADVSInputs_ligands')
AutodockVS_30.inputPorts[0].configure(datatype='LigandDB')
AutodockVS_30.inputPorts[1].configure(name='PrepareADVSInputs_autogrid_results')
AutodockVS_30.inputPorts[1].configure(datatype='autogrid_results')
AutodockVS_30.inputPorts[2].configure(name='PrepareADVSInputs_dpf_template_obj')
AutodockVS_30.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode input ports
AutodockVS_30.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AutodockVS_30.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
AutodockVS_30.shrink()
apply(AutodockVS_30.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore AutodockVS named AutodockVS in network self.macroNetwork"
print_exc()
AutodockVS_30=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network VirtualScreening ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and PrepareReceptor_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareReceptor_3, "new", "Pdb2pqrWS_CheckFileFormat_value", blocking=True
, splitratio=[0.73953989601548642, 0.35343455296743803])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptor_3 in network self.macroNetwork"
if input_Ports_1 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, ComputeGrids_21, "new", "GetComputeGridsInputs_ligands", blocking=True
, splitratio=[0.46529144721861959, 0.40210922169933605])
except:
print "WARNING: failed to restore connection between input_Ports_1 and ComputeGrids_21 in network self.macroNetwork"
if input_Ports_1 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, AutodockVS_30, "ComputeGrids_GetComputeGridsInputs_ligands", "PrepareADVSInputs_ligands", blocking=True
, splitratio=[0.48337865988456058, 0.41105508936996049])
except:
print "WARNING: failed to restore connection between input_Ports_1 and AutodockVS_30 in network self.macroNetwork"
if PrepareReceptor_3 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptor_3, ComputeGrids_21, "PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj", "GetComputeGridsInputs_receptor_pdbqt", blocking=True
, splitratio=[0.32656364590133868, 0.43316260938324158])
except:
print "WARNING: failed to restore connection between PrepareReceptor_3 and ComputeGrids_21 in network self.macroNetwork"
if ComputeGrids_21 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
ComputeGrids_21, AutodockVS_30, "MakeAutogridResultObj_autogrid_result_obj", "PrepareADVSInputs_autogrid_results", blocking=True
, splitratio=[0.25195726140883218, 0.37435524480319915])
except:
print "WARNING: failed to restore connection between ComputeGrids_21 and AutodockVS_30 in network self.macroNetwork"
if input_Ports_1 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, ComputeGrids_21, "new", "GetComputeGridsInputs_gpf_obj", blocking=True
, splitratio=[0.3610566319618409, 0.20507643166097597])
except:
print "WARNING: failed to restore connection between input_Ports_1 and ComputeGrids_21 in network self.macroNetwork"
if input_Ports_1 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, AutodockVS_30, "new", "PrepareADVSInputs_dpf_template_obj", blocking=True
, splitratio=[0.41221000935616448, 0.71284031297323347])
except:
print "WARNING: failed to restore connection between input_Ports_1 and AutodockVS_30 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if AutodockVS_30 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVS_30, output_Ports_2, "GetMainURLFromList_newurl", "new", blocking=True
, splitratio=[0.28632220295352073, 0.59933112675886213])
except:
print "WARNING: failed to restore connection between AutodockVS_30 and output_Ports_2 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareReceptor_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareReceptor_3, "new", "PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True
, splitratio=[0.66210822612399844, 0.69280049494960727])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptor_3 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
input_Ports_1.outputPorts[2].configure(name='ComputeGrids_GetComputeGridsInputs_ligands')
input_Ports_1.outputPorts[3].configure(name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
input_Ports_1.outputPorts[4].configure(name='AutodockVS_PrepareADVSInputs_dpf_template_obj')
input_Ports_1.outputPorts[5].configure(name='PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='AutodockVS_GetMainURLFromList_newurl')
## configure MacroNode input ports
VirtualScreening_0.inputPorts[0].configure(name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
VirtualScreening_0.inputPorts[0].configure(datatype='receptor')
VirtualScreening_0.inputPorts[1].configure(name='ComputeGrids_GetComputeGridsInputs_ligands')
VirtualScreening_0.inputPorts[1].configure(datatype='LigandDB')
VirtualScreening_0.inputPorts[2].configure(name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
VirtualScreening_0.inputPorts[2].configure(datatype='gpf_template')
VirtualScreening_0.inputPorts[3].configure(name='AutodockVS_PrepareADVSInputs_dpf_template_obj')
VirtualScreening_0.inputPorts[3].configure(datatype='dpf_template')
VirtualScreening_0.inputPorts[4].configure(name='PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
VirtualScreening_0.inputPorts[4].configure(datatype='boolean')
## configure MacroNode output ports
VirtualScreening_0.outputPorts[0].configure(name='AutodockVS_GetMainURLFromList_newurl')
VirtualScreening_0.outputPorts[0].configure(datatype='string')
VirtualScreening_0.shrink()
## reset modifications ##
VirtualScreening_0.resetTags()
VirtualScreening_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
VirtualScreening_0 = self
from traceback import print_exc
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(217, 346)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node PrepareReceptor ##
from Adt.Macro.PrepareReceptor import PrepareReceptor
PrepareReceptor_3 = PrepareReceptor(constrkw={},
name='PrepareReceptor',
library=Adt)
self.macroNetwork.addNode(PrepareReceptor_3, 96, 114)
apply(PrepareReceptor_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
Pdb2pqrWS_6 = PrepareReceptor_3.macroNetwork.nodes[2]
Pdb2pqrOpalService_ws_nbcr_net_10 = Pdb2pqrWS_6.macroNetwork.nodes[
3]
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'with_ph'].widget.set(r"", run=False)
apply(
Pdb2pqrOpalService_ws_nbcr_net_10.
inputPortByName['forcefield'].widget.configure, (),
{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'apbs_input'].widget.set(0, run=False)
apply(
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName['ffout'].
widget.configure, (),
{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_10.inputPortByName[
'assign_only'].widget.set(0, run=False)
GetURLFromList_11 = Pdb2pqrWS_6.macroNetwork.nodes[4]
GetURLFromList_11.inputPortByName['ext'].widget.set(r"pqr",
run=False)
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_6.macroNetwork.freeze()
Pdb2pqrWS_6.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_7 = Pdb2pqrWS_6.macroNetwork.ipNode
input_Ports_7.outputPorts[1].configure(
name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_8 = Pdb2pqrWS_6.macroNetwork.opNode
output_Ports_8.inputPorts[1].configure(singleConnection='auto')
output_Ports_8.inputPorts[2].configure(singleConnection='auto')
output_Ports_8.inputPorts[1].configure(
name='UpdateReceptor_receptor_obj')
output_Ports_8.inputPorts[2].configure(
name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_6.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_6.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_6.outputPorts[0].configure(
name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_6.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_6.outputPorts[1].configure(
name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_6.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_6.shrink()
PrepareReceptorWS_13 = PrepareReceptor_3.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_17 = PrepareReceptorWS_13.macroNetwork.nodes[
3]
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName[
'o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName[
'v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName[
'localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_17.inputPortByName[
'execPath'].widget.set(r"", run=False)
GetURLFromList_18 = PrepareReceptorWS_13.macroNetwork.nodes[4]
GetURLFromList_18.inputPortByName['ext'].widget.set(r"pdbqt",
run=False)
DownloadToFile_19 = PrepareReceptorWS_13.macroNetwork.nodes[5]
DownloadToFile_19.inputPortByName['overwrite'].widget.set(
1, run=False)
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_13.macroNetwork.freeze()
PrepareReceptorWS_13.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_14 = PrepareReceptorWS_13.macroNetwork.ipNode
input_Ports_14.outputPorts[1].configure(
name='CheckFileFormat_value')
input_Ports_14.outputPorts[2].configure(
name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_15 = PrepareReceptorWS_13.macroNetwork.opNode
output_Ports_15.inputPorts[1].configure(singleConnection='auto')
output_Ports_15.inputPorts[2].configure(singleConnection='auto')
output_Ports_15.inputPorts[1].configure(
name='UpdateReceptor_receptor_prepared_obj')
output_Ports_15.inputPorts[2].configure(
name='UpdateReceptor_receptor_result')
PrepareReceptorWS_13.inputPorts[0].configure(
name='CheckFileFormat_value')
PrepareReceptorWS_13.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_13.inputPorts[1].configure(
name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_13.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_13.outputPorts[0].configure(
name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_13.outputPorts[0].configure(
datatype='receptor_prepared')
PrepareReceptorWS_13.outputPorts[1].configure(
name='UpdateReceptor_receptor_result')
PrepareReceptorWS_13.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_13.shrink()
## saving connections for network PrepareReceptor ##
PrepareReceptor_3.macroNetwork.freeze()
PrepareReceptor_3.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_4 = PrepareReceptor_3.macroNetwork.ipNode
input_Ports_4.outputPorts[1].configure(
name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_4.outputPorts[2].configure(
name=
'PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_5 = PrepareReceptor_3.macroNetwork.opNode
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[2].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_5.inputPorts[2].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_3.inputPorts[0].configure(
name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_3.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_3.inputPorts[1].configure(
name=
'PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_3.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptor_3.outputPorts[0].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_3.outputPorts[0].configure(
datatype='receptor_prepared')
PrepareReceptor_3.outputPorts[1].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_3.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptor_3.shrink()
apply(PrepareReceptor_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore PrepareReceptor named PrepareReceptor in network self.macroNetwork"
print_exc()
PrepareReceptor_3 = None
try:
## saving node ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_21 = ComputeGrids(constrkw={},
name='ComputeGrids',
library=Adt)
self.macroNetwork.addNode(ComputeGrids_21, 187, 205)
apply(ComputeGrids_21.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
prepareGPF_kryptonite_nbcr_net_25 = ComputeGrids_21.macroNetwork.nodes[
3]
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
apply(
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['lib'].
widget.configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['p'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['o'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName['v'].widget.set(
0, run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_25.inputPortByName[
'execPath'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_26 = ComputeGrids_21.macroNetwork.nodes[
4]
autogrid_kryptonite_nbcr_net_26.inputPortByName[
'infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['l'].widget.set(
r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['o'].widget.set(
0, run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName['p'].widget.set(
r"", run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName[
'localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_26.inputPortByName[
'execPath'].widget.set(r"", run=False)
GetURLFromList_29 = ComputeGrids_21.macroNetwork.nodes[7]
GetURLFromList_29.inputPortByName['ext'].widget.set(r"gpf",
run=False)
## saving connections for network ComputeGrids ##
ComputeGrids_21.macroNetwork.freeze()
ComputeGrids_21.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_22 = ComputeGrids_21.macroNetwork.ipNode
input_Ports_22.outputPorts[1].configure(
name='GetComputeGridsInputs_ligands')
input_Ports_22.outputPorts[2].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_22.outputPorts[3].configure(
name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_23 = ComputeGrids_21.macroNetwork.opNode
output_Ports_23.inputPorts[1].configure(singleConnection='auto')
output_Ports_23.inputPorts[2].configure(singleConnection='auto')
output_Ports_23.inputPorts[1].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_23.inputPorts[2].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_21.inputPorts[0].configure(
name='GetComputeGridsInputs_ligands')
ComputeGrids_21.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_21.inputPorts[1].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_21.inputPorts[1].configure(
datatype='receptor_prepared')
ComputeGrids_21.inputPorts[2].configure(
name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_21.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode input ports
ComputeGrids_21.outputPorts[0].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_21.outputPorts[0].configure(
datatype='autogrid_results')
ComputeGrids_21.outputPorts[1].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_21.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
ComputeGrids_21.shrink()
apply(ComputeGrids_21.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore ComputeGrids named ComputeGrids in network self.macroNetwork"
print_exc()
ComputeGrids_21 = None
try:
## saving node AutodockVS ##
from Adt.Macro.AutodockVS import AutodockVS
AutodockVS_30 = AutodockVS(constrkw={},
name='AutodockVS',
library=Adt)
self.macroNetwork.addNode(AutodockVS_30, 234, 289)
apply(AutodockVS_30.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
autodock_kryptonite_nbcr_net_34 = AutodockVS_30.macroNetwork.nodes[
3]
autodock_kryptonite_nbcr_net_34.inputPortByName[
'ga_run'].widget.set(r"", run=False)
apply(
autodock_kryptonite_nbcr_net_34.inputPortByName['lib'].widget.
configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
autodock_kryptonite_nbcr_net_34.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
apply(
autodock_kryptonite_nbcr_net_34.inputPortByName['sched'].
widget.configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_34.inputPortByName[
'sched'].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_34.inputPortByName[
'execPath'].widget.set(r"", run=False)
## saving connections for network AutodockVS ##
AutodockVS_30.macroNetwork.freeze()
AutodockVS_30.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_31 = AutodockVS_30.macroNetwork.ipNode
input_Ports_31.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_31.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_31.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_32 = AutodockVS_30.macroNetwork.opNode
output_Ports_32.inputPorts[1].configure(singleConnection='auto')
output_Ports_32.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
AutodockVS_30.inputPorts[0].configure(
name='PrepareADVSInputs_ligands')
AutodockVS_30.inputPorts[0].configure(datatype='LigandDB')
AutodockVS_30.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVS_30.inputPorts[1].configure(datatype='autogrid_results')
AutodockVS_30.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVS_30.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode input ports
AutodockVS_30.outputPorts[0].configure(
name='GetMainURLFromList_newurl')
AutodockVS_30.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
AutodockVS_30.shrink()
apply(AutodockVS_30.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore AutodockVS named AutodockVS in network self.macroNetwork"
print_exc()
AutodockVS_30 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network VirtualScreening ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and PrepareReceptor_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareReceptor_3,
"new",
"Pdb2pqrWS_CheckFileFormat_value",
blocking=True,
splitratio=[0.73953989601548642, 0.35343455296743803])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptor_3 in network self.macroNetwork"
if input_Ports_1 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
ComputeGrids_21,
"new",
"GetComputeGridsInputs_ligands",
blocking=True,
splitratio=[0.46529144721861959, 0.40210922169933605])
except:
print "WARNING: failed to restore connection between input_Ports_1 and ComputeGrids_21 in network self.macroNetwork"
if input_Ports_1 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
AutodockVS_30,
"ComputeGrids_GetComputeGridsInputs_ligands",
"PrepareADVSInputs_ligands",
blocking=True,
splitratio=[0.48337865988456058, 0.41105508936996049])
except:
print "WARNING: failed to restore connection between input_Ports_1 and AutodockVS_30 in network self.macroNetwork"
if PrepareReceptor_3 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptor_3,
ComputeGrids_21,
"PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj",
"GetComputeGridsInputs_receptor_pdbqt",
blocking=True,
splitratio=[0.32656364590133868, 0.43316260938324158])
except:
print "WARNING: failed to restore connection between PrepareReceptor_3 and ComputeGrids_21 in network self.macroNetwork"
if ComputeGrids_21 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
ComputeGrids_21,
AutodockVS_30,
"MakeAutogridResultObj_autogrid_result_obj",
"PrepareADVSInputs_autogrid_results",
blocking=True,
splitratio=[0.25195726140883218, 0.37435524480319915])
except:
print "WARNING: failed to restore connection between ComputeGrids_21 and AutodockVS_30 in network self.macroNetwork"
if input_Ports_1 is not None and ComputeGrids_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
ComputeGrids_21,
"new",
"GetComputeGridsInputs_gpf_obj",
blocking=True,
splitratio=[0.3610566319618409, 0.20507643166097597])
except:
print "WARNING: failed to restore connection between input_Ports_1 and ComputeGrids_21 in network self.macroNetwork"
if input_Ports_1 is not None and AutodockVS_30 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
AutodockVS_30,
"new",
"PrepareADVSInputs_dpf_template_obj",
blocking=True,
splitratio=[0.41221000935616448, 0.71284031297323347])
except:
print "WARNING: failed to restore connection between input_Ports_1 and AutodockVS_30 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if AutodockVS_30 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVS_30,
output_Ports_2,
"GetMainURLFromList_newurl",
"new",
blocking=True,
splitratio=[0.28632220295352073, 0.59933112675886213])
except:
print "WARNING: failed to restore connection between AutodockVS_30 and output_Ports_2 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareReceptor_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareReceptor_3,
"new",
"PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C",
blocking=True,
splitratio=[0.66210822612399844, 0.69280049494960727])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptor_3 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
input_Ports_1.outputPorts[2].configure(
name='ComputeGrids_GetComputeGridsInputs_ligands')
input_Ports_1.outputPorts[3].configure(
name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
input_Ports_1.outputPorts[4].configure(
name='AutodockVS_PrepareADVSInputs_dpf_template_obj')
input_Ports_1.outputPorts[5].configure(
name=
'PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C'
)
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='AutodockVS_GetMainURLFromList_newurl')
## configure MacroNode input ports
VirtualScreening_0.inputPorts[0].configure(
name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
VirtualScreening_0.inputPorts[0].configure(datatype='receptor')
VirtualScreening_0.inputPorts[1].configure(
name='ComputeGrids_GetComputeGridsInputs_ligands')
VirtualScreening_0.inputPorts[1].configure(datatype='LigandDB')
VirtualScreening_0.inputPorts[2].configure(
name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
VirtualScreening_0.inputPorts[2].configure(datatype='gpf_template')
VirtualScreening_0.inputPorts[3].configure(
name='AutodockVS_PrepareADVSInputs_dpf_template_obj')
VirtualScreening_0.inputPorts[3].configure(datatype='dpf_template')
VirtualScreening_0.inputPorts[4].configure(
name=
'PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C'
)
VirtualScreening_0.inputPorts[4].configure(datatype='boolean')
## configure MacroNode output ports
VirtualScreening_0.outputPorts[0].configure(
name='AutodockVS_GetMainURLFromList_newurl')
VirtualScreening_0.outputPorts[0].configure(datatype='string')
VirtualScreening_0.shrink()
## reset modifications ##
VirtualScreening_0.resetTags()
VirtualScreening_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVsCSF_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory(
"http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(183, 363)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_3 = Generic(constrkw={},
name='PrepareADVSInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_3, 217, 76)
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'autogrid_results',
'cast': True,
'datatype': 'autogrid_results',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'dpf_template_obj',
'cast': True,
'datatype': 'dpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#9933FF',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'dpf_template_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'autogrid_res_url',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'autogrid_res_local',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_3.configure(function=code)
apply(PrepareADVSInputs_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
print_exc()
PrepareADVSInputs_3 = None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_4 = FunctionNode(
functionOrString='autodock_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autodock_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
}
},
name='autodock_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_4, 217, 132)
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_run'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.
inputPortByName['filter_file_url'].configure, (),
{'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_evals'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.
inputPortByName['ga_num_generations'].configure, (),
{'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].configure,
(), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['userlib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_pop_size'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['email'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_run'].widget.set(r"", run=False)
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.
configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].unbindWidget()
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.
configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.set(
r"CSF", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].rebindWidget(
)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].unbindWidget(
)
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'utar'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'utar'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['email'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_4.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autodock_kryptonite_nbcr_net_4 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_5 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_5, 217, 188)
apply(GetMainURLFromList_5.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_5.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_5 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_7 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_7, 201, 301)
apply(GetMainURLFromList_7.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_7.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_7 = None
try:
## saving node AutodockSlice_oolitevm_calit2_optiputer_net ##
from NetworkEditor.items import FunctionNode
AutodockSlice_oolitevm_calit2_optiputer_net_8 = FunctionNode(
functionOrString='AutodockSlice_oolitevm_calit2_optiputer_net',
host="http://oolitevm.calit2.optiputer.net/opal2",
namedArgs={
'execPath': '',
'localRun': False,
'divisor': '',
'lib': '',
'input_url': ''
},
constrkw={
'functionOrString':
"'AutodockSlice_oolitevm_calit2_optiputer_net'",
'host': '"http://oolitevm.calit2.optiputer.net/opal2"',
'namedArgs': {
'execPath': '',
'localRun': False,
'divisor': '',
'lib': '',
'input_url': ''
}
},
name='AutodockSlice_oolitevm_calit2_optiputer_net',
library=wslib)
self.macroNetwork.addNode(
AutodockSlice_oolitevm_calit2_optiputer_net_8, 200, 240)
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['execPath'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['localRun'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['divisor'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['lib'].configure, (), {'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['input_url'].configure, (),
{'defaultValue': None})
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'localRun'].widget.set(0, run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'divisor'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].unbindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].unbindWidget()
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.configure, (),
{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named AutodockSlice_oolitevm_calit2_optiputer_net in network self.macroNetwork"
print_exc()
AutodockSlice_oolitevm_calit2_optiputer_net_8 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVsCSF ##
if autodock_kryptonite_nbcr_net_4 is not None and GetMainURLFromList_5 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_4,
GetMainURLFromList_5,
"result",
"urls",
blocking=True,
splitratio=[0.36974288957131424, 0.63465596053596318])
except:
print "WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_4 and GetMainURLFromList_5 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.33230642287344903, 0.65770700108889613])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.50680104599665787, 0.51414170500293577])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"dpf_template_file",
"dpf",
blocking=True,
splitratio=[0.51615646597598808, 0.25661305528484007])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"autogrid_res_url",
"u",
blocking=True,
splitratio=[0.5760732944947704, 0.2032376887917188])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"autogrid_res_local",
"utar",
blocking=True,
splitratio=[0.52802808938949819, 0.66978534572736881])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"ligands",
blocking=True,
splitratio=[0.23314258225660414, 0.72184112037432979])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"autogrid_results",
blocking=True,
splitratio=[0.56916626620432731, 0.43089669830392019])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"dpf_template_obj",
blocking=True,
splitratio=[0.26502286453989665, 0.3911248444502638])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetMainURLFromList_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_7,
output_Ports_2,
"newurl",
"new",
blocking=True,
splitratio=[0.2408747073082603, 0.22897876889044461])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_7 and output_Ports_2 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
AutodockSlice_oolitevm_calit2_optiputer_net_8,
"ligand_lib",
"lib",
blocking=True,
splitratio=[0.36439875698533941, 0.58443612376117082])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if GetMainURLFromList_5 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_5,
AutodockSlice_oolitevm_calit2_optiputer_net_8,
"newurl",
"input_url",
blocking=True,
splitratio=[0.32808833199778697, 0.69237553555389719])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_5 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None and GetMainURLFromList_7 is not None:
try:
self.macroNetwork.connectNodes(
AutodockSlice_oolitevm_calit2_optiputer_net_8,
GetMainURLFromList_7,
"result",
"urls",
blocking=True,
splitratio=[0.69930142895840763, 0.2984777644803871])
except:
print "WARNING: failed to restore connection between AutodockSlice_oolitevm_calit2_optiputer_net_8 and GetMainURLFromList_7 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_1.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_1.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
AutodockVsCSF_0.inputPorts[0].configure(
name='PrepareADVSInputs_ligands')
AutodockVsCSF_0.inputPorts[0].configure(datatype='LigandDB')
AutodockVsCSF_0.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVsCSF_0.inputPorts[1].configure(datatype='autogrid_results')
AutodockVsCSF_0.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVsCSF_0.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode output ports
AutodockVsCSF_0.outputPorts[0].configure(
name='GetMainURLFromList_newurl')
AutodockVsCSF_0.outputPorts[0].configure(datatype='string')
AutodockVsCSF_0.shrink()
## reset modifications ##
AutodockVsCSF_0.resetTags()
AutodockVsCSF_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
VirtualScreeningCSF_120 = self
from traceback import print_exc
from AutoDockTools.VisionInterface.Adt import Adt
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory(
"http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_121 = self.macroNetwork.ipNode
apply(input_Ports_121.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_121 = None
try:
## saving node output Ports ##
output_Ports_122 = self.macroNetwork.opNode
apply(output_Ports_122.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_122.move(217, 330)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_122 = None
try:
## saving node PrepareReceptor ##
from Adt.Macro.PrepareReceptor import PrepareReceptor
PrepareReceptor_141 = PrepareReceptor(constrkw={},
name='PrepareReceptor',
library=Adt)
self.macroNetwork.addNode(PrepareReceptor_141, 115, 96)
apply(PrepareReceptor_141.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
Pdb2pqrWS_144 = PrepareReceptor_141.macroNetwork.nodes[2]
Pdb2pqrOpalService_ws_nbcr_net_148 = Pdb2pqrWS_144.macroNetwork.nodes[
3]
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'with_ph'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'apbs_input'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_148.inputPortByName[
'assign_only'].widget.set(0, run=False)
GetURLFromList_149 = Pdb2pqrWS_144.macroNetwork.nodes[4]
GetURLFromList_149.inputPortByName['ext'].widget.set(r"pqr",
run=False)
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_144.macroNetwork.freeze()
Pdb2pqrWS_144.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_145 = Pdb2pqrWS_144.macroNetwork.ipNode
input_Ports_145.outputPorts[1].configure(
name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_146 = Pdb2pqrWS_144.macroNetwork.opNode
output_Ports_146.inputPorts[1].configure(singleConnection='auto')
output_Ports_146.inputPorts[2].configure(singleConnection='auto')
output_Ports_146.inputPorts[1].configure(
name='UpdateReceptor_receptor_obj')
output_Ports_146.inputPorts[2].configure(
name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_144.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_144.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_144.outputPorts[0].configure(
name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_144.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_144.outputPorts[1].configure(
name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_144.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_144.shrink()
PrepareReceptorWS_151 = PrepareReceptor_141.macroNetwork.nodes[3]
PrepareReceptorOpalService_ws_nbcr_net_155 = PrepareReceptorWS_151.macroNetwork.nodes[
3]
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName[
'o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName[
'v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName[
'localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_155.inputPortByName[
'execPath'].widget.set(r"", run=False)
GetURLFromList_156 = PrepareReceptorWS_151.macroNetwork.nodes[4]
GetURLFromList_156.inputPortByName['ext'].widget.set(r"pdbqt",
run=False)
DownloadToFile_157 = PrepareReceptorWS_151.macroNetwork.nodes[5]
DownloadToFile_157.inputPortByName['overwrite'].widget.set(
1, run=False)
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_151.macroNetwork.freeze()
PrepareReceptorWS_151.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_152 = PrepareReceptorWS_151.macroNetwork.ipNode
input_Ports_152.outputPorts[1].configure(
name='CheckFileFormat_value')
input_Ports_152.outputPorts[2].configure(
name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_153 = PrepareReceptorWS_151.macroNetwork.opNode
output_Ports_153.inputPorts[1].configure(singleConnection='auto')
output_Ports_153.inputPorts[2].configure(singleConnection='auto')
output_Ports_153.inputPorts[1].configure(
name='UpdateReceptor_receptor_prepared_obj')
output_Ports_153.inputPorts[2].configure(
name='UpdateReceptor_receptor_result')
PrepareReceptorWS_151.inputPorts[0].configure(
name='CheckFileFormat_value')
PrepareReceptorWS_151.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_151.inputPorts[1].configure(
name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_151.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_151.outputPorts[0].configure(
name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_151.outputPorts[0].configure(
datatype='receptor_prepared')
PrepareReceptorWS_151.outputPorts[1].configure(
name='UpdateReceptor_receptor_result')
PrepareReceptorWS_151.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_151.shrink()
## saving connections for network PrepareReceptor ##
PrepareReceptor_141.macroNetwork.freeze()
PrepareReceptor_141.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_142 = PrepareReceptor_141.macroNetwork.ipNode
input_Ports_142.outputPorts[1].configure(
name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_142.outputPorts[2].configure(
name=
'PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_143 = PrepareReceptor_141.macroNetwork.opNode
output_Ports_143.inputPorts[1].configure(singleConnection='auto')
output_Ports_143.inputPorts[2].configure(singleConnection='auto')
output_Ports_143.inputPorts[1].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_143.inputPorts[2].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_141.inputPorts[0].configure(
name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_141.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_141.inputPorts[1].configure(
name=
'PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_141.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptor_141.outputPorts[0].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_141.outputPorts[0].configure(
datatype='receptor_prepared')
PrepareReceptor_141.outputPorts[1].configure(
name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_141.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptor_141.shrink()
apply(PrepareReceptor_141.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore PrepareReceptor named PrepareReceptor in network self.macroNetwork"
print_exc()
PrepareReceptor_141 = None
try:
## saving node ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_159 = ComputeGrids(constrkw={},
name='ComputeGrids',
library=Adt)
self.macroNetwork.addNode(ComputeGrids_159, 136, 207)
apply(ComputeGrids_159.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
prepareGPF_kryptonite_nbcr_net_163 = ComputeGrids_159.macroNetwork.nodes[
3]
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['p'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['o'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName['v'].widget.set(
0, run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_163.inputPortByName[
'execPath'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_164 = ComputeGrids_159.macroNetwork.nodes[
4]
autogrid_kryptonite_nbcr_net_164.inputPortByName[
'infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['l'].widget.set(
r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['o'].widget.set(
0, run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName['p'].widget.set(
r"", run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName[
'localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_164.inputPortByName[
'execPath'].widget.set(r"", run=False)
GetURLFromList_167 = ComputeGrids_159.macroNetwork.nodes[7]
GetURLFromList_167.inputPortByName['ext'].widget.set(r"gpf",
run=False)
## saving connections for network ComputeGrids ##
ComputeGrids_159.macroNetwork.freeze()
ComputeGrids_159.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_160 = ComputeGrids_159.macroNetwork.ipNode
input_Ports_160.outputPorts[1].configure(
name='GetComputeGridsInputs_ligands')
input_Ports_160.outputPorts[2].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_160.outputPorts[3].configure(
name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_161 = ComputeGrids_159.macroNetwork.opNode
output_Ports_161.inputPorts[1].configure(singleConnection='auto')
output_Ports_161.inputPorts[2].configure(singleConnection='auto')
output_Ports_161.inputPorts[1].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_161.inputPorts[2].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_159.inputPorts[0].configure(
name='GetComputeGridsInputs_ligands')
ComputeGrids_159.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_159.inputPorts[1].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_159.inputPorts[1].configure(
datatype='receptor_prepared')
ComputeGrids_159.inputPorts[2].configure(
name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_159.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode input ports
ComputeGrids_159.outputPorts[0].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_159.outputPorts[0].configure(
datatype='autogrid_results')
ComputeGrids_159.outputPorts[1].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_159.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
ComputeGrids_159.shrink()
apply(ComputeGrids_159.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore ComputeGrids named ComputeGrids in network self.macroNetwork"
print_exc()
ComputeGrids_159 = None
try:
## saving node AutodockVsCSF ##
from Adt.Macro.AutodockVsCSF import AutodockVsCSF
AutodockVsCSF_168 = AutodockVsCSF(constrkw={},
name='AutodockVsCSF',
library=Adt)
self.macroNetwork.addNode(AutodockVsCSF_168, 234, 272)
apply(AutodockVsCSF_168.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
autodock_kryptonite_nbcr_net_172 = AutodockVsCSF_168.macroNetwork.nodes[
3]
autodock_kryptonite_nbcr_net_172.inputPortByName[
'ga_run'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'sched'].widget.set(r"CSF", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_172.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175 = AutodockVsCSF_168.macroNetwork.nodes[
6]
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName[
'localRun'].widget.set(0, run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_175.inputPortByName[
'divisor'].widget.set(r"", run=False)
## saving connections for network AutodockVsCSF ##
AutodockVsCSF_168.macroNetwork.freeze()
AutodockVsCSF_168.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_169 = AutodockVsCSF_168.macroNetwork.ipNode
input_Ports_169.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_169.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_169.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_170 = AutodockVsCSF_168.macroNetwork.opNode
output_Ports_170.inputPorts[1].configure(singleConnection='auto')
output_Ports_170.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
AutodockVsCSF_168.inputPorts[0].configure(
name='PrepareADVSInputs_ligands')
AutodockVsCSF_168.inputPorts[0].configure(datatype='LigandDB')
AutodockVsCSF_168.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVsCSF_168.inputPorts[1].configure(
datatype='autogrid_results')
AutodockVsCSF_168.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVsCSF_168.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode input ports
AutodockVsCSF_168.outputPorts[0].configure(
name='GetMainURLFromList_newurl')
AutodockVsCSF_168.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
AutodockVsCSF_168.shrink()
apply(AutodockVsCSF_168.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore AutodockVsCSF named AutodockVsCSF in network self.macroNetwork"
print_exc()
AutodockVsCSF_168 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network VirtualScreeningCSF ##
input_Ports_121 = self.macroNetwork.ipNode
if input_Ports_121 is not None and PrepareReceptor_141 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
PrepareReceptor_141,
"new",
"Pdb2pqrWS_CheckFileFormat_value",
blocking=True,
splitratio=[0.70852617526621731, 0.39749336046566702])
except:
print "WARNING: failed to restore connection between input_Ports_121 and PrepareReceptor_141 in network self.macroNetwork"
if PrepareReceptor_141 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptor_141,
ComputeGrids_159,
"PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj",
"GetComputeGridsInputs_receptor_pdbqt",
blocking=True,
splitratio=[0.35807693100671723, 0.50862337251735745])
except:
print "WARNING: failed to restore connection between PrepareReceptor_141 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
ComputeGrids_159,
"new",
"GetComputeGridsInputs_ligands",
blocking=True,
splitratio=[0.40102167589221782, 0.6253111040879471])
except:
print "WARNING: failed to restore connection between input_Ports_121 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
AutodockVsCSF_168,
"ComputeGrids_GetComputeGridsInputs_ligands",
"PrepareADVSInputs_ligands",
blocking=True,
splitratio=[0.65260935115862417, 0.64296744661832661])
except:
print "WARNING: failed to restore connection between input_Ports_121 and AutodockVsCSF_168 in network self.macroNetwork"
if ComputeGrids_159 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
ComputeGrids_159,
AutodockVsCSF_168,
"MakeAutogridResultObj_autogrid_result_obj",
"PrepareADVSInputs_autogrid_results",
blocking=True,
splitratio=[0.50054097826587762, 0.55954672420260165])
except:
print "WARNING: failed to restore connection between ComputeGrids_159 and AutodockVsCSF_168 in network self.macroNetwork"
if input_Ports_121 is not None and ComputeGrids_159 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
ComputeGrids_159,
"new",
"GetComputeGridsInputs_gpf_obj",
blocking=True,
splitratio=[0.73607423731241384, 0.54225043834950515])
except:
print "WARNING: failed to restore connection between input_Ports_121 and ComputeGrids_159 in network self.macroNetwork"
if input_Ports_121 is not None and AutodockVsCSF_168 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
AutodockVsCSF_168,
"new",
"PrepareADVSInputs_dpf_template_obj",
blocking=True,
splitratio=[0.24404719659126095, 0.41822006352735946])
except:
print "WARNING: failed to restore connection between input_Ports_121 and AutodockVsCSF_168 in network self.macroNetwork"
if input_Ports_121 is not None and PrepareReceptor_141 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_121,
PrepareReceptor_141,
"new",
"PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C",
blocking=True,
splitratio=[0.73098254809437191, 0.23999050334763958])
except:
print "WARNING: failed to restore connection between input_Ports_121 and PrepareReceptor_141 in network self.macroNetwork"
output_Ports_122 = self.macroNetwork.opNode
if AutodockVsCSF_168 is not None and output_Ports_122 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVsCSF_168,
output_Ports_122,
"GetMainURLFromList_newurl",
"new",
blocking=True,
splitratio=[0.55528494083678659, 0.33476142488031579])
except:
print "WARNING: failed to restore connection between AutodockVsCSF_168 and output_Ports_122 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_121 = self.macroNetwork.ipNode
input_Ports_121.outputPorts[1].configure(
name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
input_Ports_121.outputPorts[2].configure(
name='ComputeGrids_GetComputeGridsInputs_ligands')
input_Ports_121.outputPorts[3].configure(
name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
input_Ports_121.outputPorts[4].configure(
name='AutodockVsCSF_PrepareADVSInputs_dpf_template_obj')
input_Ports_121.outputPorts[5].configure(
name=
'PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C'
)
## modifying MacroOutputNode dynamic ports
output_Ports_122 = self.macroNetwork.opNode
output_Ports_122.inputPorts[1].configure(singleConnection='auto')
output_Ports_122.inputPorts[1].configure(
name='AutodockVsCSF_GetMainURLFromList_newurl')
## configure MacroNode input ports
VirtualScreeningCSF_120.inputPorts[0].configure(
name='PrepareReceptor_Pdb2pqrWS_CheckFileFormat_value')
VirtualScreeningCSF_120.inputPorts[0].configure(datatype='receptor')
VirtualScreeningCSF_120.inputPorts[1].configure(
name='ComputeGrids_GetComputeGridsInputs_ligands')
VirtualScreeningCSF_120.inputPorts[1].configure(datatype='LigandDB')
VirtualScreeningCSF_120.inputPorts[2].configure(
name='ComputeGrids_GetComputeGridsInputs_gpf_obj')
VirtualScreeningCSF_120.inputPorts[2].configure(
datatype='gpf_template')
VirtualScreeningCSF_120.inputPorts[3].configure(
name='AutodockVsCSF_PrepareADVSInputs_dpf_template_obj')
VirtualScreeningCSF_120.inputPorts[3].configure(
datatype='dpf_template')
VirtualScreeningCSF_120.inputPorts[4].configure(
name=
'PrepareReceptor_PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C'
)
VirtualScreeningCSF_120.inputPorts[4].configure(datatype='boolean')
## configure MacroNode output ports
VirtualScreeningCSF_120.outputPorts[0].configure(
name='AutodockVsCSF_GetMainURLFromList_newurl')
VirtualScreeningCSF_120.outputPorts[0].configure(datatype='string')
VirtualScreeningCSF_120.shrink()
## reset modifications ##
VirtualScreeningCSF_120.resetTags()
VirtualScreeningCSF_120.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
LocalLigandDirectory_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_2.move(294, 448)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node Make Zip File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={}, name='Make Zip File', library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3,136,158)
apply(Make_Zip_File_3.inputPortByName['input_directory'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_directory'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_name'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MakeZipFileNE named Make Zip File in network self.macroNetwork"
print_exc()
Make_Zip_File_3=None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_4 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_4,312,18)
apply(Entry_4.inputPortByName['entry'].configure, (), {'defaultValue': None})
Entry_4.inputPortByName['entry'].widget.set(r"my_ligands.zip", run=False)
apply(Entry_4.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
print_exc()
Entry_4=None
try:
## saving node LigandDBUpload_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
LigandDBUpload_kryptonite_nbcr_net_5 = FunctionNode(functionOrString='LigandDBUpload_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'username': '', 'userlib': '', 'password': '', 'localRun': False, 'execPath': '', 'desc': ''}, constrkw={'functionOrString': "'LigandDBUpload_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'username': '', 'userlib': '', 'password': '', 'localRun': False, 'execPath': '', 'desc': ''}}, name='LigandDBUpload_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(LigandDBUpload_kryptonite_nbcr_net_5,136,216)
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['username'].configure, (), {'defaultValue': None})
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['userlib'].configure, (), {'defaultValue': None})
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['password'].configure, (), {'defaultValue': None})
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['execPath'].configure, (), {'defaultValue': None})
apply(LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['desc'].configure, (), {'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['username'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['userlib'].rebindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['userlib'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['userlib'].unbindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['password'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['localRun'].widget.set(0, run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['execPath'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName['desc'].widget.set(r"", run=False)
apply(LigandDBUpload_kryptonite_nbcr_net_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named LigandDBUpload_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
LigandDBUpload_kryptonite_nbcr_net_5=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6,136,273)
apply(Index_6.inputPortByName['data'].configure, (), {'defaultValue': None})
apply(Index_6.inputPortByName['index'].configure, (), {'defaultValue': None})
apply(Index_6.outputPortByName['data'].configure, (), {'datatype': 'string'})
apply(Index_6.inputPortByName['index'].widget.configure, (), {'max': 7, 'min': -8})
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_6=None
try:
## saving node ReplaceURL ##
from WebServices.VisionInterface.WSNodes import ReplaceURLNode
ReplaceURL_7 = ReplaceURLNode(constrkw={}, name='ReplaceURL', library=wslib)
self.macroNetwork.addNode(ReplaceURL_7,328,327)
apply(ReplaceURL_7.inputPortByName['url'].configure, (), {'defaultValue': None})
apply(ReplaceURL_7.inputPortByName['newfilename'].configure, (), {'defaultValue': None})
ReplaceURL_7.inputPortByName['url'].rebindWidget()
ReplaceURL_7.inputPortByName['url'].widget.set(r"", run=False)
ReplaceURL_7.inputPortByName['url'].unbindWidget()
apply(ReplaceURL_7.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore ReplaceURLNode named ReplaceURL in network self.macroNetwork"
print_exc()
ReplaceURL_7=None
try:
## saving node CreateLigandDBObj ##
from Vision.StandardNodes import Generic
CreateLigandDBObj_8 = Generic(constrkw={}, name='CreateLigandDBObj', library=stdlib)
self.macroNetwork.addNode(CreateLigandDBObj_8,217,385)
apply(CreateLigandDBObj_8.addInputPort, (), {'singleConnection': True, 'name': 'ligand_lib_url', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(CreateLigandDBObj_8.addInputPort, (), {'singleConnection': True, 'name': 'log_file', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(CreateLigandDBObj_8.addOutputPort, (), {'name': 'ligand_db_obj', 'datatype': 'LigandDB', 'height': 8, 'width': 12, 'shape': 'rect', 'color': '#FFCCFF'})
code = """def doit(self, ligand_lib_url, log_file):
if log_file == None:
log_file = "ligand_lib_uploads.log"
log_file = os.path.abspath(log_file)
if log_file != None:
from time import strftime
now = strftime("%Y-%m-%d %H:%M:%S")
log_str = '''On ''' + now + ''', you uploaded a ligand library to: \n'''
log_str = log_str + ligand_lib_url + '''\n\n'''
f = open(log_file, '''a''')
f.write(log_str)
print "This ligand library upload has been recorded in " + log_file
from AutoDockTools.VisionInterface.Adt.LigandDB import LigandDB
ligand_db_obj = LigandDB(url_lib=ligand_lib_url)
pass
## to ouput data on port ligand_db_obj use
self.outputData(ligand_db_obj=ligand_db_obj)
"""
CreateLigandDBObj_8.configure(function=code)
apply(CreateLigandDBObj_8.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named CreateLigandDBObj in network self.macroNetwork"
print_exc()
CreateLigandDBObj_8=None
try:
## saving node get_paths ##
from Vision.StandardNodes import Generic
get_paths_9 = Generic(constrkw={}, name='get_paths', library=stdlib)
self.macroNetwork.addNode(get_paths_9,136,105)
apply(get_paths_9.addInputPort, (), {'singleConnection': True, 'name': 'directory', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(get_paths_9.addInputPort, (), {'singleConnection': True, 'name': 'zip_name', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(get_paths_9.addOutputPort, (), {'name': 'input_directory', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(get_paths_9.addOutputPort, (), {'name': 'output_directory', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(get_paths_9.addOutputPort, (), {'name': 'output_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(get_paths_9.addOutputPort, (), {'name': 'output_basedir', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, directory, zip_name):
input_directory = os.path.abspath(directory)
if not(os.path.exists(input_directory)):
print "ERROR: ligand input directory " + input_directory + " does not exist"
return '''stop'''
output_directory = os.path.abspath('''.''')
