if_14, rename_stdout_13, "_if", "in_name", blocking=True
, splitratio=[0.42861758851787812, 0.59732773543810935])
except:
print "WARNING: failed to restore connection between if_14 and rename_stdout_13 in network SaveNAMDResults_5.macroNetwork"
SaveNAMDResults_5.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_6.outputPorts[1].configure(name='GetOutURLs_url')
input_Ports_6.outputPorts[2].configure(name='GetOutURLs_filename')
SaveNAMDResults_5.inputPorts[0].configure(name='GetOutURLs_url')
SaveNAMDResults_5.inputPorts[0].configure(datatype='string')
SaveNAMDResults_5.inputPorts[1].configure(name='GetOutURLs_filename')
SaveNAMDResults_5.inputPorts[1].configure(datatype='string')
## configure MacroNode input ports
## configure MacroNode output ports
SaveNAMDResults_5.shrink()
apply(SaveNAMDResults_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet"
print_exc()
SaveNAMDResults_5=None
try:
## saving node NamdWS ##
from NetworkEditor.macros import MacroNode
NamdWS_15 = MacroNode(name='NamdWS')
masterNet.addNode(NamdWS_15, 455, 313)
output_Ports_17 = NamdWS_15.macroNetwork.opNode
apply(output_Ports_17.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_17.move(211, 381)
from NetworkEditor.items import FunctionNode
if_101, rename_stdout_100, "_if", "in_name", blocking=True
, splitratio=[0.42861758851787812, 0.59732773543810935])
except:
print "WARNING: failed to restore connection between if_101 and rename_stdout_100 in network SaveNAMDResults_92.macroNetwork"
SaveNAMDResults_92.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_93.outputPorts[1].configure(name='GetOutURLs_url')
input_Ports_93.outputPorts[2].configure(name='GetOutURLs_filename')
SaveNAMDResults_92.inputPorts[0].configure(name='GetOutURLs_url')
SaveNAMDResults_92.inputPorts[0].configure(datatype='string')
SaveNAMDResults_92.inputPorts[1].configure(name='GetOutURLs_filename')
SaveNAMDResults_92.inputPorts[1].configure(datatype='string')
## configure MacroNode input ports
## configure MacroNode output ports
SaveNAMDResults_92.shrink()
apply(SaveNAMDResults_92.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet"
print_exc()
SaveNAMDResults_92=None
try:
## saving node NamdWS ##
from NetworkEditor.macros import MacroNode
NamdWS_102 = MacroNode(name='NamdWS')
masterNet.addNode(NamdWS_102, 455, 294)
output_Ports_104 = NamdWS_102.macroNetwork.opNode
apply(output_Ports_104.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_104.move(211, 381)
from NetworkEditor.items import FunctionNode
## modifying MacroInputNode dynamic ports
input_Ports_32.outputPorts[1].configure(name='getMolePath_mol')
input_Ports_32.outputPorts[2].configure(name='getMolePath_mol_paths')
## modifying MacroOutputNode dynamic ports
output_Ports_33.inputPorts[1].configure(singleConnection='auto')
output_Ports_33.inputPorts[1].configure(name='getMolePath_mol_path')
LoadMolecule_31.inputPorts[0].configure(name='getMolePath_mol')
LoadMolecule_31.inputPorts[0].configure(datatype='string')
LoadMolecule_31.inputPorts[1].configure(name='getMolePath_mol_paths')
LoadMolecule_31.inputPorts[1].configure(datatype='list')
## configure MacroNode input ports
LoadMolecule_31.outputPorts[0].configure(name='getMolePath_mol_path')
LoadMolecule_31.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
LoadMolecule_31.shrink()
apply(LoadMolecule_31.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named LoadMolecule in network masterNet"
print_exc()
LoadMolecule_31=None
try:
## saving node GetLigands ##
from Vision.StandardNodes import Generic
GetLigands_41 = Generic(constrkw={}, name='GetLigands', library=stdlib)
masterNet.addNode(GetLigands_41,332,135)
apply(GetLigands_41.addInputPort, (), {'singleConnection': True, 'name': 'rps', 'cast': True, 'datatype': 'list', 'defaultValue': None, 'required': True, 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan', 'originalDatatype': 'None'})
apply(GetLigands_41.addInputPort, (), {'singleConnection': True, 'name': 'r', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetLigands_41.addOutputPort, (), {'name': 'ligands', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
code = """def doit(self, rps, r):
input_Ports_21.outputPorts[3].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config')
