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"
print_exc()
iterate_0=None
try:
## saving node VirtualScreening ##
from Adt.Macro.VirtualScreening import VirtualScreening
VirtualScreening_1 = VirtualScreening(constrkw={}, name='VirtualScreening', library=Adt)
masterNet.addNode(VirtualScreening_1,216,497)
apply(VirtualScreening_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
PrepareReceptor_4 = VirtualScreening_1.macroNetwork.nodes[2]
Pdb2pqrWS_7 = PrepareReceptor_4.macroNetwork.nodes[2]
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 ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_0 = ComputeGrids(constrkw={},
name='ComputeGrids',
library=Adt)
masterNet.addNode(ComputeGrids_0, 391, 290)
apply(ComputeGrids_0.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
prepareGPF_kryptonite_nbcr_net_4 = ComputeGrids_0.macroNetwork.nodes[3]
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['singlelib'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['r_url'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zpoints'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
apply(
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.
"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"
print_exc()
iterate_0 = None
try:
## saving node VirtualScreening ##
from Adt.Macro.VirtualScreening import VirtualScreening
VirtualScreening_1 = VirtualScreening(constrkw={},
name='VirtualScreening',
library=Adt)
masterNet.addNode(VirtualScreening_1, 216, 497)
apply(VirtualScreening_1.configure, (), {
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)
GROMOS_ClusterFiles_kryptonite_nbcr_net_3.inputPortByName['execPath'].widget.set(r"", run=False)
Entry_6 = GromosCluster_0.macroNetwork.nodes[5]
Entry_6.inputPortByName['entry'].widget.set(r"3", run=False)
## saving connections for network GromosCluster ##
GromosCluster_0.macroNetwork.freeze()
GromosCluster_0.macroNetwork.unfreeze()
masterNet
except (NameError, AttributeError): # we run the network outside Vision
from NetworkEditor.net import Network
masterNet = Network()
masterNet.getEditor().addLibraryInstance(matplotliblib,"Vision.matplotlibNodes", "matplotliblib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
masterNet.getEditor().addLibraryInstance(vizlib,"DejaVu.VisionInterface.DejaVuNodes", "vizlib")
try:
## saving node Histogram ##
from Vision.matplotlibNodes import HistogramNE
Histogram_0 = HistogramNE(constrkw={}, name='Histogram', library=matplotliblib)
masterNet.addNode(Histogram_0,108,243)
Histogram_0.inputPortByName['bins'].widget.set(50, run=False)
Histogram_0.inputPortByName['normed'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_antialiased'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_linewidth'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_edgecolor'].widget.set(r"black", run=False)
Histogram_0.inputPortByName['patch_facecolor'].widget.set(r"green", run=False)
apply(Histogram_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore HistogramNE named Histogram in network masterNet"
print_exc()
Histogram_0=None
try:
## saving node Draw Area ##
from Vision.matplotlibNodes import MPLDrawAreaNE
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"
print_exc()
iterate_0=None
try:
## saving node VirtualScreening ##
from Adt.Macro.VirtualScreening import VirtualScreening
VirtualScreening_1 = VirtualScreening(constrkw={}, name='VirtualScreening', library=Adt)
masterNet.addNode(VirtualScreening_1,216,497)
apply(VirtualScreening_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
PrepareReceptor_4 = VirtualScreening_1.macroNetwork.nodes[2]
Pdb2pqrWS_7 = PrepareReceptor_4.macroNetwork.nodes[2]
'namedArgs': {
'i': False,
'k': False,
'l': '',
'o': False,
'pdbq': '',
'p': '',
't': False,
'url': '',
'localRun': False,
'execPath': ''
}
},
name='AutodockOpalService_kryptonite_nbcr_net',
library=wslib)
masterNet.addNode(AutodockOpalService_kryptonite_nbcr_net_0, 173, 245)
apply(
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['l'].
configure, (), {'defaultValue': None})
apply(
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['pdbq'].