output_name = zip_name
output_basedir = zip_name.rstrip('''.zip''')
pass
self.outputData(input_directory=input_directory, output_directory=output_directory, output_name=zip_name, output_basedir=output_basedir)
## to ouput data on port input_directory use
## self.outputData(input_directory=data)
## to ouput data on port output_directory use
## self.outputData(output_directory=data)
## to ouput data on port output_name use
## self.outputData(output_name=data)
## to ouput data on port output_basedir use
## self.outputData(output_basedir=data)
"""
get_paths_9.configure(function=code)
apply(get_paths_9.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named get_paths in network self.macroNetwork"
print_exc()
get_paths_9=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network LocalLigandDirectory ##
if Make_Zip_File_3 is not None and LigandDBUpload_kryptonite_nbcr_net_5 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3, LigandDBUpload_kryptonite_nbcr_net_5, "zipfile", "userlib", blocking=True
, splitratio=[0.67700056401206909, 0.41786522052018427])
except:
print "WARNING: failed to restore connection between Make_Zip_File_3 and LigandDBUpload_kryptonite_nbcr_net_5 in network self.macroNetwork"
if LigandDBUpload_kryptonite_nbcr_net_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
LigandDBUpload_kryptonite_nbcr_net_5, Index_6, "result", "data", blocking=True
, splitratio=[0.27868065815947218, 0.69101010116597561])
except:
print "WARNING: failed to restore connection between LigandDBUpload_kryptonite_nbcr_net_5 and Index_6 in network self.macroNetwork"
if Index_6 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6, ReplaceURL_7, "data", "url", blocking=True
, splitratio=[0.0, 0.50910496731074983])
except:
print "WARNING: failed to restore connection between Index_6 and ReplaceURL_7 in network self.macroNetwork"
if ReplaceURL_7 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7, CreateLigandDBObj_8, "newurl", "ligand_lib_url", blocking=True
, splitratio=[0.7375258387145982, 0.34433018843468416])
except:
print "WARNING: failed to restore connection between ReplaceURL_7 and CreateLigandDBObj_8 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if CreateLigandDBObj_8 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
CreateLigandDBObj_8, output_Ports_2, "ligand_db_obj", "new", blocking=True
, splitratio=[0.25450332220506922, 0.49254602433654382])
except:
print "WARNING: failed to restore connection between CreateLigandDBObj_8 and output_Ports_2 in network self.macroNetwork"
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, get_paths_9, "new", "directory", blocking=True
, splitratio=[0.73592256661833422, 0.40050624233195609])
except:
print "WARNING: failed to restore connection between input_Ports_1 and get_paths_9 in network self.macroNetwork"
if Entry_4 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
Entry_4, get_paths_9, "string", "zip_name", blocking=True
, splitratio=[0.74641701362897139, 0.56047721560743557])
except:
print "WARNING: failed to restore connection between Entry_4 and get_paths_9 in network self.macroNetwork"
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9, Make_Zip_File_3, "input_directory", "input_directory", blocking=True
, splitratio=[0.24975092021298884, 0.59053364249853169])
except:
print "WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9, Make_Zip_File_3, "output_name", "output_name", blocking=True
, splitratio=[0.44934886807300634, 0.5145630699734256])
except:
print "WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9, Make_Zip_File_3, "output_directory", "output_directory", blocking=True
, splitratio=[0.65054191214838031, 0.31030412383438832])
except:
print "WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
if get_paths_9 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9, ReplaceURL_7, "output_basedir", "newfilename", blocking=True
, splitratio=[0.5380996717918376, 0.39023381726820411])
except:
print "WARNING: failed to restore connection between get_paths_9 and ReplaceURL_7 in network self.macroNetwork"
if input_Ports_1 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, CreateLigandDBObj_8, "new", "log_file", blocking=True
, splitratio=[0.49268182912115838, 0.67412763774649975])
except:
print "WARNING: failed to restore connection between input_Ports_1 and CreateLigandDBObj_8 in network self.macroNetwork"
if ReplaceURL_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7, output_Ports_2, "newurl", "new", blocking=True
, splitratio=[0.67446600768034171, 0.74989471765767979])
except:
print "WARNING: failed to restore connection between ReplaceURL_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(name='CreateLigandDBObj_log_file')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='CreateLigandDBObj_ligand_db_obj')
output_Ports_2.inputPorts[2].configure(name='ReplaceURL_newurl')
## configure MacroNode input ports
LocalLigandDirectory_0.inputPorts[0].configure(name='Make_Zip_File_input_directory')
LocalLigandDirectory_0.inputPorts[0].configure(datatype='string')
LocalLigandDirectory_0.inputPorts[1].configure(name='CreateLigandDBObj_log_file')
LocalLigandDirectory_0.inputPorts[1].configure(datatype='string')
## configure MacroNode output ports
LocalLigandDirectory_0.outputPorts[0].configure(name='CreateLigandDBObj_ligand_db_obj')
LocalLigandDirectory_0.outputPorts[0].configure(datatype='LigandDB')
LocalLigandDirectory_0.outputPorts[1].configure(name='ReplaceURL_newurl')
LocalLigandDirectory_0.outputPorts[1].configure(datatype='string')
LocalLigandDirectory_0.shrink()
## reset modifications ##
LocalLigandDirectory_0.resetTags()
LocalLigandDirectory_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
PrepareReceptor_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node Pdb2pqrWS ##
from NetworkEditor.macros import MacroNode
Pdb2pqrWS_3 = MacroNode(name='Pdb2pqrWS')
self.macroNetwork.addNode(Pdb2pqrWS_3, 153, 86)
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
apply(input_Ports_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
input_Ports_4.move(65, 10)
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
apply(output_Ports_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_5.move(65, 310)
from Vision.StandardNodes import Generic
CheckFileFormat_6 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(CheckFileFormat_6,82,62)
apply(CheckFileFormat_6.addInputPort, (), {'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
apply(CheckFileFormat_6.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
apply(CheckFileFormat_6.addOutputPort, (), {'name': 'pqr_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(CheckFileFormat_6.addOutputPort, (), {'name': 'pdb_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pqr''') != None or value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr_name = value.get_id() + '''.pqr'''
pdb_path = value.get_ext_loc('''pdb''')
self.outputData(receptor_obj=value, pqr_name=pqr_name, pdb_path=pdb_path)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''pqr_name'''), self.getOutputPortByName('''pdb_path''')])
"""
CheckFileFormat_6.configure(function=code)
apply(CheckFileFormat_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
Pdb2pqrOpalService_ws_nbcr_net_7 = FunctionNode(functionOrString='Pdb2pqrOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}, constrkw={'functionOrString': "'Pdb2pqrOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}}, name='Pdb2pqrOpalService_ws_nbcr_net', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(Pdb2pqrOpalService_ws_nbcr_net_7,99,115)
apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].configure, (), {'defaultValue': None, 'required': True})
apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].configure, (), {'defaultValue': None, 'required': True})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False)
apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['apbs_input'].widget.set(0, run=False)
apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['assign_only'].widget.set(0, run=False)
apply(Pdb2pqrOpalService_ws_nbcr_net_7.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_8 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(GetURLFromList_8,117,169)
GetURLFromList_8.inputPortByName['ext'].widget.set(r"pqr", run=False)
apply(GetURLFromList_8.configure, (), {'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_9 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(UpdateReceptor_9,82,256)
apply(UpdateReceptor_9.addInputPort, (), {'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
apply(UpdateReceptor_9.addInputPort, (), {'singleConnection': True, 'name': 'pqr', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(UpdateReceptor_9.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
apply(UpdateReceptor_9.addOutputPort, (), {'name': 'pdb2pqr_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pqr):
if pqr != '''no data yet''':
pdb2pqr_result = pqr
receptor_obj.set_ext_loc(pqr)
else:
pdbqt = receptor_obj.get_ext_loc('''pdbqt''')
pqr = receptor_obj.get_ext_loc('''pqr''')
if pdbqt != None:
pdb2pqr_result = pdbqt
elif pqr != None:
pdb2pqr_result = pqr
pass
self.outputData(receptor_obj=receptor_obj, pdb2pqr_result=pdb2pqr_result)
"""
UpdateReceptor_9.configure(function=code)
apply(UpdateReceptor_9.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_3.macroNetwork.freeze()
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pqr_name", "output_file", blocking=True
, splitratio=[0.43278717885693868, 0.65281492247209427])
except:
print "WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork"
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pdb_path", "inFile", blocking=True
, splitratio=[0.61978340673276544, 0.69977512898866912])
except:
print "WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork"
if Pdb2pqrOpalService_ws_nbcr_net_7 is not None and GetURLFromList_8 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
Pdb2pqrOpalService_ws_nbcr_net_7, GetURLFromList_8, "result", "urllist", blocking=True
, splitratio=[0.73247388879852338, 0.69014271703344965])
except:
print "WARNING: failed to restore connection between Pdb2pqrOpalService_ws_nbcr_net_7 and GetURLFromList_8 in network Pdb2pqrWS_3.macroNetwork"
if GetURLFromList_8 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
GetURLFromList_8, UpdateReceptor_9, "url", "pqr", blocking=True
, splitratio=[0.35224914715245104, 0.47693375858097758])
except:
print "WARNING: failed to restore connection between GetURLFromList_8 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork"
if CheckFileFormat_6 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, UpdateReceptor_9, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.57865377076653579, 0.45824116584600394])
except:
print "WARNING: failed to restore connection between CheckFileFormat_6 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork"
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
if input_Ports_4 is not None and CheckFileFormat_6 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
input_Ports_4, CheckFileFormat_6, "new", "value", blocking=True
, splitratio=[0.28291581858817416, 0.70581213384962171])
except:
print "WARNING: failed to restore connection between input_Ports_4 and CheckFileFormat_6 in network Pdb2pqrWS_3.macroNetwork"
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "receptor_obj", "new", blocking=True
, splitratio=[0.24354423773729619, 0.72115604180615911])
except:
print "WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork"
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "pdb2pqr_result", "new", blocking=True
, splitratio=[0.31141907324539131, 0.41794097665671487])
except:
print "WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork"
Pdb2pqrWS_3.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_4.outputPorts[1].configure(name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[2].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(name='UpdateReceptor_receptor_obj')
output_Ports_5.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_3.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_3.outputPorts[0].configure(name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_3.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_3.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_3.shrink()
apply(Pdb2pqrWS_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named Pdb2pqrWS in network self.macroNetwork"
print_exc()
Pdb2pqrWS_3=None
try:
## saving node PrepareReceptorWS ##
from NetworkEditor.macros import MacroNode
PrepareReceptorWS_10 = MacroNode(name='PrepareReceptorWS')
self.macroNetwork.addNode(PrepareReceptorWS_10, 217, 140)
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
apply(input_Ports_11.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
input_Ports_11.move(145, 8)
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
apply(output_Ports_12.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_12.move(29, 412)
from Vision.StandardNodes import Generic
CheckFileFormat_13 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(CheckFileFormat_13,46,64)
apply(CheckFileFormat_13.addInputPort, (), {'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(CheckFileFormat_13.addOutputPort, (), {'name': 'download_loc', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr = value.get_ext_loc('''pqr''')
pdb = value.get_ext_loc('''pdb''')
download_loc = value.get_workdir() + os.sep + value.get_id() + '''.pdbqt'''
if pqr != None:
if value.get_ext_type('''pqr''') == '''url''':
receptor_url = pqr
receptor_local = ""
else:
receptor_url = ""
receptor_local = pqr
elif pdb != None:
if value.get_ext_type('''pdb''') == '''url''':
receptor_url = pdb
receptor_local = ""
else:
receptor_url = ""
receptor_local = pdb
else:
print "*** ERROR: pqr and pqr both missing from receptor object"
print receptor_obj.ext_loc
return '''stop'''
self.outputData(receptor_obj=value, receptor_url=receptor_url, receptor_local=receptor_local, download_loc=download_loc)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''receptor_url'''), self.getOutputPortByName('''receptor_local'''), self.getOutputPortByName('''download_loc''')])
"""
CheckFileFormat_13.configure(function=code)
apply(CheckFileFormat_13.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
PrepareReceptorOpalService_ws_nbcr_net_14 = FunctionNode(functionOrString='PrepareReceptorOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'PrepareReceptorOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}}, name='PrepareReceptorOpalService_ws_nbcr_net', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(PrepareReceptorOpalService_ws_nbcr_net_14,180,128)
apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].configure, (), {'defaultValue': None})
apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].configure, (), {'defaultValue': None, 'required': True})
apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].configure, (), {'defaultValue': None, 'required': True})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['execPath'].widget.set(r"", run=False)
apply(PrepareReceptorOpalService_ws_nbcr_net_14.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_15 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(GetURLFromList_15,180,186)
GetURLFromList_15.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
apply(GetURLFromList_15.configure, (), {'paramPanelImmediate': 1})
from WebServices.VisionInterface.WSNodes import DownloadToFileNode
DownloadToFile_16 = DownloadToFileNode(constrkw={}, name='DownloadToFile', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(DownloadToFile_16,80,272)
apply(DownloadToFile_16.inputPortByName['url'].configure, (), {'defaultValue': None})
apply(DownloadToFile_16.inputPortByName['filename'].configure, (), {'defaultValue': None})
DownloadToFile_16.inputPortByName['url'].rebindWidget()
DownloadToFile_16.inputPortByName['url'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['url'].unbindWidget()
DownloadToFile_16.inputPortByName['filename'].rebindWidget()
DownloadToFile_16.inputPortByName['filename'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['filename'].unbindWidget()
DownloadToFile_16.inputPortByName['overwrite'].widget.set(1, run=False)
apply(DownloadToFile_16.configure, (), {'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_17 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(UpdateReceptor_17,46,358)
apply(UpdateReceptor_17.addInputPort, (), {'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
apply(UpdateReceptor_17.addInputPort, (), {'singleConnection': True, 'name': 'pdbqt', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(UpdateReceptor_17.addOutputPort, (), {'name': 'receptor_prepared_obj', 'datatype': 'receptor_prepared', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900'})
apply(UpdateReceptor_17.addOutputPort, (), {'name': 'receptor_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pdbqt):
from AutoDockTools.VisionInterface.Adt.receptor_prepared import receptor_prepared
if pdbqt != '''no data yet''':
receptor_prepared_obj = receptor_prepared(pdbqt)
receptor_obj.set_ext_loc(pdbqt)
receptor_result = pdbqt
else:
pdbqt_org = receptor_obj.get_ext_loc('''pdbqt''')
receptor_prepared_obj = receptor_prepared(pdbqt_org)
receptor_result = pdbqt_org
pass
self.outputData(receptor_prepared_obj = receptor_prepared_obj, receptor_result=receptor_result)
"""
UpdateReceptor_17.configure(function=code)
apply(UpdateReceptor_17.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_10.macroNetwork.freeze()
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
if input_Ports_11 is not None and CheckFileFormat_13 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, CheckFileFormat_13, "new", "value", blocking=True
, splitratio=[0.64907843562020084, 0.47057253960060474])
except:
print "WARNING: failed to restore connection between input_Ports_11 and CheckFileFormat_13 in network PrepareReceptorWS_10.macroNetwork"
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_url", "url", blocking=True
, splitratio=[0.6171192646814192, 0.42883431331137822])
except:
print "WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork"
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_local", "r", blocking=True
, splitratio=[0.66136144381723583, 0.28482114514549767])
except:
print "WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork"
if input_Ports_11 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, PrepareReceptorOpalService_ws_nbcr_net_14, "new", "C", blocking=True
, splitratio=[0.53817543437956172, 0.61119702937572407])
except:
print "WARNING: failed to restore connection between input_Ports_11 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork"
if PrepareReceptorOpalService_ws_nbcr_net_14 is not None and GetURLFromList_15 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
PrepareReceptorOpalService_ws_nbcr_net_14, GetURLFromList_15, "result", "urllist", blocking=True
, splitratio=[0.43369347916867251, 0.26566786648658042])
except:
print "WARNING: failed to restore connection between PrepareReceptorOpalService_ws_nbcr_net_14 and GetURLFromList_15 in network PrepareReceptorWS_10.macroNetwork"
if GetURLFromList_15 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
GetURLFromList_15, DownloadToFile_16, "url", "url", blocking=True
, splitratio=[0.70502483723033316, 0.71683158018466053])
except:
print "WARNING: failed to restore connection between GetURLFromList_15 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork"
if CheckFileFormat_13 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, DownloadToFile_16, "download_loc", "filename", blocking=True
, splitratio=[0.60455581032885575, 0.35606890231085681])
except:
print "WARNING: failed to restore connection between CheckFileFormat_13 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork"
if CheckFileFormat_13 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, UpdateReceptor_17, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.74908230670336207, 0.38226563370205602])
except:
print "WARNING: failed to restore connection between CheckFileFormat_13 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork"
if DownloadToFile_16 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
DownloadToFile_16, UpdateReceptor_17, "filename", "pdbqt", blocking=True
, splitratio=[0.38698393490575966, 0.2874426709930199])
except:
print "WARNING: failed to restore connection between DownloadToFile_16 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork"
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_prepared_obj", "new", blocking=True
, splitratio=[0.69589857263374943, 0.59566078506240416])
except:
print "WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork"
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_result", "new", blocking=True
, splitratio=[0.44926362052272689, 0.38628711158860896])
except:
print "WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork"
PrepareReceptorWS_10.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_11.outputPorts[1].configure(name='CheckFileFormat_value')
input_Ports_11.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_12.inputPorts[1].configure(singleConnection='auto')
output_Ports_12.inputPorts[2].configure(singleConnection='auto')
output_Ports_12.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj')
output_Ports_12.inputPorts[2].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.inputPorts[0].configure(name='CheckFileFormat_value')
PrepareReceptorWS_10.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_10.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_10.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_10.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_10.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptorWS_10.outputPorts[1].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_10.shrink()
apply(PrepareReceptorWS_10.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named PrepareReceptorWS in network self.macroNetwork"
print_exc()
PrepareReceptorWS_10=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network PrepareReceptor ##
input_Ports_1 = self.macroNetwork.ipNode
Pdb2pqrWS_3 = self.macroNetwork.nodes[2]
if input_Ports_1 is not None and Pdb2pqrWS_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Pdb2pqrWS_3, "new", "CheckFileFormat_value", blocking=True
, splitratio=[0.73531020066010289, 0.24042404972613104])
except:
print "WARNING: failed to restore connection between input_Ports_1 and Pdb2pqrWS_3 in network self.macroNetwork"
PrepareReceptorWS_10 = self.macroNetwork.nodes[3]
if Pdb2pqrWS_3 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
Pdb2pqrWS_3, PrepareReceptorWS_10, "UpdateReceptor_receptor_obj", "CheckFileFormat_value", blocking=True
, splitratio=[0.54479169827535734, 0.4847384502006486])
except:
print "WARNING: failed to restore connection between Pdb2pqrWS_3 and PrepareReceptorWS_10 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareReceptorWS_10, "new", "PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True
, splitratio=[0.37730151685222141, 0.48897820190498614])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptorWS_10 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_prepared_obj", "new", blocking=True
, splitratio=[0.64110508898616414, 0.45535290355389196])
except:
print "WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork"
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_result", "new", blocking=True
, splitratio=[0.45846842546122241, 0.44240009354017412])
except:
print "WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_1.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_2.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
## configure MacroNode input ports
PrepareReceptor_0.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_0.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_0.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_0.inputPorts[1].configure(datatype='boolean')
## configure MacroNode output ports
PrepareReceptor_0.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_0.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptor_0.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_0.outputPorts[1].configure(datatype='string')
PrepareReceptor_0.shrink()
## reset modifications ##
PrepareReceptor_0.resetTags()
PrepareReceptor_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVsCSF_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_2.move(183, 363)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_3 = Generic(constrkw={}, name='PrepareADVSInputs', library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_3,217,76)
apply(PrepareADVSInputs_3.addInputPort, (), {'singleConnection': True, 'name': 'ligands', 'cast': True, 'datatype': 'LigandDB', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'rect', 'color': '#FFCCFF', 'originalDatatype': 'None'})
apply(PrepareADVSInputs_3.addInputPort, (), {'singleConnection': True, 'name': 'autogrid_results', 'cast': True, 'datatype': 'autogrid_results', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#FF33CC', 'originalDatatype': 'None'})
apply(PrepareADVSInputs_3.addInputPort, (), {'singleConnection': True, 'name': 'dpf_template_obj', 'cast': True, 'datatype': 'dpf_template', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#9933FF', 'originalDatatype': 'None'})
apply(PrepareADVSInputs_3.addOutputPort, (), {'name': 'filter_file', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareADVSInputs_3.addOutputPort, (), {'name': 'ligand_lib', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareADVSInputs_3.addOutputPort, (), {'name': 'dpf_template_file', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareADVSInputs_3.addOutputPort, (), {'name': 'autogrid_res_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareADVSInputs_3.addOutputPort, (), {'name': 'autogrid_res_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_3.configure(function=code)
apply(PrepareADVSInputs_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
print_exc()
PrepareADVSInputs_3=None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_4 = FunctionNode(functionOrString='autodock_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'ga_run': '', 'lib': '', 'filter_file_url': '', 'ga_num_evals': '', 'filter_file': '', 'sched': 'SGE', 'urllib': '', 'ga_num_generations': '', 'dpf': '', 'u': '', 'utar': '', 'userlib': '', 'ga_pop_size': '', 'localRun': False, 'email': '', 'execPath': ''}, constrkw={'functionOrString': "'autodock_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'ga_run': '', 'lib': '', 'filter_file_url': '', 'ga_num_evals': '', 'filter_file': '', 'sched': 'SGE', 'urllib': '', 'ga_num_generations': '', 'dpf': '', 'u': '', 'utar': '', 'userlib': '', 'ga_pop_size': '', 'localRun': False, 'email': '', 'execPath': ''}}, name='autodock_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_4,217,132)
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['ga_run'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file_url'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_evals'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_generations'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['u'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['userlib'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['ga_pop_size'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['email'].configure, (), {'defaultValue': None})
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['execPath'].configure, (), {'defaultValue': None})
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_run'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].unbindWidget()
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.set(r"CSF", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['execPath'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autodock_kryptonite_nbcr_net_4=None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_5 = GetMainURLFromListNode(constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_5,217,188)
apply(GetMainURLFromList_5.inputPortByName['urls'].configure, (), {'defaultValue': None})
apply(GetMainURLFromList_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_5=None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_7 = GetMainURLFromListNode(constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_7,201,301)
apply(GetMainURLFromList_7.inputPortByName['urls'].configure, (), {'defaultValue': None})
apply(GetMainURLFromList_7.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_7=None
try:
## saving node AutodockSlice_oolitevm_calit2_optiputer_net ##
from NetworkEditor.items import FunctionNode
AutodockSlice_oolitevm_calit2_optiputer_net_8 = FunctionNode(functionOrString='AutodockSlice_oolitevm_calit2_optiputer_net', host="http://oolitevm.calit2.optiputer.net/opal2", namedArgs={'execPath': '', 'localRun': False, 'divisor': '', 'lib': '', 'input_url': ''}, constrkw={'functionOrString': "'AutodockSlice_oolitevm_calit2_optiputer_net'", 'host': '"http://oolitevm.calit2.optiputer.net/opal2"', 'namedArgs': {'execPath': '', 'localRun': False, 'divisor': '', 'lib': '', 'input_url': ''}}, name='AutodockSlice_oolitevm_calit2_optiputer_net', library=wslib)
self.macroNetwork.addNode(AutodockSlice_oolitevm_calit2_optiputer_net_8,200,240)
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['execPath'].configure, (), {'defaultValue': None})