## modifying MacroOutputNode dynamic ports
output_Ports_22.inputPorts[1].configure(singleConnection='auto')
output_Ports_22.inputPorts[1].configure(name='GetMainURLFromList_newurl')
Vina_20.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_20.inputPorts[0].configure(datatype='receptor_prepared')
Vina_20.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_20.inputPorts[1].configure(datatype='LigandDB')
Vina_20.inputPorts[2].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_20.inputPorts[2].configure(datatype='string')
## configure MacroNode input ports
Vina_20.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_20.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
Vina_20.shrink()
apply(Vina_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named Vina in network masterNet"
print_exc()
Vina_20=None
try:
## saving node DownloadSaveDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadSaveDir_26 = DownloadSaveDirNode(constrkw={}, name='DownloadSaveDir', library=wslib)
masterNet.addNode(DownloadSaveDir_26,350,411)
apply(DownloadSaveDir_26.inputPortByName['url'].configure, (), {'defaultValue': None})
DownloadSaveDir_26.inputPortByName['url'].rebindWidget()
DownloadSaveDir_26.inputPortByName['url'].widget.set(r"", run=False)
DownloadSaveDir_26.inputPortByName['url'].unbindWidget()
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()
input_Ports_5.outputPorts[3].configure(name='NAMD_rocce_ucsd_edu_procs')
## modifying MacroOutputNode dynamic ports
output_Ports_6.inputPorts[1].configure(singleConnection='auto')
output_Ports_6.inputPorts[1].configure(name='GetMainURLFromList_newurl')
AMDws_4.inputPorts[0].configure(name='eval_in1')
AMDws_4.inputPorts[0].configure(datatype='string')
AMDws_4.inputPorts[1].configure(name='prepareForZip_in1')
AMDws_4.inputPorts[1].configure(datatype='string')
AMDws_4.inputPorts[2].configure(name='NAMD_rocce_ucsd_edu_procs')
AMDws_4.inputPorts[2].configure(datatype='string')
## configure MacroNode input ports
AMDws_4.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AMDws_4.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
AMDws_4.shrink()
apply(AMDws_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named AMDws in network masterNet"
print_exc()
AMDws_4=None
try:
## saving node DownloadDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadDir_12 = DownloadSaveDirNode(constrkw={}, name='DownloadDir', library=wslib)
masterNet.addNode(DownloadDir_12,494,320)
apply(DownloadDir_12.inputPortByName['url'].configure, (), {'defaultValue': None})
DownloadDir_12.inputPortByName['url'].rebindWidget()
DownloadDir_12.inputPortByName['url'].widget.set(r"", run=False)
DownloadDir_12.inputPortByName['url'].unbindWidget()
blocking=True,
splitratio=[0.42861758851787812, 0.59732773543810935])
except:
print "WARNING: failed to restore connection between if_14 and rename_stdout_13 in network SaveNAMDResults_5.macroNetwork"
SaveNAMDResults_5.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_6.outputPorts[1].configure(name='GetOutURLs_url')
input_Ports_6.outputPorts[2].configure(name='GetOutURLs_filename')
SaveNAMDResults_5.inputPorts[0].configure(name='GetOutURLs_url')
SaveNAMDResults_5.inputPorts[0].configure(datatype='string')
SaveNAMDResults_5.inputPorts[1].configure(name='GetOutURLs_filename')
SaveNAMDResults_5.inputPorts[1].configure(datatype='string')
## configure MacroNode input ports
## configure MacroNode output ports
SaveNAMDResults_5.shrink()
apply(SaveNAMDResults_5.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet"
print_exc()
SaveNAMDResults_5 = None
try:
## saving node NamdWS ##
from NetworkEditor.macros import MacroNode
NamdWS_15 = MacroNode(name='NamdWS')
masterNet.addNode(NamdWS_15, 455, 313)
output_Ports_17 = NamdWS_15.macroNetwork.opNode
## modifying MacroOutputNode dynamic ports
output_Ports_23.inputPorts[1].configure(singleConnection='auto')
output_Ports_23.inputPorts[1].configure(name='GetMainURLFromList_newurl')
Vina_21.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_21.inputPorts[0].configure(datatype='receptor_prepared')
Vina_21.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_21.inputPorts[1].configure(datatype='LigandDB')
Vina_21.inputPorts[2].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_21.inputPorts[2].configure(datatype='string')