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['divisor'].configure, (), {'defaultValue': None})
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['lib'].configure, (), {'defaultValue': None})
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['input_url'].configure, (), {'defaultValue': None})
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['localRun'].widget.set(0, run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['divisor'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['lib'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['lib'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['lib'].unbindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['input_url'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['input_url'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName['input_url'].unbindWidget()
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named AutodockSlice_oolitevm_calit2_optiputer_net in network self.macroNetwork"
print_exc()
AutodockSlice_oolitevm_calit2_optiputer_net_8=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVsCSF ##
if autodock_kryptonite_nbcr_net_4 is not None and GetMainURLFromList_5 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_4, GetMainURLFromList_5, "result", "urls", blocking=True
, splitratio=[0.36974288957131424, 0.63465596053596318])
except:
print "WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_4 and GetMainURLFromList_5 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, autodock_kryptonite_nbcr_net_4, "filter_file", "filter_file", blocking=True
, splitratio=[0.33230642287344903, 0.65770700108889613])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, autodock_kryptonite_nbcr_net_4, "ligand_lib", "urllib", blocking=True
, splitratio=[0.50680104599665787, 0.51414170500293577])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, autodock_kryptonite_nbcr_net_4, "dpf_template_file", "dpf", blocking=True
, splitratio=[0.51615646597598808, 0.25661305528484007])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, autodock_kryptonite_nbcr_net_4, "autogrid_res_url", "u", blocking=True
, splitratio=[0.5760732944947704, 0.2032376887917188])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, autodock_kryptonite_nbcr_net_4, "autogrid_res_local", "utar", blocking=True
, splitratio=[0.52802808938949819, 0.66978534572736881])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareADVSInputs_3, "new", "ligands", blocking=True
, splitratio=[0.23314258225660414, 0.72184112037432979])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareADVSInputs_3, "new", "autogrid_results", blocking=True
, splitratio=[0.56916626620432731, 0.43089669830392019])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareADVSInputs_3, "new", "dpf_template_obj", blocking=True
, splitratio=[0.26502286453989665, 0.3911248444502638])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetMainURLFromList_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_7, output_Ports_2, "newurl", "new", blocking=True
, splitratio=[0.2408747073082603, 0.22897876889044461])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_7 and output_Ports_2 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3, AutodockSlice_oolitevm_calit2_optiputer_net_8, "ligand_lib", "lib", blocking=True
, splitratio=[0.36439875698533941, 0.58443612376117082])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if GetMainURLFromList_5 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_5, AutodockSlice_oolitevm_calit2_optiputer_net_8, "newurl", "input_url", blocking=True
, splitratio=[0.32808833199778697, 0.69237553555389719])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_5 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None and GetMainURLFromList_7 is not None:
try:
self.macroNetwork.connectNodes(
AutodockSlice_oolitevm_calit2_optiputer_net_8, GetMainURLFromList_7, "result", "urls", blocking=True
, splitratio=[0.69930142895840763, 0.2984777644803871])
except:
print "WARNING: failed to restore connection between AutodockSlice_oolitevm_calit2_optiputer_net_8 and GetMainURLFromList_7 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='PrepareADVSInputs_ligands')
input_Ports_1.outputPorts[2].configure(name='PrepareADVSInputs_autogrid_results')
input_Ports_1.outputPorts[3].configure(name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='GetMainURLFromList_newurl')
## configure MacroNode input ports
AutodockVsCSF_0.inputPorts[0].configure(name='PrepareADVSInputs_ligands')
AutodockVsCSF_0.inputPorts[0].configure(datatype='LigandDB')
AutodockVsCSF_0.inputPorts[1].configure(name='PrepareADVSInputs_autogrid_results')
AutodockVsCSF_0.inputPorts[1].configure(datatype='autogrid_results')
AutodockVsCSF_0.inputPorts[2].configure(name='PrepareADVSInputs_dpf_template_obj')
AutodockVsCSF_0.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode output ports
AutodockVsCSF_0.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AutodockVsCSF_0.outputPorts[0].configure(datatype='string')
AutodockVsCSF_0.shrink()
## reset modifications ##
AutodockVsCSF_0.resetTags()
AutodockVsCSF_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
PrepareSingleLigand_18 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_19 = self.macroNetwork.ipNode
apply(input_Ports_19.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_19=None
try:
## saving node output Ports ##
output_Ports_20 = self.macroNetwork.opNode
apply(output_Ports_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_20=None
try:
## saving node PrepareLigandSingle_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
PrepareLigandSingle_kryptonite_nbcr_net_21 = FunctionNode(functionOrString='PrepareLigandSingle_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'A': '', 'C': False, 'B': '', 'ligand': '', 'g': False, 'F': False, 'I': '', 'M': False, 'p': '', 'R': '', 'U': '', 'v': False, 'Z': False, 'localRun': False, 'execPath': '', 'd': ''}, constrkw={'functionOrString': "'PrepareLigandSingle_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'A': '', 'C': False, 'B': '', 'ligand': '', 'g': False, 'F': False, 'I': '', 'M': False, 'p': '', 'R': '', 'U': '', 'v': False, 'Z': False, 'localRun': False, 'execPath': '', 'd': ''}}, name='PrepareLigandSingle_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(PrepareLigandSingle_kryptonite_nbcr_net_21,217,92)
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['A'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['C'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['B'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['ligand'].configure, (), {'defaultValue': None, 'required': True})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['g'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['F'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['I'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['M'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['p'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['R'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['U'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['v'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['Z'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['execPath'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['d'].configure, (), {'defaultValue': None})
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['A'].widget.configure, (), {'choices': ('bonds_hydrogens', 'bonds', 'hydrogens')})
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['A'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['C'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['B'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['ligand'].rebindWidget()
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['ligand'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['ligand'].unbindWidget()
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['g'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['F'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['I'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['M'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['p'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['R'].widget.set(r"", run=False)
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['U'].widget.configure, (), {'choices': ('nphs_lps', 'nphs', 'lps')})
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['U'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['v'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['Z'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['localRun'].widget.set(0, run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['execPath'].widget.set(r"", run=False)
PrepareLigandSingle_kryptonite_nbcr_net_21.inputPortByName['d'].widget.set(r"", run=False)
apply(PrepareLigandSingle_kryptonite_nbcr_net_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named PrepareLigandSingle_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
PrepareLigandSingle_kryptonite_nbcr_net_21=None
try:
## saving node GetURLFromList ##
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_22 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
self.macroNetwork.addNode(GetURLFromList_22,217,171)
apply(GetURLFromList_22.inputPortByName['urllist'].configure, (), {'defaultValue': None})
apply(GetURLFromList_22.inputPortByName['ext'].configure, (), {'defaultValue': None})
GetURLFromList_22.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
apply(GetURLFromList_22.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore GetURLFromListNode named GetURLFromList in network self.macroNetwork"
print_exc()
GetURLFromList_22=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network PrepareSingleLigand ##
if PrepareLigandSingle_kryptonite_nbcr_net_21 is not None and GetURLFromList_22 is not None:
try:
self.macroNetwork.connectNodes(
PrepareLigandSingle_kryptonite_nbcr_net_21, GetURLFromList_22, "result", "urllist", blocking=True
, splitratio=[0.32868238447942777, 0.66102005033481848])
except:
print "WARNING: failed to restore connection between PrepareLigandSingle_kryptonite_nbcr_net_21 and GetURLFromList_22 in network self.macroNetwork"
output_Ports_20 = self.macroNetwork.opNode
if GetURLFromList_22 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
GetURLFromList_22, output_Ports_20, "url", "new", blocking=True
, splitratio=[0.24357139972148803, 0.60352121442381113])
except:
print "WARNING: failed to restore connection between GetURLFromList_22 and output_Ports_20 in network self.macroNetwork"
input_Ports_19 = self.macroNetwork.ipNode
if input_Ports_19 is not None and PrepareLigandSingle_kryptonite_nbcr_net_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19, PrepareLigandSingle_kryptonite_nbcr_net_21, "new", "ligand", blocking=True
, splitratio=[0.58130558930809739, 0.62673128127582967])
except:
print "WARNING: failed to restore connection between input_Ports_19 and PrepareLigandSingle_kryptonite_nbcr_net_21 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_19 = self.macroNetwork.ipNode
input_Ports_19.outputPorts[1].configure(name='PrepareLigandSingle_kryptonite_nbcr_net_ligand')
## modifying MacroOutputNode dynamic ports
output_Ports_20 = self.macroNetwork.opNode
output_Ports_20.inputPorts[1].configure(singleConnection='auto')
output_Ports_20.inputPorts[1].configure(name='GetURLFromList_url')
## configure MacroNode input ports
PrepareSingleLigand_18.inputPorts[0].configure(name='PrepareLigandSingle_kryptonite_nbcr_net_ligand')
PrepareSingleLigand_18.inputPorts[0].configure(datatype='string')
## configure MacroNode output ports
PrepareSingleLigand_18.outputPorts[0].configure(name='GetURLFromList_url')
PrepareSingleLigand_18.outputPorts[0].configure(datatype='string')
PrepareSingleLigand_18.shrink()
## reset modifications ##
PrepareSingleLigand_18.resetTags()
PrepareSingleLigand_18.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
GromosCluster_33 = self
from traceback import print_exc
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_34 = self.macroNetwork.ipNode
input_Ports_34.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_34 = None
try:
## saving node output Ports ##
output_Ports_35 = self.macroNetwork.opNode
output_Ports_35.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_35.move(236, 302)
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_35 = None
try:
## saving node GROMOS_ClusterFiles_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
GROMOS_ClusterFiles_kryptonite_nbcr_net_36 = FunctionNode(
functionOrString='GROMOS_ClusterFiles_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'expert_options': '',
'rmsd': '0.125',
'traj': '',
'prefix': '',
'default_options':
'-o -g -dist -ev -sz -tr -ntr -clid -cl',
'active': '',
'localRun': False,
'method': 'gromos',
'execPath': ''
},
constrkw={
'functionOrString':
"'GROMOS_ClusterFiles_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'expert_options': '',
'rmsd': '0.125',
'traj': '',
'prefix': '',
'default_options':
'-o -g -dist -ev -sz -tr -ntr -clid -cl',
'active': '',
'localRun': False,
'method': 'gromos',
'execPath': ''
}
},
name='GROMOS_ClusterFiles_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(
GROMOS_ClusterFiles_kryptonite_nbcr_net_36, 200, 98)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'expert_options'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'rmsd'].configure(*(), **{
'defaultValue': None,
'required': True
})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'traj'].configure(*(), **{
'defaultValue': None,
'required': True
})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'prefix'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'default_options'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'active'].configure(*(), **{
'defaultValue': None,
'required': True
})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'method'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'expert_options'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'rmsd'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'rmsd'].widget.set(r"0.125", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'rmsd'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'traj'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'traj'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'traj'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'prefix'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'default_options'].widget.set(
r"-o -g -dist -ev -sz -tr -ntr -clid -cl", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'active'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'active'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'active'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'localRun'].widget.set(0, run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'method'].widget.configure(
*(), **{
'choices': ('gromos', 'linkage', 'jarvis-patrick',
'monte-carlo', 'diagonalization')
})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'method'].widget.set(r"gromos", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName[
'execPath'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named GROMOS_ClusterFiles_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36 = None
try:
## saving node GetClusterFrameLink ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetClusterFrameLink_46 = GetMainURLFromListNode(
constrkw={}, name='GetClusterFrameLink', library=wslib)
self.macroNetwork.addNode(GetClusterFrameLink_46, 200, 164)
GetClusterFrameLink_46.inputPortByName['urls'].configure(
*(), **{'defaultValue': None})
code = """def doit(self, urls):
url = urls[0]
filename = url.split('''/''')[len(url.split('''/'''))-1]
nurl = url.strip(filename)
nurl = nurl + '''cluster_frames'''
pass
self.outputData(newurl=nurl)
"""
GetClusterFrameLink_46.configure(function=code)
GetClusterFrameLink_46.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore GetMainURLFromListNode named GetClusterFrameLink in network self.macroNetwork"
)
print_exc()
GetClusterFrameLink_46 = None
try:
## saving node DownloadSaveDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadSaveDir_51 = DownloadSaveDirNode(constrkw={},
name='DownloadSaveDir',
library=wslib)
self.macroNetwork.addNode(DownloadSaveDir_51, 253, 241)
DownloadSaveDir_51.inputPortByName['url'].configure(
*(), **{'defaultValue': None})
DownloadSaveDir_51.inputPortByName['path'].configure(
*(), **{'defaultValue': None})
DownloadSaveDir_51.inputPortByName['cutdirs'].configure(
*(), **{'defaultValue': None})
DownloadSaveDir_51.inputPortByName['url'].rebindWidget()
DownloadSaveDir_51.inputPortByName['url'].widget.set(r"",
run=False)
DownloadSaveDir_51.inputPortByName['url'].unbindWidget()
DownloadSaveDir_51.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore DownloadSaveDirNode named DownloadSaveDir in network self.macroNetwork"
)
print_exc()
DownloadSaveDir_51 = None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_54 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_54, 347, 154)
Entry_54.inputPortByName['entry'].configure(
*(), **{'defaultValue': None})
Entry_54.inputPortByName['entry'].widget.set(r"3", run=False)
Entry_54.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
)
print_exc()
Entry_54 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network GromosCluster ##
input_Ports_34 = self.macroNetwork.ipNode
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34,
GROMOS_ClusterFiles_kryptonite_nbcr_net_36,
"new",
"traj",
blocking=True,
splitratio=[0.45411042113261574, 0.54335719372693991])
except:
print(
"WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
)
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34,
GROMOS_ClusterFiles_kryptonite_nbcr_net_36,
"new",
"active",
blocking=True,
splitratio=[0.50935546751136695, 0.51596797621119816])
except:
print(
"WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
)
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34,
GROMOS_ClusterFiles_kryptonite_nbcr_net_36,
"new",
"rmsd",
blocking=True,
splitratio=[0.72697457023572398, 0.5609730307022871])
except:
print(
"WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
)
if GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None and GetClusterFrameLink_46 is not None:
try:
self.macroNetwork.connectNodes(
GROMOS_ClusterFiles_kryptonite_nbcr_net_36,
GetClusterFrameLink_46,
"result",
"urls",
blocking=True,
splitratio=[0.72920790745169972, 0.25586352865051565])
except:
print(
"WARNING: failed to restore connection between GROMOS_ClusterFiles_kryptonite_nbcr_net_36 and GetClusterFrameLink_46 in network self.macroNetwork"
)
if GetClusterFrameLink_46 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
GetClusterFrameLink_46,
DownloadSaveDir_51,
"newurl",
"url",
blocking=True,
splitratio=[0.6813604229397745, 0.24060738045908744])
except:
print(
"WARNING: failed to restore connection between GetClusterFrameLink_46 and DownloadSaveDir_51 in network self.macroNetwork"
)
if input_Ports_34 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34,
DownloadSaveDir_51,
"new",
"path",
blocking=True,
splitratio=[0.26234570709625593, 0.71051250549253275])
except:
print(
"WARNING: failed to restore connection between input_Ports_34 and DownloadSaveDir_51 in network self.macroNetwork"
)
output_Ports_35 = self.macroNetwork.opNode
if DownloadSaveDir_51 is not None and output_Ports_35 is not None:
try:
self.macroNetwork.connectNodes(
DownloadSaveDir_51,
output_Ports_35,
"output",
"new",
blocking=True,
splitratio=[0.32827353595918307, 0.22147048732628238])
except:
print(
"WARNING: failed to restore connection between DownloadSaveDir_51 and output_Ports_35 in network self.macroNetwork"
)
if Entry_54 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
Entry_54,
DownloadSaveDir_51,
"string",
"cutdirs",
blocking=True,
splitratio=[0.28715327854931738, 0.50903858482741082])
except:
print(
"WARNING: failed to restore connection between Entry_54 and DownloadSaveDir_51 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_34 = self.macroNetwork.ipNode
input_Ports_34.outputPorts[1].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_traj')
input_Ports_34.outputPorts[2].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_active')
input_Ports_34.outputPorts[3].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_rmsd')
input_Ports_34.outputPorts[4].configure(name='DownloadSaveDir_path')
## modifying MacroOutputNode dynamic ports
output_Ports_35 = self.macroNetwork.opNode
output_Ports_35.inputPorts[1].configure(singleConnection='auto')
output_Ports_35.inputPorts[1].configure(name='DownloadSaveDir_output')
## configure MacroNode input ports
GromosCluster_33.inputPorts[0].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_traj')
GromosCluster_33.inputPorts[0].configure(datatype='string')
GromosCluster_33.inputPorts[1].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_active')
GromosCluster_33.inputPorts[1].configure(datatype='string')
GromosCluster_33.inputPorts[2].configure(
name='GROMOS_ClusterFiles_kryptonite_nbcr_net_rmsd')
GromosCluster_33.inputPorts[2].configure(datatype='string')
GromosCluster_33.inputPorts[3].configure(name='DownloadSaveDir_path')
GromosCluster_33.inputPorts[3].configure(datatype='string')
## configure MacroNode output ports
GromosCluster_33.outputPorts[0].configure(
name='DownloadSaveDir_output')
GromosCluster_33.outputPorts[0].configure(datatype='string')
GromosCluster_33.shrink()
## reset modifications ##
GromosCluster_33.resetTags()
GromosCluster_33.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
GromosCluster_33 = self
from traceback import print_exc
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_34 = self.macroNetwork.ipNode
apply(input_Ports_34.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_34=None
try:
## saving node output Ports ##
output_Ports_35 = self.macroNetwork.opNode
apply(output_Ports_35.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_35.move(236, 302)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_35=None
try:
## saving node GROMOS_ClusterFiles_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
GROMOS_ClusterFiles_kryptonite_nbcr_net_36 = FunctionNode(functionOrString='GROMOS_ClusterFiles_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'expert_options': '', 'rmsd': '0.125', 'traj': '', 'prefix': '', 'default_options': '-o -g -dist -ev -sz -tr -ntr -clid -cl', 'active': '', 'localRun': False, 'method': 'gromos', 'execPath': ''}, constrkw={'functionOrString': "'GROMOS_ClusterFiles_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'expert_options': '', 'rmsd': '0.125', 'traj': '', 'prefix': '', 'default_options': '-o -g -dist -ev -sz -tr -ntr -clid -cl', 'active': '', 'localRun': False, 'method': 'gromos', 'execPath': ''}}, name='GROMOS_ClusterFiles_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(GROMOS_ClusterFiles_kryptonite_nbcr_net_36,200,98)
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['expert_options'].configure, (), {'defaultValue': None})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['rmsd'].configure, (), {'defaultValue': None, 'required': True})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['traj'].configure, (), {'defaultValue': None, 'required': True})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['prefix'].configure, (), {'defaultValue': None})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['default_options'].configure, (), {'defaultValue': None})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['active'].configure, (), {'defaultValue': None, 'required': True})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['method'].configure, (), {'defaultValue': None})
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['execPath'].configure, (), {'defaultValue': None})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['expert_options'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['rmsd'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['rmsd'].widget.set(r"0.125", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['rmsd'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['traj'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['traj'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['traj'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['prefix'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['default_options'].widget.set(r"-o -g -dist -ev -sz -tr -ntr -clid -cl", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['active'].rebindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['active'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['active'].unbindWidget()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['localRun'].widget.set(0, run=False)
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['method'].widget.configure, (), {'choices': ('gromos', 'linkage', 'jarvis-patrick', 'monte-carlo', 'diagonalization')})
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['method'].widget.set(r"gromos", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_36.inputPortByName['execPath'].widget.set(r"", run=False)
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_36.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named GROMOS_ClusterFiles_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
GROMOS_ClusterFiles_kryptonite_nbcr_net_36=None
try:
## saving node GetClusterFrameLink ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetClusterFrameLink_46 = GetMainURLFromListNode(constrkw={}, name='GetClusterFrameLink', library=wslib)
self.macroNetwork.addNode(GetClusterFrameLink_46,200,164)
apply(GetClusterFrameLink_46.inputPortByName['urls'].configure, (), {'defaultValue': None})
code = """def doit(self, urls):
url = urls[0]
filename = url.split('''/''')[len(url.split('''/'''))-1]
nurl = url.strip(filename)
nurl = nurl + '''cluster_frames'''
pass
self.outputData(newurl=nurl)
"""
GetClusterFrameLink_46.configure(function=code)
apply(GetClusterFrameLink_46.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetClusterFrameLink in network self.macroNetwork"
print_exc()
GetClusterFrameLink_46=None
try:
## saving node DownloadSaveDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadSaveDir_51 = DownloadSaveDirNode(constrkw={}, name='DownloadSaveDir', library=wslib)
self.macroNetwork.addNode(DownloadSaveDir_51,253,241)
apply(DownloadSaveDir_51.inputPortByName['url'].configure, (), {'defaultValue': None})
apply(DownloadSaveDir_51.inputPortByName['path'].configure, (), {'defaultValue': None})
apply(DownloadSaveDir_51.inputPortByName['cutdirs'].configure, (), {'defaultValue': None})
DownloadSaveDir_51.inputPortByName['url'].rebindWidget()
DownloadSaveDir_51.inputPortByName['url'].widget.set(r"", run=False)
DownloadSaveDir_51.inputPortByName['url'].unbindWidget()
apply(DownloadSaveDir_51.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore DownloadSaveDirNode named DownloadSaveDir in network self.macroNetwork"
print_exc()
DownloadSaveDir_51=None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_54 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_54,347,154)
apply(Entry_54.inputPortByName['entry'].configure, (), {'defaultValue': None})
Entry_54.inputPortByName['entry'].widget.set(r"3", run=False)
apply(Entry_54.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
print_exc()
Entry_54=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network GromosCluster ##
input_Ports_34 = self.macroNetwork.ipNode
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34, GROMOS_ClusterFiles_kryptonite_nbcr_net_36, "new", "traj", blocking=True
, splitratio=[0.45411042113261574, 0.54335719372693991])
except:
print "WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34, GROMOS_ClusterFiles_kryptonite_nbcr_net_36, "new", "active", blocking=True
, splitratio=[0.50935546751136695, 0.51596797621119816])
except:
print "WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
if input_Ports_34 is not None and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34, GROMOS_ClusterFiles_kryptonite_nbcr_net_36, "new", "rmsd", blocking=True
, splitratio=[0.72697457023572398, 0.5609730307022871])
except:
print "WARNING: failed to restore connection between input_Ports_34 and GROMOS_ClusterFiles_kryptonite_nbcr_net_36 in network self.macroNetwork"
if GROMOS_ClusterFiles_kryptonite_nbcr_net_36 is not None and GetClusterFrameLink_46 is not None:
try:
self.macroNetwork.connectNodes(
GROMOS_ClusterFiles_kryptonite_nbcr_net_36, GetClusterFrameLink_46, "result", "urls", blocking=True
, splitratio=[0.72920790745169972, 0.25586352865051565])
except:
print "WARNING: failed to restore connection between GROMOS_ClusterFiles_kryptonite_nbcr_net_36 and GetClusterFrameLink_46 in network self.macroNetwork"
if GetClusterFrameLink_46 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
GetClusterFrameLink_46, DownloadSaveDir_51, "newurl", "url", blocking=True
, splitratio=[0.6813604229397745, 0.24060738045908744])
except:
print "WARNING: failed to restore connection between GetClusterFrameLink_46 and DownloadSaveDir_51 in network self.macroNetwork"
if input_Ports_34 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_34, DownloadSaveDir_51, "new", "path", blocking=True
, splitratio=[0.26234570709625593, 0.71051250549253275])
except:
print "WARNING: failed to restore connection between input_Ports_34 and DownloadSaveDir_51 in network self.macroNetwork"
output_Ports_35 = self.macroNetwork.opNode
if DownloadSaveDir_51 is not None and output_Ports_35 is not None:
try:
self.macroNetwork.connectNodes(
DownloadSaveDir_51, output_Ports_35, "output", "new", blocking=True
, splitratio=[0.32827353595918307, 0.22147048732628238])
except:
print "WARNING: failed to restore connection between DownloadSaveDir_51 and output_Ports_35 in network self.macroNetwork"
if Entry_54 is not None and DownloadSaveDir_51 is not None:
try:
self.macroNetwork.connectNodes(
Entry_54, DownloadSaveDir_51, "string", "cutdirs", blocking=True
, splitratio=[0.28715327854931738, 0.50903858482741082])
except:
print "WARNING: failed to restore connection between Entry_54 and DownloadSaveDir_51 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_34 = self.macroNetwork.ipNode
input_Ports_34.outputPorts[1].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_traj')
input_Ports_34.outputPorts[2].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_active')
input_Ports_34.outputPorts[3].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_rmsd')
input_Ports_34.outputPorts[4].configure(name='DownloadSaveDir_path')
## modifying MacroOutputNode dynamic ports
output_Ports_35 = self.macroNetwork.opNode
output_Ports_35.inputPorts[1].configure(singleConnection='auto')
output_Ports_35.inputPorts[1].configure(name='DownloadSaveDir_output')
## configure MacroNode input ports
GromosCluster_33.inputPorts[0].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_traj')
GromosCluster_33.inputPorts[0].configure(datatype='string')
GromosCluster_33.inputPorts[1].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_active')
GromosCluster_33.inputPorts[1].configure(datatype='string')
GromosCluster_33.inputPorts[2].configure(name='GROMOS_ClusterFiles_kryptonite_nbcr_net_rmsd')
GromosCluster_33.inputPorts[2].configure(datatype='string')
GromosCluster_33.inputPorts[3].configure(name='DownloadSaveDir_path')
GromosCluster_33.inputPorts[3].configure(datatype='string')
## configure MacroNode output ports
GromosCluster_33.outputPorts[0].configure(name='DownloadSaveDir_output')
GromosCluster_33.outputPorts[0].configure(datatype='string')
GromosCluster_33.shrink()
## reset modifications ##
GromosCluster_33.resetTags()
GromosCluster_33.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
PrepareReceptor_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork")
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork")
print_exc()
output_Ports_2=None
try:
## saving node Pdb2pqrWS ##
from NetworkEditor.macros import MacroNode
Pdb2pqrWS_3 = MacroNode(name='Pdb2pqrWS')
self.macroNetwork.addNode(Pdb2pqrWS_3, 153, 86)
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
input_Ports_4.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
input_Ports_4.move(65, 10)
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
output_Ports_5.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
output_Ports_5.move(65, 310)
from Vision.StandardNodes import Generic
CheckFileFormat_6 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(CheckFileFormat_6,82,62)
CheckFileFormat_6.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'pqr_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'pdb_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pqr''') != None or value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr_name = value.get_id() + '''.pqr'''
pdb_path = value.get_ext_loc('''pdb''')
self.outputData(receptor_obj=value, pqr_name=pqr_name, pdb_path=pdb_path)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''pqr_name'''), self.getOutputPortByName('''pdb_path''')])
"""
CheckFileFormat_6.configure(function=code)
CheckFileFormat_6.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
Pdb2pqrOpalService_ws_nbcr_net_7 = FunctionNode(functionOrString='Pdb2pqrOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}, constrkw={'functionOrString': "'Pdb2pqrOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}}, name='Pdb2pqrOpalService_ws_nbcr_net', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(Pdb2pqrOpalService_ws_nbcr_net_7,99,115)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].configure(*(), **{'defaultValue': None, 'required': True})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].configure(*(), **{'defaultValue': None, 'required': True})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['apbs_input'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['assign_only'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_8 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(GetURLFromList_8,117,169)
GetURLFromList_8.inputPortByName['ext'].widget.set(r"pqr", run=False)
GetURLFromList_8.configure(*(), **{'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_9 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(UpdateReceptor_9,82,256)
UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'pqr', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
UpdateReceptor_9.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
UpdateReceptor_9.addOutputPort(*(), **{'name': 'pdb2pqr_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pqr):
if pqr != '''no data yet''':
pdb2pqr_result = pqr
receptor_obj.set_ext_loc(pqr)
else:
pdbqt = receptor_obj.get_ext_loc('''pdbqt''')
pqr = receptor_obj.get_ext_loc('''pqr''')
if pdbqt != None:
pdb2pqr_result = pdbqt
elif pqr != None:
pdb2pqr_result = pqr
pass
self.outputData(receptor_obj=receptor_obj, pdb2pqr_result=pdb2pqr_result)
"""
UpdateReceptor_9.configure(function=code)
UpdateReceptor_9.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_3.macroNetwork.freeze()
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pqr_name", "output_file", blocking=True
, splitratio=[0.43278717885693868, 0.65281492247209427])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork")
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pdb_path", "inFile", blocking=True
, splitratio=[0.61978340673276544, 0.69977512898866912])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork")
if Pdb2pqrOpalService_ws_nbcr_net_7 is not None and GetURLFromList_8 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
Pdb2pqrOpalService_ws_nbcr_net_7, GetURLFromList_8, "result", "urllist", blocking=True
, splitratio=[0.73247388879852338, 0.69014271703344965])
except:
print("WARNING: failed to restore connection between Pdb2pqrOpalService_ws_nbcr_net_7 and GetURLFromList_8 in network Pdb2pqrWS_3.macroNetwork")
if GetURLFromList_8 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
GetURLFromList_8, UpdateReceptor_9, "url", "pqr", blocking=True
, splitratio=[0.35224914715245104, 0.47693375858097758])
except:
print("WARNING: failed to restore connection between GetURLFromList_8 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork")
if CheckFileFormat_6 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, UpdateReceptor_9, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.57865377076653579, 0.45824116584600394])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork")
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
if input_Ports_4 is not None and CheckFileFormat_6 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
input_Ports_4, CheckFileFormat_6, "new", "value", blocking=True
, splitratio=[0.28291581858817416, 0.70581213384962171])
except:
print("WARNING: failed to restore connection between input_Ports_4 and CheckFileFormat_6 in network Pdb2pqrWS_3.macroNetwork")
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "receptor_obj", "new", blocking=True
, splitratio=[0.24354423773729619, 0.72115604180615911])
except:
print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork")
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "pdb2pqr_result", "new", blocking=True
, splitratio=[0.31141907324539131, 0.41794097665671487])
except:
print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork")
Pdb2pqrWS_3.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_4.outputPorts[1].configure(name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[2].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(name='UpdateReceptor_receptor_obj')
output_Ports_5.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_3.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_3.outputPorts[0].configure(name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_3.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_3.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_3.shrink()
Pdb2pqrWS_3.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroNode named Pdb2pqrWS in network self.macroNetwork")
print_exc()
Pdb2pqrWS_3=None
try:
## saving node PrepareReceptorWS ##
from NetworkEditor.macros import MacroNode
PrepareReceptorWS_10 = MacroNode(name='PrepareReceptorWS')
self.macroNetwork.addNode(PrepareReceptorWS_10, 217, 140)
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
input_Ports_11.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
input_Ports_11.move(145, 8)
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
output_Ports_12.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
output_Ports_12.move(29, 412)
from Vision.StandardNodes import Generic
CheckFileFormat_13 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(CheckFileFormat_13,46,64)
CheckFileFormat_13.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'download_loc', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr = value.get_ext_loc('''pqr''')
pdb = value.get_ext_loc('''pdb''')
download_loc = value.get_workdir() + os.sep + value.get_id() + '''.pdbqt'''
if pqr != None:
if value.get_ext_type('''pqr''') == '''url''':
receptor_url = pqr
receptor_local = ""
else:
receptor_url = ""
receptor_local = pqr
elif pdb != None:
if value.get_ext_type('''pdb''') == '''url''':
receptor_url = pdb
receptor_local = ""
else:
receptor_url = ""
receptor_local = pdb
else:
print "*** ERROR: pqr and pqr both missing from receptor object"
print receptor_obj.ext_loc
return '''stop'''
self.outputData(receptor_obj=value, receptor_url=receptor_url, receptor_local=receptor_local, download_loc=download_loc)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''receptor_url'''), self.getOutputPortByName('''receptor_local'''), self.getOutputPortByName('''download_loc''')])
"""
CheckFileFormat_13.configure(function=code)
CheckFileFormat_13.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
PrepareReceptorOpalService_ws_nbcr_net_14 = FunctionNode(functionOrString='PrepareReceptorOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'PrepareReceptorOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}}, name='PrepareReceptorOpalService_ws_nbcr_net', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(PrepareReceptorOpalService_ws_nbcr_net_14,180,128)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].configure(*(), **{'defaultValue': None})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].configure(*(), **{'defaultValue': None, 'required': True})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].configure(*(), **{'defaultValue': None, 'required': True})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['execPath'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_15 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(GetURLFromList_15,180,186)
GetURLFromList_15.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
GetURLFromList_15.configure(*(), **{'paramPanelImmediate': 1})
from WebServices.VisionInterface.WSNodes import DownloadToFileNode
DownloadToFile_16 = DownloadToFileNode(constrkw={}, name='DownloadToFile', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(DownloadToFile_16,80,272)
DownloadToFile_16.inputPortByName['url'].configure(*(), **{'defaultValue': None})
DownloadToFile_16.inputPortByName['filename'].configure(*(), **{'defaultValue': None})
DownloadToFile_16.inputPortByName['url'].rebindWidget()
DownloadToFile_16.inputPortByName['url'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['url'].unbindWidget()
DownloadToFile_16.inputPortByName['filename'].rebindWidget()
DownloadToFile_16.inputPortByName['filename'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['filename'].unbindWidget()
DownloadToFile_16.inputPortByName['overwrite'].widget.set(1, run=False)
DownloadToFile_16.configure(*(), **{'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_17 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(UpdateReceptor_17,46,358)
UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'pdbqt', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_prepared_obj', 'datatype': 'receptor_prepared', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900'})
UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pdbqt):
from AutoDockTools.VisionInterface.Adt.receptor_prepared import receptor_prepared
if pdbqt != '''no data yet''':
receptor_prepared_obj = receptor_prepared(pdbqt)
receptor_obj.set_ext_loc(pdbqt)
receptor_result = pdbqt
else:
pdbqt_org = receptor_obj.get_ext_loc('''pdbqt''')
receptor_prepared_obj = receptor_prepared(pdbqt_org)
receptor_result = pdbqt_org
pass
self.outputData(receptor_prepared_obj = receptor_prepared_obj, receptor_result=receptor_result)
"""
UpdateReceptor_17.configure(function=code)
UpdateReceptor_17.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_10.macroNetwork.freeze()
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
if input_Ports_11 is not None and CheckFileFormat_13 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, CheckFileFormat_13, "new", "value", blocking=True
, splitratio=[0.64907843562020084, 0.47057253960060474])
except:
print("WARNING: failed to restore connection between input_Ports_11 and CheckFileFormat_13 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_url", "url", blocking=True
, splitratio=[0.6171192646814192, 0.42883431331137822])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_local", "r", blocking=True
, splitratio=[0.66136144381723583, 0.28482114514549767])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if input_Ports_11 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, PrepareReceptorOpalService_ws_nbcr_net_14, "new", "C", blocking=True
, splitratio=[0.53817543437956172, 0.61119702937572407])
except:
print("WARNING: failed to restore connection between input_Ports_11 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if PrepareReceptorOpalService_ws_nbcr_net_14 is not None and GetURLFromList_15 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
PrepareReceptorOpalService_ws_nbcr_net_14, GetURLFromList_15, "result", "urllist", blocking=True
, splitratio=[0.43369347916867251, 0.26566786648658042])
except:
print("WARNING: failed to restore connection between PrepareReceptorOpalService_ws_nbcr_net_14 and GetURLFromList_15 in network PrepareReceptorWS_10.macroNetwork")
if GetURLFromList_15 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
GetURLFromList_15, DownloadToFile_16, "url", "url", blocking=True
, splitratio=[0.70502483723033316, 0.71683158018466053])
except:
print("WARNING: failed to restore connection between GetURLFromList_15 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, DownloadToFile_16, "download_loc", "filename", blocking=True
, splitratio=[0.60455581032885575, 0.35606890231085681])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, UpdateReceptor_17, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.74908230670336207, 0.38226563370205602])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork")
if DownloadToFile_16 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
DownloadToFile_16, UpdateReceptor_17, "filename", "pdbqt", blocking=True
, splitratio=[0.38698393490575966, 0.2874426709930199])
except:
print("WARNING: failed to restore connection between DownloadToFile_16 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork")
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_prepared_obj", "new", blocking=True
, splitratio=[0.69589857263374943, 0.59566078506240416])
except:
print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork")
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_result", "new", blocking=True
, splitratio=[0.44926362052272689, 0.38628711158860896])
except:
print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork")
PrepareReceptorWS_10.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_11.outputPorts[1].configure(name='CheckFileFormat_value')
input_Ports_11.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_12.inputPorts[1].configure(singleConnection='auto')
output_Ports_12.inputPorts[2].configure(singleConnection='auto')
output_Ports_12.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj')
output_Ports_12.inputPorts[2].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.inputPorts[0].configure(name='CheckFileFormat_value')
PrepareReceptorWS_10.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_10.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_10.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_10.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_10.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptorWS_10.outputPorts[1].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_10.shrink()
PrepareReceptorWS_10.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroNode named PrepareReceptorWS in network self.macroNetwork")
print_exc()
PrepareReceptorWS_10=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network PrepareReceptor ##
input_Ports_1 = self.macroNetwork.ipNode
Pdb2pqrWS_3 = self.macroNetwork.nodes[2]
if input_Ports_1 is not None and Pdb2pqrWS_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Pdb2pqrWS_3, "new", "CheckFileFormat_value", blocking=True
, splitratio=[0.73531020066010289, 0.24042404972613104])
except:
print("WARNING: failed to restore connection between input_Ports_1 and Pdb2pqrWS_3 in network self.macroNetwork")
PrepareReceptorWS_10 = self.macroNetwork.nodes[3]
if Pdb2pqrWS_3 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
Pdb2pqrWS_3, PrepareReceptorWS_10, "UpdateReceptor_receptor_obj", "CheckFileFormat_value", blocking=True
, splitratio=[0.54479169827535734, 0.4847384502006486])
except:
print("WARNING: failed to restore connection between Pdb2pqrWS_3 and PrepareReceptorWS_10 in network self.macroNetwork")
if input_Ports_1 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareReceptorWS_10, "new", "PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True
, splitratio=[0.37730151685222141, 0.48897820190498614])
except:
print("WARNING: failed to restore connection between input_Ports_1 and PrepareReceptorWS_10 in network self.macroNetwork")
output_Ports_2 = self.macroNetwork.opNode
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_prepared_obj", "new", blocking=True
, splitratio=[0.64110508898616414, 0.45535290355389196])
except:
print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork")
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_result", "new", blocking=True
, splitratio=[0.45846842546122241, 0.44240009354017412])
except:
print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork")
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_1.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_2.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
## configure MacroNode input ports
PrepareReceptor_0.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_0.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_0.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_0.inputPorts[1].configure(datatype='boolean')
## configure MacroNode output ports
PrepareReceptor_0.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_0.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptor_0.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_0.outputPorts[1].configure(datatype='string')
PrepareReceptor_0.shrink()
## reset modifications ##
PrepareReceptor_0.resetTags()
PrepareReceptor_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVS_9 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_10 = self.macroNetwork.ipNode
input_Ports_10.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_10 = None
try:
## saving node output Ports ##
output_Ports_11 = self.macroNetwork.opNode
output_Ports_11.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_11 = None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_12 = Generic(constrkw={},
name='PrepareADVSInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_12, 217, 76)
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'autogrid_results',
'cast': True,
'datatype': 'autogrid_results',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'dpf_template_obj',
'cast': True,
'datatype': 'dpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#9933FF',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'dpf_template_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'autogrid_res_url',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'autogrid_res_local',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_12.configure(function=code)
PrepareADVSInputs_12.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
)
print_exc()
PrepareADVSInputs_12 = None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_13 = FunctionNode(
functionOrString='autodock_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autodock_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
}
},
name='autodock_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_13, 217,
132)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_run'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['lib'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file_url'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_evals'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['sched'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_generations'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['dpf'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['utar'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_pop_size'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['email'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_run'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'lib'].widget.configure(
*(), **{
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
autodock_kryptonite_nbcr_net_13.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'sched'].widget.configure(*(), **{'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'sched'].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'dpf'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['dpf'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'dpf'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'utar'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['utar'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'utar'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'execPath'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
autodock_kryptonite_nbcr_net_13 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_14 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_14, 217, 188)
GetMainURLFromList_14.inputPortByName['urls'].configure(
*(), **{'defaultValue': None})
GetMainURLFromList_14.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
)
print_exc()
GetMainURLFromList_14 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVS ##
input_Ports_10 = self.macroNetwork.ipNode
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"ligands",
blocking=True,
splitratio=[0.60597534741634829, 0.41083180453223428])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"autogrid_results",
blocking=True,
splitratio=[0.64561658610430228, 0.21974682015753622])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"dpf_template_obj",
blocking=True,
splitratio=[0.52491295380143521, 0.32751034461281114])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if autodock_kryptonite_nbcr_net_13 is not None and GetMainURLFromList_14 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_13,
GetMainURLFromList_14,
"result",
"urls",
blocking=True,
splitratio=[0.36974288957131424, 0.63465596053596318])
except:
print(
"WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_13 and GetMainURLFromList_14 in network self.macroNetwork"
)
output_Ports_11 = self.macroNetwork.opNode
if GetMainURLFromList_14 is not None and output_Ports_11 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_14,
output_Ports_11,
"newurl",
"new",
blocking=True,
splitratio=[0.34850477186787743, 0.35637513198385085])
except:
print(
"WARNING: failed to restore connection between GetMainURLFromList_14 and output_Ports_11 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.33230642287344903, 0.65770700108889613])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.50680104599665787, 0.51414170500293577])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"dpf_template_file",
"dpf",
blocking=True,
splitratio=[0.51615646597598808, 0.25661305528484007])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_url",
"u",
blocking=True,
splitratio=[0.5760732944947704, 0.2032376887917188])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_local",
"utar",
blocking=True,
splitratio=[0.52802808938949819, 0.66978534572736881])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_10 = self.macroNetwork.ipNode
input_Ports_10.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_10.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_10.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_11 = self.macroNetwork.opNode
output_Ports_11.inputPorts[1].configure(singleConnection='auto')
output_Ports_11.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
AutodockVS_9.inputPorts[0].configure(name='PrepareADVSInputs_ligands')
AutodockVS_9.inputPorts[0].configure(datatype='LigandDB')
AutodockVS_9.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVS_9.inputPorts[1].configure(datatype='autogrid_results')
AutodockVS_9.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVS_9.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode output ports
AutodockVS_9.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AutodockVS_9.outputPorts[0].configure(datatype='string')
AutodockVS_9.shrink()
## reset modifications ##
AutodockVS_9.resetTags()
AutodockVS_9.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
ComputeGrids_18 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_19 = self.macroNetwork.ipNode
apply(input_Ports_19.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_19 = None
try:
## saving node output Ports ##
output_Ports_20 = self.macroNetwork.opNode
apply(output_Ports_20.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_20.move(217, 471)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_20 = None
try:
## saving node GetComputeGridsInputs ##
from Vision.StandardNodes import Generic
GetComputeGridsInputs_21 = Generic(constrkw={},
name='GetComputeGridsInputs',
library=stdlib)
self.macroNetwork.addNode(GetComputeGridsInputs_21, 217, 79)
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'receptor_pdbqt',
'cast': True,
'datatype': 'receptor_prepared',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#009900',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'gpf_obj',
'cast': True,
'datatype': 'gpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF3333',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'gpf_template_path',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'prepared_receptor',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, receptor_pdbqt, gpf_obj):
gpf_path = gpf_obj.fullpath
if not(os.path.exists(gpf_path)):
print "ERROR: GPF template " + gpf_path + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
ligand_lib = ligands.loc
prepared_receptor = receptor_pdbqt.path
pass
self.outputData(gpf_template_path=gpf_path, filter_file=filter_file, ligand_lib=ligand_lib, prepared_receptor=prepared_receptor)
## to ouput data on port gpf_template_path use
## self.outputData(gpf_template_path=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port prepared_receptor use
## self.outputData(prepared_receptor=data)
"""
GetComputeGridsInputs_21.configure(function=code)
apply(GetComputeGridsInputs_21.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named GetComputeGridsInputs in network self.macroNetwork"
print_exc()
GetComputeGridsInputs_21 = None
try:
## saving node prepareGPF_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
prepareGPF_kryptonite_nbcr_net_22 = FunctionNode(
functionOrString='prepareGPF_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'singlelib': '',
'r_url': '',
'zpoints': '',
'filter_file_url': '',
'lib': '',
'ypoints': '',
'filter_file': '',
'gpf': '',
'xcenter': 'auto',
'urllib': '',
'p': '',
'r': '',
'o': '',
'zcenter': 'auto',
'v': False,
'userlib': '',
'xpoints': '',
'localRun': False,
'ycenter': 'auto',
'execPath': ''
},
constrkw={
'functionOrString': "'prepareGPF_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'singlelib': '',
'r_url': '',
'zpoints': '',
'filter_file_url': '',
'lib': '',
'ypoints': '',
'filter_file': '',
'gpf': '',
'xcenter': 'auto',
'urllib': '',
'p': '',
'r': '',
'o': '',
'zcenter': 'auto',
'v': False,
'userlib': '',
'xpoints': '',
'localRun': False,
'ycenter': 'auto',
'execPath': ''
}
},
name='prepareGPF_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(prepareGPF_kryptonite_nbcr_net_22, 217,
141)
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['singlelib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r_url'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zpoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.