## configure MacroNode input ports
Vina_21.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_21.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
Vina_21.shrink()
apply(Vina_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named Vina in network masterNet"
print_exc()
Vina_21 = None
try:
## saving node DownloadSaveDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadSaveDir_27 = DownloadSaveDirNode(constrkw={},
name='DownloadSaveDir',
library=wslib)
masterNet.addNode(DownloadSaveDir_27, 402, 366)
apply(DownloadSaveDir_27.inputPortByName['url'].configure, (),
{'defaultValue': None})
## modifying MacroInputNode dynamic ports
input_Ports_4.outputPorts[1].configure(name='FindMolPath_molname')
input_Ports_4.outputPorts[2].configure(name='abs_path_in1')
## modifying MacroOutputNode dynamic ports
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(name='FindMolPath_molpath')
LoadMolecule5_3.inputPorts[0].configure(name='FindMolPath_molname')
LoadMolecule5_3.inputPorts[0].configure(datatype='string')
LoadMolecule5_3.inputPorts[1].configure(name='abs_path_in1')
LoadMolecule5_3.inputPorts[1].configure(datatype='string')
## configure MacroNode input ports
LoadMolecule5_3.outputPorts[0].configure(name='FindMolPath_molpath')
LoadMolecule5_3.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
LoadMolecule5_3.shrink()
apply(LoadMolecule5_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named LoadMolecule5 in network masterNet"
print_exc()
LoadMolecule5_3=None
try:
## saving node ShowConformations6 ##
from NetworkEditor.macros import MacroNode
ShowConformations6_14 = MacroNode(name='ShowConformations6')
masterNet.addNode(ShowConformations6_14, 543, 541)
output_Ports_16 = ShowConformations6_14.macroNetwork.opNode
apply(output_Ports_16.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
output_Ports_16.move(220, 365)
from Vision.StandardNodes import Generic
## modifying MacroOutputNode dynamic ports
output_Ports_22.inputPorts[1].configure(singleConnection='auto')
output_Ports_22.inputPorts[1].configure(name='GetMainURLFromList_newurl')
Vina_20.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_20.inputPorts[0].configure(datatype='receptor_prepared')
Vina_20.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_20.inputPorts[1].configure(datatype='LigandDB')
Vina_20.inputPorts[2].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_20.inputPorts[2].configure(datatype='string')
## configure MacroNode input ports
Vina_20.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_20.outputPorts[0].configure(datatype='string')
## configure MacroNode output ports
Vina_20.shrink()
apply(Vina_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore MacroNode named Vina in network masterNet"
print_exc()
Vina_20 = None
try:
## saving node DownloadSaveDir ##
from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode
DownloadSaveDir_26 = DownloadSaveDirNode(constrkw={},
name='DownloadSaveDir',
library=wslib)
masterNet.addNode(DownloadSaveDir_26, 350, 411)
apply(DownloadSaveDir_26.inputPortByName['url'].configure, (),
{'defaultValue': None})
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()
blocking=True,
splitratio=[0.42861758851787812, 0.59732773543810935])
except:
print "WARNING: failed to restore connection between if_101 and rename_stdout_100 in network SaveNAMDResults_92.macroNetwork"
SaveNAMDResults_92.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_93.outputPorts[1].configure(name='GetOutURLs_url')
input_Ports_93.outputPorts[2].configure(name='GetOutURLs_filename')
SaveNAMDResults_92.inputPorts[0].configure(name='GetOutURLs_url')
SaveNAMDResults_92.inputPorts[0].configure(datatype='string')
SaveNAMDResults_92.inputPorts[1].configure(name='GetOutURLs_filename')
SaveNAMDResults_92.inputPorts[1].configure(datatype='string')
## configure MacroNode input ports
## configure MacroNode output ports
SaveNAMDResults_92.shrink()
apply(SaveNAMDResults_92.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet"
print_exc()
SaveNAMDResults_92 = None
try:
## saving node NamdWS ##
from NetworkEditor.macros import MacroNode
NamdWS_102 = MacroNode(name='NamdWS')
masterNet.addNode(NamdWS_102, 455, 294)
output_Ports_104 = NamdWS_102.macroNetwork.opNode