inputPortByName['filter_file_url'].configure, (),
{'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ypoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.
inputPortByName['filter_file'].configure, (),
{'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xcenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zcenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['userlib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xpoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ycenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].
widget.configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].widget.set(
0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_22.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named prepareGPF_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
prepareGPF_kryptonite_nbcr_net_22 = None
try:
## saving node autogrid_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autogrid_kryptonite_nbcr_net_23 = FunctionNode(
functionOrString='autogrid_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'p_url': '',
'infile_url': '',
'l': 'output.glg',
'o': False,
'p': '',
'localRun': False,
'inFile': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autogrid_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'p_url': '',
'infile_url': '',
'l': 'output.glg',
'o': False,
'p': '',
'localRun': False,
'inFile': '',
'execPath': ''
}
},
name='autogrid_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autogrid_kryptonite_nbcr_net_23, 251,
292)
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['infile_url'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].widget.set(
r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].widget.set(
0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].widget.set(
r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(autogrid_kryptonite_nbcr_net_23.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named autogrid_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autogrid_kryptonite_nbcr_net_23 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_24 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_24, 251, 348)
apply(GetMainURLFromList_24.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_24.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_24 = None
try:
## saving node MakeAutogridResultObj ##
from Vision.StandardNodes import Generic
MakeAutogridResultObj_25 = Generic(constrkw={},
name='MakeAutogridResultObj',
library=stdlib)
self.macroNetwork.addNode(MakeAutogridResultObj_25, 121, 402)
apply(
MakeAutogridResultObj_25.addInputPort, (), {
'singleConnection': True,
'name': 'autogrid_result_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
MakeAutogridResultObj_25.addOutputPort, (), {
'name': 'autogrid_result_obj',
'datatype': 'autogrid_results',
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC'
})
code = """def doit(self, autogrid_result_url):
from AutoDockTools.VisionInterface.Adt.autogrid_results import autogrid_results
agro = autogrid_results(autogrid_result_url, '''url''')
pass
## to ouput data on port autogrid_result_obj use
self.outputData(autogrid_result_obj=agro)
"""
MakeAutogridResultObj_25.configure(function=code)
apply(MakeAutogridResultObj_25.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named MakeAutogridResultObj in network self.macroNetwork"
print_exc()
MakeAutogridResultObj_25 = None
try:
## saving node GetURLFromList ##
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_26 = GetURLFromListNode(constrkw={},
name='GetURLFromList',
library=wslib)
self.macroNetwork.addNode(GetURLFromList_26, 110, 198)
apply(GetURLFromList_26.inputPortByName['urllist'].configure, (),
{'defaultValue': None})
apply(GetURLFromList_26.inputPortByName['ext'].configure, (),
{'defaultValue': None})
GetURLFromList_26.inputPortByName['ext'].widget.set(r"gpf",
run=False)
apply(GetURLFromList_26.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore GetURLFromListNode named GetURLFromList in network self.macroNetwork"
print_exc()
GetURLFromList_26 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network ComputeGrids ##
input_Ports_19 = self.macroNetwork.ipNode
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"ligands",
blocking=True,
splitratio=[0.25038057532685992, 0.40242243717082576])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"receptor_pdbqt",
blocking=True,
splitratio=[0.31642654296910228, 0.49356822236979669])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"gpf_obj",
blocking=True,
splitratio=[0.57570983312901203, 0.33826779179418875])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"gpf_template_path",
"gpf",
blocking=True,
splitratio=[0.37911517364560754, 0.49588454022594075])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.51555458245420727, 0.58910990532612562])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.45378244060628786, 0.49829462092378918])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"prepared_receptor",
"r",
blocking=True,
splitratio=[0.30158184825681655, 0.46256232709378253])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
autogrid_kryptonite_nbcr_net_23,
"prepared_receptor",
"inFile",
blocking=True,
splitratio=[0.63016045430148715, 0.62091422998177115])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
if autogrid_kryptonite_nbcr_net_23 is not None and GetMainURLFromList_24 is not None:
try:
self.macroNetwork.connectNodes(
autogrid_kryptonite_nbcr_net_23,
GetMainURLFromList_24,
"result",
"urls",
blocking=True,
splitratio=[0.4713453370864038, 0.73699665503637379])
except:
print "WARNING: failed to restore connection between autogrid_kryptonite_nbcr_net_23 and GetMainURLFromList_24 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and MakeAutogridResultObj_25 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24,
MakeAutogridResultObj_25,
"newurl",
"autogrid_result_url",
blocking=True,
splitratio=[0.37530325590010172, 0.67260462300696811])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and MakeAutogridResultObj_25 in network self.macroNetwork"
output_Ports_20 = self.macroNetwork.opNode
if MakeAutogridResultObj_25 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
MakeAutogridResultObj_25,
output_Ports_20,
"autogrid_result_obj",
"new",
blocking=True,
splitratio=[0.54860274312929591, 0.61692487705230459])
except:
print "WARNING: failed to restore connection between MakeAutogridResultObj_25 and output_Ports_20 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24,
output_Ports_20,
"newurl",
"new",
blocking=True,
splitratio=[0.56961778623989434, 0.55443680742298707])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and output_Ports_20 in network self.macroNetwork"
if prepareGPF_kryptonite_nbcr_net_22 is not None and GetURLFromList_26 is not None:
try:
self.macroNetwork.connectNodes(
prepareGPF_kryptonite_nbcr_net_22,
GetURLFromList_26,
"result",
"urllist",
blocking=True,
splitratio=[0.38550670487593142, 0.45424125807822219])
except:
print "WARNING: failed to restore connection between prepareGPF_kryptonite_nbcr_net_22 and GetURLFromList_26 in network self.macroNetwork"
if GetURLFromList_26 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetURLFromList_26,
autogrid_kryptonite_nbcr_net_23,
"url",
"p_url",
blocking=True,
splitratio=[0.65566147293832433, 0.57782517914212228])
except:
print "WARNING: failed to restore connection between GetURLFromList_26 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_19 = self.macroNetwork.ipNode
input_Ports_19.outputPorts[1].configure(
name='GetComputeGridsInputs_ligands')
input_Ports_19.outputPorts[2].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_19.outputPorts[3].configure(
name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_20 = self.macroNetwork.opNode
output_Ports_20.inputPorts[1].configure(singleConnection='auto')
output_Ports_20.inputPorts[2].configure(singleConnection='auto')
output_Ports_20.inputPorts[1].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_20.inputPorts[2].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
ComputeGrids_18.inputPorts[0].configure(
name='GetComputeGridsInputs_ligands')
ComputeGrids_18.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_18.inputPorts[1].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_18.inputPorts[1].configure(datatype='receptor_prepared')
ComputeGrids_18.inputPorts[2].configure(
name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_18.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode output ports
ComputeGrids_18.outputPorts[0].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_18.outputPorts[0].configure(datatype='autogrid_results')
ComputeGrids_18.outputPorts[1].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_18.outputPorts[1].configure(datatype='string')
ComputeGrids_18.shrink()
## reset modifications ##
ComputeGrids_18.resetTags()
ComputeGrids_18.buildOriginalList()
from Vision.StandardNodes import stdlib
try:
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node PrepareReceptor2 ##
from Adt.Macro.PrepareReceptor import PrepareReceptor
PrepareReceptor2_0 = PrepareReceptor(constrkw={}, name='PrepareReceptor2', library=Adt)
masterNet.addNode(PrepareReceptor2_0,301,206)
apply(PrepareReceptor2_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
Pdb2pqrWS_3 = PrepareReceptor2_0.macroNetwork.nodes[2]
Pdb2pqrOpalService_ws_nbcr_net_7 = Pdb2pqrWS_3.macroNetwork.nodes[3]
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False)
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
TrajQR_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(183, 405)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node Make_Zip_File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make_Zip_File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 47, 75)
apply(Make_Zip_File_3.inputPortByName['input_directory'].configure,
(), {'defaultValue': None})
apply(
Make_Zip_File_3.inputPortByName['output_directory'].configure,
(), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_name'].configure, (),
{'defaultValue': None})
apply(Make_Zip_File_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MakeZipFileNE named Make_Zip_File in network self.macroNetwork"
print_exc()
Make_Zip_File_3 = None
try:
## saving node TrajQR_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
TrajQR_kryptonite_nbcr_net_4 = FunctionNode(
functionOrString='TrajQR_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
},
constrkw={
'functionOrString': "'TrajQR_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
}
},
name='TrajQR_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(TrajQR_kryptonite_nbcr_net_4, 279, 135)
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].configure,
(), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qh_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qr_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.
inputPortByName['compressed_pdbs'].configure, (), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].widget.set(
0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].widget.set(
r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qh_filename'].widget.set(r"qh.tre", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qr_filename'].widget.set(r"qr.out", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].widget.set(r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'localRun'].widget.set(0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(TrajQR_kryptonite_nbcr_net_4.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named TrajQR_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
TrajQR_kryptonite_nbcr_net_4 = None
try:
## saving node SelectOnExtension ##
from Vision.StandardNodes import SelectOnExtension
SelectOnExtension_5 = SelectOnExtension(constrkw={},
name='SelectOnExtension',
library=stdlib)
self.macroNetwork.addNode(SelectOnExtension_5, 279, 192)
apply(SelectOnExtension_5.inputPortByName['filenames'].configure,
(), {'defaultValue': None})
apply(SelectOnExtension_5.inputPortByName['extension'].configure,
(), {'defaultValue': None})
SelectOnExtension_5.inputPortByName['extension'].widget.set(
r".out", run=False)
apply(SelectOnExtension_5.configure, (),
{'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore SelectOnExtension named SelectOnExtension in network self.macroNetwork"
print_exc()
SelectOnExtension_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 123, 281)
apply(
Index_6.inputPortByName['data'].configure, (), {
'datatype': 'list',
'defaultValue': None,
'originalDatatype': 'None'
})
apply(Index_6.inputPortByName['index'].configure, (),
{'defaultValue': None})
apply(Index_6.outputPortByName['data'].configure, (),
{'datatype': 'string'})
apply(Index_6.inputPortByName['index'].widget.configure, (), {
'max': 0,
'min': -1
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_6 = None
try:
## saving node GetSelectedPDBs ##
from Vision.StandardNodes import Generic
GetSelectedPDBs_7 = Generic(constrkw={},
name='GetSelectedPDBs',
library=stdlib)
self.macroNetwork.addNode(GetSelectedPDBs_7, 200, 346)
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'trajqr_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_in_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_out_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addOutputPort, (), {
'name': 'pdb_out_dir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, trajqr_url, pdb_in_dir, pdb_out_dir):
pdb_in_dir = os.path.abspath(pdb_in_dir)
pdb_out_dir = os.path.abspath(pdb_out_dir)
import urllib
import shutil
pdb_list = []
f = urllib.urlopen(trajqr_url)
for i in f.readlines():
pdb_file = i.strip('''
''')+'''.pdb'''
infile = pdb_in_dir + os.sep + pdb_file
outfile = pdb_out_dir + os.sep + pdb_file
shutil.copyfile(infile, outfile)
f.close
pass
## to ouput data on port pdb_list use
self.outputData(pdb_out_dir=pdb_out_dir)
"""
GetSelectedPDBs_7.configure(function=code)
apply(GetSelectedPDBs_7.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named GetSelectedPDBs in network self.macroNetwork"
print_exc()
GetSelectedPDBs_7 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network TrajQR ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
Make_Zip_File_3,
"new",
"input_directory",
blocking=True,
splitratio=[0.67469172328672133, 0.50941480178765064])
except:
print "WARNING: failed to restore connection between input_Ports_1 and Make_Zip_File_3 in network self.macroNetwork"
if input_Ports_1 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
TrajQR_kryptonite_nbcr_net_4,
"new",
"rmsd",
blocking=True,
splitratio=[0.45681934134493246, 0.33803410340720857])
except:
print "WARNING: failed to restore connection between input_Ports_1 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if Make_Zip_File_3 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
TrajQR_kryptonite_nbcr_net_4,
"zipfile",
"compressed_pdbs",
blocking=True,
splitratio=[0.71081093868178202, 0.43908686250860129])
except:
print "WARNING: failed to restore connection between Make_Zip_File_3 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if TrajQR_kryptonite_nbcr_net_4 is not None and SelectOnExtension_5 is not None:
try:
self.macroNetwork.connectNodes(
TrajQR_kryptonite_nbcr_net_4,
SelectOnExtension_5,
"result",
"filenames",
blocking=True,
splitratio=[0.63533198718963335, 0.2560040659014205])
except:
print "WARNING: failed to restore connection between TrajQR_kryptonite_nbcr_net_4 and SelectOnExtension_5 in network self.macroNetwork"
if SelectOnExtension_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
SelectOnExtension_5,
Index_6,
"matching",
"data",
blocking=True,
splitratio=[0.65832290589891362, 0.21624347250969889])
except:
print "WARNING: failed to restore connection between SelectOnExtension_5 and Index_6 in network self.macroNetwork"
if Index_6 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
GetSelectedPDBs_7,
"data",
"trajqr_url",
blocking=True,
splitratio=[0.51754619993986595, 0.63949220525823236])
except:
print "WARNING: failed to restore connection between Index_6 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"Make_Zip_File_input_directory",
"pdb_in_dir",
blocking=True,
splitratio=[0.7121964126696847, 0.42697952864467786])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"new",
"pdb_out_dir",
blocking=True,
splitratio=[0.62460995639428174, 0.60275185701976297])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetSelectedPDBs_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetSelectedPDBs_7,
output_Ports_2,
"pdb_out_dir",
"new",
blocking=True,
splitratio=[0.7431176169343523, 0.73697976585137526])
except:
print "WARNING: failed to restore connection between GetSelectedPDBs_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
input_Ports_1.outputPorts[3].configure(
name='GetSelectedPDBs_pdb_out_dir')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='GetSelectedPDBs_pdb_out_dir')
## configure MacroNode input ports
TrajQR_0.inputPorts[0].configure(name='Make_Zip_File_input_directory')
TrajQR_0.inputPorts[0].configure(datatype='string')
TrajQR_0.inputPorts[1].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
TrajQR_0.inputPorts[1].configure(datatype='string')
TrajQR_0.inputPorts[2].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
TrajQR_0.outputPorts[0].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.outputPorts[0].configure(datatype='string')
TrajQR_0.shrink()
## reset modifications ##
TrajQR_0.resetTags()
TrajQR_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
Vina_30 = self
from traceback import print_exc
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_31 = self.macroNetwork.ipNode
apply(input_Ports_31.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_31=None
try:
## saving node output Ports ##
output_Ports_32 = self.macroNetwork.opNode
apply(output_Ports_32.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_32=None
try:
## saving node AutodockVina_Screening_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
AutodockVina_Screening_kryptonite_nbcr_net_33 = FunctionNode(functionOrString='AutodockVina_Screening_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'num_modes': '', 'energy_range': '', 'seed': '', 'receptor': '', 'size_y': '', 'size_z': '', 'out': '', 'log': '', 'urllib': '', 'exhaustiveness': '', 'localRun': False, 'flex': '', 'center_z': '', 'center_x': '', 'center_y': '', 'userlib': '', 'size_x': '', 'config': '', 'filter': '', 'ligand_db': '', 'cpu': '', 'execPath': ''}, constrkw={'functionOrString': "'AutodockVina_Screening_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'num_modes': '', 'energy_range': '', 'seed': '', 'receptor': '', 'size_y': '', 'size_z': '', 'out': '', 'log': '', 'urllib': '', 'exhaustiveness': '', 'localRun': False, 'flex': '', 'center_z': '', 'center_x': '', 'center_y': '', 'userlib': '', 'size_x': '', 'config': '', 'filter': '', 'ligand_db': '', 'cpu': '', 'execPath': ''}}, name='AutodockVina_Screening_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(AutodockVina_Screening_kryptonite_nbcr_net_33,217,185)
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['num_modes'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['energy_range'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['seed'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['receptor'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_y'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_z'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['out'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['log'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['urllib'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['exhaustiveness'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['flex'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_z'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_x'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_y'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['userlib'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_x'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['config'].configure, (), {'defaultValue': None, 'required': True})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['filter'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['ligand_db'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['cpu'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['execPath'].configure, (), {'defaultValue': None})
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['num_modes'].widget.configure, (), {'choices': ('1', '2', '3', '4', '5', '6', '7', '8', '9', '10')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['num_modes'].widget.set(r"", run=False)
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['energy_range'].widget.configure, (), {'choices': ('1', '2', '3')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['energy_range'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['seed'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['receptor'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['receptor'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['receptor'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['out'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['log'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['urllib'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['urllib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['urllib'].unbindWidget()
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['exhaustiveness'].widget.configure, (), {'choices': ('1', '2', '3', '4', '5', '6', '7', '8')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['exhaustiveness'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['localRun'].widget.set(0, run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['flex'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['center_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['userlib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['size_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['config'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['config'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['config'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['filter'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['filter'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['filter'].unbindWidget()
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['ligand_db'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'asinex', 'fda_approved', 'otava', 'zinc_natural_products')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['ligand_db'].widget.set(r"", run=False)
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['cpu'].widget.configure, (), {'choices': ('1', '2')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['cpu'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName['execPath'].widget.set(r"", run=False)
apply(AutodockVina_Screening_kryptonite_nbcr_net_33.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named AutodockVina_Screening_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
AutodockVina_Screening_kryptonite_nbcr_net_33=None
try:
## saving node PrepareVinaInputs ##
from Vision.StandardNodes import Generic
PrepareVinaInputs_34 = Generic(constrkw={}, name='PrepareVinaInputs', library=stdlib)
self.macroNetwork.addNode(PrepareVinaInputs_34,140,107)
apply(PrepareVinaInputs_34.addInputPort, (), {'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor_prepared', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900', 'originalDatatype': 'None'})
apply(PrepareVinaInputs_34.addInputPort, (), {'singleConnection': True, 'name': 'ligand_obj', 'cast': True, 'datatype': 'LigandDB', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'rect', 'color': '#FFCCFF', 'originalDatatype': 'None'})
apply(PrepareVinaInputs_34.addOutputPort, (), {'name': 'receptor_file', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareVinaInputs_34.addOutputPort, (), {'name': 'ligand_lib', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(PrepareVinaInputs_34.addOutputPort, (), {'name': 'filter_file', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, ligand_obj):
receptor_file = receptor_obj.path
filter_file = ligand_obj.filter_file
ligand_lib = ligand_obj.loc
if receptor_obj.type == "local":
if not(os.path.exists(receptor_file)):
print "ERROR: receptor_file " + receptor_file + " does not exist"
return '''stop'''
pass
self.outputData(receptor_file=receptor_file, ligand_lib=ligand_lib, filter_file=filter_file)
## to ouput data on port receptor_file use
## self.outputData(receptor_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
"""
PrepareVinaInputs_34.configure(function=code)
apply(PrepareVinaInputs_34.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named PrepareVinaInputs in network self.macroNetwork"
print_exc()
PrepareVinaInputs_34=None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_35 = GetMainURLFromListNode(constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_35,217,248)
apply(GetMainURLFromList_35.inputPortByName['urls'].configure, (), {'defaultValue': None})
apply(GetMainURLFromList_35.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_35=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network Vina ##
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34, AutodockVina_Screening_kryptonite_nbcr_net_33, "receptor_file", "receptor", blocking=True
, splitratio=[0.48630431331124768, 0.72717758735716731])
except:
print "WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34, AutodockVina_Screening_kryptonite_nbcr_net_33, "ligand_lib", "urllib", blocking=True
, splitratio=[0.61963739449043087, 0.74955133389937689])
except:
print "WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34, AutodockVina_Screening_kryptonite_nbcr_net_33, "filter_file", "filter", blocking=True
, splitratio=[0.32670226336274166, 0.25123642944789149])
except:
print "WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
if AutodockVina_Screening_kryptonite_nbcr_net_33 is not None and GetMainURLFromList_35 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVina_Screening_kryptonite_nbcr_net_33, GetMainURLFromList_35, "result", "urls", blocking=True
, splitratio=[0.23401196873379349, 0.68593608346615742])
except:
print "WARNING: failed to restore connection between AutodockVina_Screening_kryptonite_nbcr_net_33 and GetMainURLFromList_35 in network self.macroNetwork"
output_Ports_32 = self.macroNetwork.opNode
if GetMainURLFromList_35 is not None and output_Ports_32 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_35, output_Ports_32, "newurl", "new", blocking=True
, splitratio=[0.26588001265563421, 0.34355863787969732])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_35 and output_Ports_32 in network self.macroNetwork"
input_Ports_31 = self.macroNetwork.ipNode
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31, PrepareVinaInputs_34, "new", "receptor_obj", blocking=True
, splitratio=[0.59193136382656331, 0.41134942510734418])
except:
print "WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31, PrepareVinaInputs_34, "new", "ligand_obj", blocking=True
, splitratio=[0.29092159940560591, 0.60619808825531374])
except:
print "WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
if input_Ports_31 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31, AutodockVina_Screening_kryptonite_nbcr_net_33, "new", "config", blocking=True
, splitratio=[0.24239548372031838, 0.55842775396640953])
except:
print "WARNING: failed to restore connection between input_Ports_31 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_31 = self.macroNetwork.ipNode
input_Ports_31.outputPorts[1].configure(name='PrepareVinaInputs_receptor_obj')
input_Ports_31.outputPorts[2].configure(name='PrepareVinaInputs_ligand_obj')
input_Ports_31.outputPorts[3].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config')
## modifying MacroOutputNode dynamic ports
output_Ports_32 = self.macroNetwork.opNode
output_Ports_32.inputPorts[1].configure(singleConnection='auto')
output_Ports_32.inputPorts[1].configure(name='GetMainURLFromList_newurl')
## configure MacroNode input ports
Vina_30.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_30.inputPorts[0].configure(datatype='receptor_prepared')
Vina_30.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_30.inputPorts[1].configure(datatype='LigandDB')
Vina_30.inputPorts[2].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_30.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
Vina_30.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_30.outputPorts[0].configure(datatype='string')
Vina_30.shrink()
## reset modifications ##
Vina_30.resetTags()
Vina_30.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVS_9 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_10 = self.macroNetwork.ipNode
apply(input_Ports_10.configure, (), {"paramPanelImmediate": 1, "expanded": False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_10 = None
try:
## saving node output Ports ##
output_Ports_11 = self.macroNetwork.opNode
apply(output_Ports_11.configure, (), {"paramPanelImmediate": 1, "expanded": False})
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_11 = None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_12 = Generic(constrkw={}, name="PrepareADVSInputs", library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_12, 217, 76)
apply(
PrepareADVSInputs_12.addInputPort,
(),
{
"singleConnection": True,
"name": "ligands",
"cast": True,
"datatype": "LigandDB",
"defaultValue": None,
"required": True,
"height": 8,
"width": 12,
"shape": "rect",
"color": "#FFCCFF",
"originalDatatype": "None",
},
)
apply(
PrepareADVSInputs_12.addInputPort,
(),
{
"singleConnection": True,
"name": "autogrid_results",
"cast": True,
"datatype": "autogrid_results",
"defaultValue": None,
"required": True,
"height": 8,
"width": 12,
"shape": "triangle",
"color": "#FF33CC",
"originalDatatype": "None",
},
)
apply(
PrepareADVSInputs_12.addInputPort,
(),
{
"singleConnection": True,
"name": "dpf_template_obj",
"cast": True,
"datatype": "dpf_template",
"defaultValue": None,
"required": True,
"height": 8,
"width": 12,
"shape": "triangle",
"color": "#9933FF",
"originalDatatype": "None",
},
)
apply(
PrepareADVSInputs_12.addOutputPort,
(),
{
"name": "filter_file",
"datatype": "string",
"height": 8,
"width": 12,
"shape": "oval",
"color": "white",
},
)
apply(
PrepareADVSInputs_12.addOutputPort,
(),
{
"name": "ligand_lib",
"datatype": "string",
"height": 8,
"width": 12,
"shape": "oval",
"color": "white",
},
)
apply(
PrepareADVSInputs_12.addOutputPort,
(),
{
"name": "dpf_template_file",
"datatype": "string",
"height": 8,
"width": 12,
"shape": "oval",
"color": "white",
},
)
apply(
PrepareADVSInputs_12.addOutputPort,
(),
{
"name": "autogrid_res_url",
"datatype": "string",
"height": 8,
"width": 12,
"shape": "oval",
"color": "white",
},
)
apply(
PrepareADVSInputs_12.addOutputPort,
(),
{
"name": "autogrid_res_local",
"datatype": "string",
"height": 8,
"width": 12,
"shape": "oval",
"color": "white",
},
)
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_12.configure(function=code)
apply(PrepareADVSInputs_12.configure, (), {"paramPanelImmediate": 1, "expanded": False})
except:
print "WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
print_exc()
PrepareADVSInputs_12 = None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_13 = FunctionNode(
functionOrString="autodock_kryptonite_nbcr_net",
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
"ga_run": "",
"lib": "",
"filter_file_url": "",
"ga_num_evals": "",
"filter_file": "",
"sched": "SGE",
"urllib": "",
"ga_num_generations": "",
"dpf": "",
"u": "",
"utar": "",
"userlib": "",
"ga_pop_size": "",
"localRun": False,
"email": "",
"execPath": "",
},
constrkw={
"functionOrString": "'autodock_kryptonite_nbcr_net'",
"host": '"http://kryptonite.nbcr.net/opal2"',
"namedArgs": {
"ga_run": "",
"lib": "",
"filter_file_url": "",
"ga_num_evals": "",
"filter_file": "",
"sched": "SGE",
"urllib": "",
"ga_num_generations": "",
"dpf": "",
"u": "",
"utar": "",
"userlib": "",
"ga_pop_size": "",
"localRun": False,
"email": "",
"execPath": "",
},
},
name="autodock_kryptonite_nbcr_net",
library=wslib,
)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_13, 217, 132)
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["ga_run"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["lib"].configure, (), {"defaultValue": None})
apply(
autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file_url"].configure, (), {"defaultValue": None}
)
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["ga_num_evals"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["sched"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["urllib"].configure, (), {"defaultValue": None})
apply(
autodock_kryptonite_nbcr_net_13.inputPortByName["ga_num_generations"].configure,
(),
{"defaultValue": None},
)
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["dpf"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["u"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["utar"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["userlib"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["ga_pop_size"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["localRun"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["email"].configure, (), {"defaultValue": None})
apply(autodock_kryptonite_nbcr_net_13.inputPortByName["execPath"].configure, (), {"defaultValue": None})
autodock_kryptonite_nbcr_net_13.inputPortByName["ga_run"].widget.set(r"", run=False)
apply(
autodock_kryptonite_nbcr_net_13.inputPortByName["lib"].widget.configure,
(),
{
"choices": (
"sample",
"NCIDS_SC",
"NCI_DS1",
"NCI_DS2",
"human_metabolome",
"chembridge_building_blocks",
"drugbank_nutraceutics",
"drugbank_smallmol",
"fda_approved",
)
},
)
autodock_kryptonite_nbcr_net_13.inputPortByName["lib"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file_url"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["ga_num_evals"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file"].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["filter_file"].unbindWidget()
apply(
autodock_kryptonite_nbcr_net_13.inputPortByName["sched"].widget.configure,
(),
{"choices": ("SGE", "CSF")},
)
autodock_kryptonite_nbcr_net_13.inputPortByName["sched"].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["urllib"].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["urllib"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["urllib"].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["ga_num_generations"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["dpf"].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["dpf"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["dpf"].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["u"].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["u"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["u"].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["utar"].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["utar"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["utar"].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName["userlib"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["ga_pop_size"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["localRun"].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["email"].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName["execPath"].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_13.configure, (), {"paramPanelImmediate": 1, "expanded": False})
except:
print "WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autodock_kryptonite_nbcr_net_13 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_14 = GetMainURLFromListNode(constrkw={}, name="GetMainURLFromList", library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_14, 217, 188)
apply(GetMainURLFromList_14.inputPortByName["urls"].configure, (), {"defaultValue": None})
apply(GetMainURLFromList_14.configure, (), {"paramPanelImmediate": 1, "expanded": False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_14 = None
# self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVS ##
input_Ports_10 = self.macroNetwork.ipNode
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"ligands",
blocking=True,
splitratio=[0.60597534741634829, 0.41083180453223428],
)
except:
print "WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"autogrid_results",
blocking=True,
splitratio=[0.64561658610430228, 0.21974682015753622],
)
except:
print "WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"dpf_template_obj",
blocking=True,
splitratio=[0.52491295380143521, 0.32751034461281114],
)
except:
print "WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
if autodock_kryptonite_nbcr_net_13 is not None and GetMainURLFromList_14 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_13,
GetMainURLFromList_14,
"result",
"urls",
blocking=True,
splitratio=[0.36974288957131424, 0.63465596053596318],
)
except:
print "WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_13 and GetMainURLFromList_14 in network self.macroNetwork"
output_Ports_11 = self.macroNetwork.opNode
if GetMainURLFromList_14 is not None and output_Ports_11 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_14,
output_Ports_11,
"newurl",
"new",
blocking=True,
splitratio=[0.34850477186787743, 0.35637513198385085],
)
except:
print "WARNING: failed to restore connection between GetMainURLFromList_14 and output_Ports_11 in network self.macroNetwork"
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.33230642287344903, 0.65770700108889613],
)
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.50680104599665787, 0.51414170500293577],
)
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"dpf_template_file",
"dpf",
blocking=True,
splitratio=[0.51615646597598808, 0.25661305528484007],
)
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_url",
"u",
blocking=True,
splitratio=[0.5760732944947704, 0.2032376887917188],
)
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_local",
"utar",
blocking=True,
splitratio=[0.52802808938949819, 0.66978534572736881],
)
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_10 = self.macroNetwork.ipNode
input_Ports_10.outputPorts[1].configure(name="PrepareADVSInputs_ligands")
input_Ports_10.outputPorts[2].configure(name="PrepareADVSInputs_autogrid_results")
input_Ports_10.outputPorts[3].configure(name="PrepareADVSInputs_dpf_template_obj")
## modifying MacroOutputNode dynamic ports
output_Ports_11 = self.macroNetwork.opNode
output_Ports_11.inputPorts[1].configure(singleConnection="auto")
output_Ports_11.inputPorts[1].configure(name="GetMainURLFromList_newurl")
## configure MacroNode input ports
AutodockVS_9.inputPorts[0].configure(name="PrepareADVSInputs_ligands")
AutodockVS_9.inputPorts[0].configure(datatype="LigandDB")
AutodockVS_9.inputPorts[1].configure(name="PrepareADVSInputs_autogrid_results")
AutodockVS_9.inputPorts[1].configure(datatype="autogrid_results")
AutodockVS_9.inputPorts[2].configure(name="PrepareADVSInputs_dpf_template_obj")
AutodockVS_9.inputPorts[2].configure(datatype="dpf_template")
## configure MacroNode output ports
AutodockVS_9.outputPorts[0].configure(name="GetMainURLFromList_newurl")
AutodockVS_9.outputPorts[0].configure(datatype="string")
AutodockVS_9.shrink()
## reset modifications ##
AutodockVS_9.resetTags()
AutodockVS_9.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
Vina_30 = self
from traceback import print_exc
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_31 = self.macroNetwork.ipNode
input_Ports_31.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_31 = None
try:
## saving node output Ports ##
output_Ports_32 = self.macroNetwork.opNode
output_Ports_32.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_32 = None
try:
## saving node AutodockVina_Screening_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
AutodockVina_Screening_kryptonite_nbcr_net_33 = FunctionNode(
functionOrString='AutodockVina_Screening_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'num_modes': '',
'energy_range': '',
'seed': '',
'receptor': '',
'size_y': '',
'size_z': '',
'out': '',
'log': '',
'urllib': '',
'exhaustiveness': '',
'localRun': False,
'flex': '',
'center_z': '',
'center_x': '',
'center_y': '',
'userlib': '',
'size_x': '',
'config': '',
'filter': '',
'ligand_db': '',
'cpu': '',
'execPath': ''
},
constrkw={
'functionOrString':
"'AutodockVina_Screening_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'num_modes': '',
'energy_range': '',
'seed': '',
'receptor': '',
'size_y': '',
'size_z': '',
'out': '',
'log': '',
'urllib': '',
'exhaustiveness': '',
'localRun': False,
'flex': '',
'center_z': '',
'center_x': '',
'center_y': '',
'userlib': '',
'size_x': '',
'config': '',
'filter': '',
'ligand_db': '',
'cpu': '',
'execPath': ''
}
},
name='AutodockVina_Screening_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(
AutodockVina_Screening_kryptonite_nbcr_net_33, 217, 185)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'seed'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_y'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_z'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'out'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'log'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'flex'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_z'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_x'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_y'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_x'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].configure(*(), **{
'defaultValue': None,
'required': True
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].widget.configure(
*(), **{
'choices':
('1', '2', '3', '4', '5', '6', '7', '8', '9', '10')
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].widget.configure(
*(), **{'choices': ('1', '2', '3')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'seed'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'out'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'log'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].widget.configure(
*(),
**{'choices': ('1', '2', '3', '4', '5', '6', '7', '8')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'localRun'].widget.set(0, run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'flex'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'userlib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].widget.configure(
*(), **{
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'asinex', 'fda_approved', 'otava',
'zinc_natural_products')
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].widget.configure(*(), **{'choices': ('1', '2')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named AutodockVina_Screening_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
AutodockVina_Screening_kryptonite_nbcr_net_33 = None
try:
## saving node PrepareVinaInputs ##
from Vision.StandardNodes import Generic
PrepareVinaInputs_34 = Generic(constrkw={},
name='PrepareVinaInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareVinaInputs_34, 140, 107)
PrepareVinaInputs_34.addInputPort(
*(), **{
'singleConnection': True,
'name': 'receptor_obj',
'cast': True,
'datatype': 'receptor_prepared',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#009900',
'originalDatatype': 'None'
})
PrepareVinaInputs_34.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligand_obj',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'receptor_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, receptor_obj, ligand_obj):
receptor_file = receptor_obj.path
filter_file = ligand_obj.filter_file
ligand_lib = ligand_obj.loc
if receptor_obj.type == "local":
if not(os.path.exists(receptor_file)):
print "ERROR: receptor_file " + receptor_file + " does not exist"
return '''stop'''
pass
self.outputData(receptor_file=receptor_file, ligand_lib=ligand_lib, filter_file=filter_file)
## to ouput data on port receptor_file use
## self.outputData(receptor_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
"""
PrepareVinaInputs_34.configure(function=code)
PrepareVinaInputs_34.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named PrepareVinaInputs in network self.macroNetwork"
)
print_exc()
PrepareVinaInputs_34 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_35 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_35, 217, 248)
GetMainURLFromList_35.inputPortByName['urls'].configure(
*(), **{'defaultValue': None})
GetMainURLFromList_35.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
)
print_exc()
GetMainURLFromList_35 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network Vina ##
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"receptor_file",
"receptor",
blocking=True,
splitratio=[0.48630431331124768, 0.72717758735716731])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.61963739449043087, 0.74955133389937689])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"filter_file",
"filter",
blocking=True,
splitratio=[0.32670226336274166, 0.25123642944789149])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if AutodockVina_Screening_kryptonite_nbcr_net_33 is not None and GetMainURLFromList_35 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVina_Screening_kryptonite_nbcr_net_33,
GetMainURLFromList_35,
"result",
"urls",
blocking=True,
splitratio=[0.23401196873379349, 0.68593608346615742])
except:
print(
"WARNING: failed to restore connection between AutodockVina_Screening_kryptonite_nbcr_net_33 and GetMainURLFromList_35 in network self.macroNetwork"
)
output_Ports_32 = self.macroNetwork.opNode
if GetMainURLFromList_35 is not None and output_Ports_32 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_35,
output_Ports_32,
"newurl",
"new",
blocking=True,
splitratio=[0.26588001265563421, 0.34355863787969732])
except:
print(
"WARNING: failed to restore connection between GetMainURLFromList_35 and output_Ports_32 in network self.macroNetwork"
)
input_Ports_31 = self.macroNetwork.ipNode
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
PrepareVinaInputs_34,
"new",
"receptor_obj",
blocking=True,
splitratio=[0.59193136382656331, 0.41134942510734418])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
)
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
PrepareVinaInputs_34,
"new",
"ligand_obj",
blocking=True,
splitratio=[0.29092159940560591, 0.60619808825531374])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
)
if input_Ports_31 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"new",
"config",
blocking=True,
splitratio=[0.24239548372031838, 0.55842775396640953])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_31 = self.macroNetwork.ipNode
input_Ports_31.outputPorts[1].configure(
name='PrepareVinaInputs_receptor_obj')
input_Ports_31.outputPorts[2].configure(
name='PrepareVinaInputs_ligand_obj')
input_Ports_31.outputPorts[3].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
## modifying MacroOutputNode dynamic ports
output_Ports_32 = self.macroNetwork.opNode
output_Ports_32.inputPorts[1].configure(singleConnection='auto')
output_Ports_32.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
Vina_30.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_30.inputPorts[0].configure(datatype='receptor_prepared')
Vina_30.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_30.inputPorts[1].configure(datatype='LigandDB')
Vina_30.inputPorts[2].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_30.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
Vina_30.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_30.outputPorts[0].configure(datatype='string')
Vina_30.shrink()
## reset modifications ##
Vina_30.resetTags()
Vina_30.buildOriginalList()
from WebServices.VisionInterface.WSNodes import wslib
try:
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(Adt,"AutoDockTools.VisionInterface.Adt", "Adt")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node GromosCluster ##
from Adt.Macro.GromosCluster import GromosCluster
GromosCluster_0 = GromosCluster(constrkw={}, name='GromosCluster', library=Adt)
masterNet.addNode(GromosCluster_0,396,213)
apply(GromosCluster_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
GROMOS_ClusterFiles_kryptonite_nbcr_net_3 = GromosCluster_0.macroNetwork.nodes[2]
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['expert_options'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['prefix'].widget.set(r"", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['default_options'].widget.set(r"-o -g -dist -ev -sz -tr -ntr -clid -cl", run=False)
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['localRun'].widget.set(0, run=False)
apply(GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['method'].widget.configure, (), {'choices': ('gromos', 'linkage', 'jarvis-patrick', 'monte-carlo', 'diagonalization')})
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['method'].widget.set(r"gromos", run=False)
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
ComputeGrids_18 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_19 = self.macroNetwork.ipNode
apply(input_Ports_19.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_19=None
try:
## saving node output Ports ##
output_Ports_20 = self.macroNetwork.opNode
apply(output_Ports_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_20.move(217, 471)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_20=None
try:
## saving node GetComputeGridsInputs ##
from Vision.StandardNodes import Generic
GetComputeGridsInputs_21 = Generic(constrkw={}, name='GetComputeGridsInputs', library=stdlib)
self.macroNetwork.addNode(GetComputeGridsInputs_21,217,79)
apply(GetComputeGridsInputs_21.addInputPort, (), {'singleConnection': True, 'name': 'ligands', 'cast': True, 'datatype': 'LigandDB', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'rect', 'color': '#FFCCFF', 'originalDatatype': 'None'})
apply(GetComputeGridsInputs_21.addInputPort, (), {'singleConnection': True, 'name': 'receptor_pdbqt', 'cast': True, 'datatype': 'receptor_prepared', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900', 'originalDatatype': 'None'})
apply(GetComputeGridsInputs_21.addInputPort, (), {'singleConnection': True, 'name': 'gpf_obj', 'cast': True, 'datatype': 'gpf_template', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#FF3333', 'originalDatatype': 'None'})
apply(GetComputeGridsInputs_21.addOutputPort, (), {'name': 'gpf_template_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(GetComputeGridsInputs_21.addOutputPort, (), {'name': 'filter_file', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(GetComputeGridsInputs_21.addOutputPort, (), {'name': 'ligand_lib', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
apply(GetComputeGridsInputs_21.addOutputPort, (), {'name': 'prepared_receptor', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, ligands, receptor_pdbqt, gpf_obj):
gpf_path = gpf_obj.fullpath
if not(os.path.exists(gpf_path)):
print "ERROR: GPF template " + gpf_path + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
ligand_lib = ligands.loc
prepared_receptor = receptor_pdbqt.path
pass
self.outputData(gpf_template_path=gpf_path, filter_file=filter_file, ligand_lib=ligand_lib, prepared_receptor=prepared_receptor)
## to ouput data on port gpf_template_path use
## self.outputData(gpf_template_path=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port prepared_receptor use
## self.outputData(prepared_receptor=data)
"""
GetComputeGridsInputs_21.configure(function=code)
apply(GetComputeGridsInputs_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named GetComputeGridsInputs in network self.macroNetwork"
print_exc()
GetComputeGridsInputs_21=None
try:
## saving node prepareGPF_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
prepareGPF_kryptonite_nbcr_net_22 = FunctionNode(functionOrString='prepareGPF_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'singlelib': '', 'r_url': '', 'zpoints': '', 'filter_file_url': '', 'lib': '', 'ypoints': '', 'filter_file': '', 'gpf': '', 'xcenter': 'auto', 'urllib': '', 'p': '', 'r': '', 'o': '', 'zcenter': 'auto', 'v': False, 'userlib': '', 'xpoints': '', 'localRun': False, 'ycenter': 'auto', 'execPath': ''}, constrkw={'functionOrString': "'prepareGPF_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'singlelib': '', 'r_url': '', 'zpoints': '', 'filter_file_url': '', 'lib': '', 'ypoints': '', 'filter_file': '', 'gpf': '', 'xcenter': 'auto', 'urllib': '', 'p': '', 'r': '', 'o': '', 'zcenter': 'auto', 'v': False, 'userlib': '', 'xpoints': '', 'localRun': False, 'ycenter': 'auto', 'execPath': ''}}, name='prepareGPF_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(prepareGPF_kryptonite_nbcr_net_22,217,141)
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['singlelib'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r_url'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zpoints'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file_url'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ypoints'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xcenter'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zcenter'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['userlib'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xpoints'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ycenter'].configure, (), {'defaultValue': None})
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['execPath'].configure, (), {'defaultValue': None})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file_url'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].widget.configure, (), {'choices': ('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI', 'human_metabolome', 'chembridge_building_blocks', 'drugbank_nutraceutics', 'drugbank_smallmol', 'fda_approved')})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['filter_file'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['execPath'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_22.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named prepareGPF_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
prepareGPF_kryptonite_nbcr_net_22=None
try:
## saving node autogrid_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autogrid_kryptonite_nbcr_net_23 = FunctionNode(functionOrString='autogrid_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'p_url': '', 'infile_url': '', 'l': 'output.glg', 'o': False, 'p': '', 'localRun': False, 'inFile': '', 'execPath': ''}, constrkw={'functionOrString': "'autogrid_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'p_url': '', 'infile_url': '', 'l': 'output.glg', 'o': False, 'p': '', 'localRun': False, 'inFile': '', 'execPath': ''}}, name='autogrid_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(autogrid_kryptonite_nbcr_net_23,251,292)
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['infile_url'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].configure, (), {'defaultValue': None})
apply(autogrid_kryptonite_nbcr_net_23.inputPortByName['execPath'].configure, (), {'defaultValue': None})
autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName['infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].widget.set(r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName['execPath'].widget.set(r"", run=False)
apply(autogrid_kryptonite_nbcr_net_23.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named autogrid_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autogrid_kryptonite_nbcr_net_23=None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_24 = GetMainURLFromListNode(constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_24,251,348)
apply(GetMainURLFromList_24.inputPortByName['urls'].configure, (), {'defaultValue': None})
apply(GetMainURLFromList_24.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_24=None
try:
## saving node MakeAutogridResultObj ##
from Vision.StandardNodes import Generic
MakeAutogridResultObj_25 = Generic(constrkw={}, name='MakeAutogridResultObj', library=stdlib)
self.macroNetwork.addNode(MakeAutogridResultObj_25,121,402)
apply(MakeAutogridResultObj_25.addInputPort, (), {'singleConnection': True, 'name': 'autogrid_result_url', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(MakeAutogridResultObj_25.addOutputPort, (), {'name': 'autogrid_result_obj', 'datatype': 'autogrid_results', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#FF33CC'})
code = """def doit(self, autogrid_result_url):
from AutoDockTools.VisionInterface.Adt.autogrid_results import autogrid_results
agro = autogrid_results(autogrid_result_url, '''url''')
pass
## to ouput data on port autogrid_result_obj use
self.outputData(autogrid_result_obj=agro)
"""
MakeAutogridResultObj_25.configure(function=code)
apply(MakeAutogridResultObj_25.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named MakeAutogridResultObj in network self.macroNetwork"
print_exc()
MakeAutogridResultObj_25=None
try:
## saving node GetURLFromList ##
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_26 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
self.macroNetwork.addNode(GetURLFromList_26,110,198)
apply(GetURLFromList_26.inputPortByName['urllist'].configure, (), {'defaultValue': None})
apply(GetURLFromList_26.inputPortByName['ext'].configure, (), {'defaultValue': None})
GetURLFromList_26.inputPortByName['ext'].widget.set(r"gpf", run=False)
apply(GetURLFromList_26.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore GetURLFromListNode named GetURLFromList in network self.macroNetwork"
print_exc()
GetURLFromList_26=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network ComputeGrids ##
input_Ports_19 = self.macroNetwork.ipNode
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19, GetComputeGridsInputs_21, "new", "ligands", blocking=True
, splitratio=[0.25038057532685992, 0.40242243717082576])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19, GetComputeGridsInputs_21, "new", "receptor_pdbqt", blocking=True
, splitratio=[0.31642654296910228, 0.49356822236979669])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19, GetComputeGridsInputs_21, "new", "gpf_obj", blocking=True
, splitratio=[0.57570983312901203, 0.33826779179418875])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21, prepareGPF_kryptonite_nbcr_net_22, "gpf_template_path", "gpf", blocking=True
, splitratio=[0.37911517364560754, 0.49588454022594075])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21, prepareGPF_kryptonite_nbcr_net_22, "filter_file", "filter_file", blocking=True
, splitratio=[0.51555458245420727, 0.58910990532612562])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21, prepareGPF_kryptonite_nbcr_net_22, "ligand_lib", "urllib", blocking=True
, splitratio=[0.45378244060628786, 0.49829462092378918])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21, prepareGPF_kryptonite_nbcr_net_22, "prepared_receptor", "r", blocking=True
, splitratio=[0.30158184825681655, 0.46256232709378253])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21, autogrid_kryptonite_nbcr_net_23, "prepared_receptor", "inFile", blocking=True
, splitratio=[0.63016045430148715, 0.62091422998177115])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
if autogrid_kryptonite_nbcr_net_23 is not None and GetMainURLFromList_24 is not None:
try:
self.macroNetwork.connectNodes(
autogrid_kryptonite_nbcr_net_23, GetMainURLFromList_24, "result", "urls", blocking=True
, splitratio=[0.4713453370864038, 0.73699665503637379])
except:
print "WARNING: failed to restore connection between autogrid_kryptonite_nbcr_net_23 and GetMainURLFromList_24 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and MakeAutogridResultObj_25 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24, MakeAutogridResultObj_25, "newurl", "autogrid_result_url", blocking=True
, splitratio=[0.37530325590010172, 0.67260462300696811])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and MakeAutogridResultObj_25 in network self.macroNetwork"
output_Ports_20 = self.macroNetwork.opNode
if MakeAutogridResultObj_25 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
MakeAutogridResultObj_25, output_Ports_20, "autogrid_result_obj", "new", blocking=True
, splitratio=[0.54860274312929591, 0.61692487705230459])
except:
print "WARNING: failed to restore connection between MakeAutogridResultObj_25 and output_Ports_20 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24, output_Ports_20, "newurl", "new", blocking=True
, splitratio=[0.56961778623989434, 0.55443680742298707])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and output_Ports_20 in network self.macroNetwork"
if prepareGPF_kryptonite_nbcr_net_22 is not None and GetURLFromList_26 is not None:
try:
self.macroNetwork.connectNodes(
prepareGPF_kryptonite_nbcr_net_22, GetURLFromList_26, "result", "urllist", blocking=True
, splitratio=[0.38550670487593142, 0.45424125807822219])
except:
print "WARNING: failed to restore connection between prepareGPF_kryptonite_nbcr_net_22 and GetURLFromList_26 in network self.macroNetwork"
if GetURLFromList_26 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetURLFromList_26, autogrid_kryptonite_nbcr_net_23, "url", "p_url", blocking=True
, splitratio=[0.65566147293832433, 0.57782517914212228])
except:
print "WARNING: failed to restore connection between GetURLFromList_26 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_19 = self.macroNetwork.ipNode
input_Ports_19.outputPorts[1].configure(name='GetComputeGridsInputs_ligands')
input_Ports_19.outputPorts[2].configure(name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_19.outputPorts[3].configure(name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_20 = self.macroNetwork.opNode
output_Ports_20.inputPorts[1].configure(singleConnection='auto')
output_Ports_20.inputPorts[2].configure(singleConnection='auto')
output_Ports_20.inputPorts[1].configure(name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_20.inputPorts[2].configure(name='GetMainURLFromList_newurl')
## configure MacroNode input ports
ComputeGrids_18.inputPorts[0].configure(name='GetComputeGridsInputs_ligands')
ComputeGrids_18.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_18.inputPorts[1].configure(name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_18.inputPorts[1].configure(datatype='receptor_prepared')
ComputeGrids_18.inputPorts[2].configure(name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_18.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode output ports
ComputeGrids_18.outputPorts[0].configure(name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_18.outputPorts[0].configure(datatype='autogrid_results')
ComputeGrids_18.outputPorts[1].configure(name='GetMainURLFromList_newurl')
ComputeGrids_18.outputPorts[1].configure(datatype='string')
ComputeGrids_18.shrink()
## reset modifications ##
ComputeGrids_18.resetTags()
ComputeGrids_18.buildOriginalList()
## loading libraries ##
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
try:
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://rocce.ucsd.edu/opal2", replace=False)
except:
pass
try:
## saving node Input Directory Browser ##
from Vision.StandardNodes import DirBrowserNE
Input_Directory_Browser_0 = DirBrowserNE(constrkw={}, name='Input Directory Browser', library=stdlib)
masterNet.addNode(Input_Directory_Browser_0,375,8)
Input_Directory_Browser_0.inputPortByName['directory'].widget.set(r"AMDNBCR_0.2_input", run=False)
apply(Input_Directory_Browser_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore DirBrowserNE named Input Directory Browser in network masterNet"
print_exc()
Input_Directory_Browser_0=None
try:
from Vision.StandardNodes import stdlib
try:
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
"stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2",
replace=False)
except:
pass
try:
## saving node FileWithCommandOrdering ##
from Vision.StandardNodes import FileBrowserNE
FileWithCommandOrdering_0 = FileBrowserNE(constrkw={},
name='FileWithCommandOrdering',
library=stdlib)
masterNet.addNode(FileWithCommandOrdering_0, 30, 10)
FileWithCommandOrdering_0.inputPortByName['filename'].widget.set(
r"NAMDTeragridGPU_0.1_input/order.txt", run=False)
apply(FileWithCommandOrdering_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
print_exc()
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(Adt,
"AutoDockTools.VisionInterface.Adt",
"Adt")
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
"stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node iterate ##
from Vision.StandardNodes import Iterate
iterate_0 = Iterate(constrkw={}, name='iterate', library=stdlib)
masterNet.addNode(iterate_0, 16, 228)
iterate_0.inputPortByName['stopOnFailure'].widget.set(0, run=False)
apply(iterate_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore Iterate named iterate in network masterNet"
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
TrajQR_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_2.move(183, 405)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node Make_Zip_File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={}, name='Make_Zip_File', library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3,47,75)
apply(Make_Zip_File_3.inputPortByName['input_directory'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_directory'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_name'].configure, (), {'defaultValue': None})
apply(Make_Zip_File_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MakeZipFileNE named Make_Zip_File in network self.macroNetwork"
print_exc()
Make_Zip_File_3=None
try:
## saving node TrajQR_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
TrajQR_kryptonite_nbcr_net_4 = FunctionNode(functionOrString='TrajQR_kryptonite_nbcr_net', host="http://kryptonite.nbcr.net/opal2", namedArgs={'license': False, 'rmsd': '', 'qh_filename': 'qh.tre', 'qr_filename': 'qr.out', 'compressed_pdbs': '', 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'TrajQR_kryptonite_nbcr_net'", 'host': '"http://kryptonite.nbcr.net/opal2"', 'namedArgs': {'license': False, 'rmsd': '', 'qh_filename': 'qh.tre', 'qr_filename': 'qr.out', 'compressed_pdbs': '', 'localRun': False, 'execPath': ''}}, name='TrajQR_kryptonite_nbcr_net', library=wslib)
self.macroNetwork.addNode(TrajQR_kryptonite_nbcr_net_4,279,135)
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].configure, (), {'defaultValue': None})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].configure, (), {'defaultValue': None, 'required': True})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['qh_filename'].configure, (), {'defaultValue': None})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['qr_filename'].configure, (), {'defaultValue': None})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['compressed_pdbs'].configure, (), {'defaultValue': None, 'required': True})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['localRun'].configure, (), {'defaultValue': None})
apply(TrajQR_kryptonite_nbcr_net_4.inputPortByName['execPath'].configure, (), {'defaultValue': None})
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].widget.set(0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].widget.set(r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qh_filename'].widget.set(r"qh.tre", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qr_filename'].widget.set(r"qr.out", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['compressed_pdbs'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['compressed_pdbs'].widget.set(r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['compressed_pdbs'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['localRun'].widget.set(0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['execPath'].widget.set(r"", run=False)
apply(TrajQR_kryptonite_nbcr_net_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore FunctionNode named TrajQR_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
TrajQR_kryptonite_nbcr_net_4=None
try:
## saving node SelectOnExtension ##
from Vision.StandardNodes import SelectOnExtension
SelectOnExtension_5 = SelectOnExtension(constrkw={}, name='SelectOnExtension', library=stdlib)
self.macroNetwork.addNode(SelectOnExtension_5,279,192)
apply(SelectOnExtension_5.inputPortByName['filenames'].configure, (), {'defaultValue': None})
apply(SelectOnExtension_5.inputPortByName['extension'].configure, (), {'defaultValue': None})
SelectOnExtension_5.inputPortByName['extension'].widget.set(r".out", run=False)
apply(SelectOnExtension_5.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore SelectOnExtension named SelectOnExtension in network self.macroNetwork"
print_exc()
SelectOnExtension_5=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6,123,281)
apply(Index_6.inputPortByName['data'].configure, (), {'datatype': 'list', 'defaultValue': None, 'originalDatatype': 'None'})
apply(Index_6.inputPortByName['index'].configure, (), {'defaultValue': None})
apply(Index_6.outputPortByName['data'].configure, (), {'datatype': 'string'})
apply(Index_6.inputPortByName['index'].widget.configure, (), {'max': 0, 'min': -1})
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_6=None
try:
## saving node GetSelectedPDBs ##
from Vision.StandardNodes import Generic
GetSelectedPDBs_7 = Generic(constrkw={}, name='GetSelectedPDBs', library=stdlib)
self.macroNetwork.addNode(GetSelectedPDBs_7,200,346)
apply(GetSelectedPDBs_7.addInputPort, (), {'singleConnection': True, 'name': 'trajqr_url', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetSelectedPDBs_7.addInputPort, (), {'singleConnection': True, 'name': 'pdb_in_dir', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetSelectedPDBs_7.addInputPort, (), {'singleConnection': True, 'name': 'pdb_out_dir', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetSelectedPDBs_7.addOutputPort, (), {'name': 'pdb_out_dir', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, trajqr_url, pdb_in_dir, pdb_out_dir):
pdb_in_dir = os.path.abspath(pdb_in_dir)
pdb_out_dir = os.path.abspath(pdb_out_dir)
import urllib
import shutil
pdb_list = []
f = urllib.urlopen(trajqr_url)
for i in f.readlines():
pdb_file = i.strip('''
''')+'''.pdb'''
infile = pdb_in_dir + os.sep + pdb_file
outfile = pdb_out_dir + os.sep + pdb_file
shutil.copyfile(infile, outfile)
f.close
pass
## to ouput data on port pdb_list use
self.outputData(pdb_out_dir=pdb_out_dir)
"""
GetSelectedPDBs_7.configure(function=code)
apply(GetSelectedPDBs_7.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore Generic named GetSelectedPDBs in network self.macroNetwork"
print_exc()
GetSelectedPDBs_7=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network TrajQR ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Make_Zip_File_3, "new", "input_directory", blocking=True
, splitratio=[0.67469172328672133, 0.50941480178765064])
except:
print "WARNING: failed to restore connection between input_Ports_1 and Make_Zip_File_3 in network self.macroNetwork"
if input_Ports_1 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, TrajQR_kryptonite_nbcr_net_4, "new", "rmsd", blocking=True
, splitratio=[0.45681934134493246, 0.33803410340720857])
except:
print "WARNING: failed to restore connection between input_Ports_1 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if Make_Zip_File_3 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3, TrajQR_kryptonite_nbcr_net_4, "zipfile", "compressed_pdbs", blocking=True
, splitratio=[0.71081093868178202, 0.43908686250860129])
except:
print "WARNING: failed to restore connection between Make_Zip_File_3 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if TrajQR_kryptonite_nbcr_net_4 is not None and SelectOnExtension_5 is not None:
try:
self.macroNetwork.connectNodes(
TrajQR_kryptonite_nbcr_net_4, SelectOnExtension_5, "result", "filenames", blocking=True
, splitratio=[0.63533198718963335, 0.2560040659014205])
except:
print "WARNING: failed to restore connection between TrajQR_kryptonite_nbcr_net_4 and SelectOnExtension_5 in network self.macroNetwork"
if SelectOnExtension_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
SelectOnExtension_5, Index_6, "matching", "data", blocking=True
, splitratio=[0.65832290589891362, 0.21624347250969889])
except:
print "WARNING: failed to restore connection between SelectOnExtension_5 and Index_6 in network self.macroNetwork"
if Index_6 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6, GetSelectedPDBs_7, "data", "trajqr_url", blocking=True
, splitratio=[0.51754619993986595, 0.63949220525823236])
except:
print "WARNING: failed to restore connection between Index_6 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, GetSelectedPDBs_7, "Make_Zip_File_input_directory", "pdb_in_dir", blocking=True
, splitratio=[0.7121964126696847, 0.42697952864467786])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, GetSelectedPDBs_7, "new", "pdb_out_dir", blocking=True
, splitratio=[0.62460995639428174, 0.60275185701976297])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetSelectedPDBs_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetSelectedPDBs_7, output_Ports_2, "pdb_out_dir", "new", blocking=True
, splitratio=[0.7431176169343523, 0.73697976585137526])
except:
print "WARNING: failed to restore connection between GetSelectedPDBs_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(name='TrajQR_kryptonite_nbcr_net_rmsd')
input_Ports_1.outputPorts[3].configure(name='GetSelectedPDBs_pdb_out_dir')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='GetSelectedPDBs_pdb_out_dir')
## configure MacroNode input ports
TrajQR_0.inputPorts[0].configure(name='Make_Zip_File_input_directory')
TrajQR_0.inputPorts[0].configure(datatype='string')
TrajQR_0.inputPorts[1].configure(name='TrajQR_kryptonite_nbcr_net_rmsd')
TrajQR_0.inputPorts[1].configure(datatype='string')
TrajQR_0.inputPorts[2].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
TrajQR_0.outputPorts[0].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.outputPorts[0].configure(datatype='string')
TrajQR_0.shrink()
## reset modifications ##
TrajQR_0.resetTags()
TrajQR_0.buildOriginalList()