configure, (), {'defaultValue': None})
apply(
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['p'].
configure, (), {'defaultValue': None})
apply(
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['url'].
configure, (), {'defaultValue': None})
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['i'].widget.set(
0, run=False)
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName['k'].widget.set(
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://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node AutodockVS ##
from Adt.Macro.AutodockVS import AutodockVS
AutodockVS_0 = AutodockVS(constrkw={}, name='AutodockVS', library=Adt)
masterNet.addNode(AutodockVS_0,357,292)
apply(AutodockVS_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
autodock_kryptonite_nbcr_net_4 = AutodockVS_0.macroNetwork.nodes[3]
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)
apply(autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_generations'].widget.set(r"", run=False)
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)
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(
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(pmvlib,"Pmv.VisionInterface.PmvNodes", "pmvlib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
try:
## saving node GetReceptors ##
from Vision.StandardNodes import Generic
GetReceptors_0 = Generic(constrkw={}, name='GetReceptors', library=stdlib)
masterNet.addNode(GetReceptors_0,12,104)
apply(GetReceptors_0.addInputPort, (), {'singleConnection': True, 'name': 'directory', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetReceptors_0.addOutputPort, (), {'name': 'filelist', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
apply(GetReceptors_0.addOutputPort, (), {'name': 'filelist_paths', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
code = """def doit(self, directory):
import glob, os
match_str = "*"
if directory is not None:
cwd = os.getcwd()
os.chdir(directory)
try:
pdirs = glob.glob(match_str)
values = []
for i in pdirs:
if os.path.exists(i + os.sep + '''summarize_results.txt'''):
"matplotliblib")
masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
"stdlib")
masterNet.getEditor().addLibraryInstance(vizlib,
"DejaVu.VisionInterface.DejaVuNodes",
"vizlib")
try:
## saving node Histogram ##
from Vision.matplotlibNodes import HistogramNE
Histogram_0 = HistogramNE(constrkw={},
name='Histogram',
library=matplotliblib)
masterNet.addNode(Histogram_0, 108, 243)
Histogram_0.inputPortByName['bins'].widget.set(50, run=False)
Histogram_0.inputPortByName['normed'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_antialiased'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_linewidth'].widget.set(1, run=False)
Histogram_0.inputPortByName['patch_edgecolor'].widget.set(r"black",
run=False)
Histogram_0.inputPortByName['patch_facecolor'].widget.set(r"green",
run=False)
apply(Histogram_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore HistogramNE named Histogram in network masterNet"
print_exc()
Histogram_0 = None
try:
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)
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['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False)
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)
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 StructureBrowser ##
from Adt.Input.StructureBrowser import StructureBrowser
StructureBrowser_0 = StructureBrowser(constrkw={},
name='StructureBrowser',
library=Adt)
masterNet.addNode(StructureBrowser_0, 32, 37)
StructureBrowser_0.inputPortByName['receptor_file'].widget.set(
r"VinaVSlocal_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
print_exc()
StructureBrowser_0 = None
try:
## saving node Vina Config File Browser ##
from Vision.StandardNodes import FileBrowserNE
Vina_Config_File_Browser_1 = FileBrowserNE(constrkw={},
name='Vina Config File Browser',
library=stdlib)
masterNet.addNode(Vina_Config_File_Browser_1, 849, 41)
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 ComputeGrids ##
from Adt.Macro.ComputeGrids import ComputeGrids
ComputeGrids_0 = ComputeGrids(constrkw={}, name='ComputeGrids', library=Adt)
masterNet.addNode(ComputeGrids_0,391,290)
apply(ComputeGrids_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
prepareGPF_kryptonite_nbcr_net_4 = ComputeGrids_0.macroNetwork.nodes[3]
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['filter_file_url'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_4.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_4.inputPortByName['lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['p'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['o'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['v'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_4.inputPortByName['userlib'].widget.set(r"", run=False)
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 StructureBrowser ##
from Adt.Input.StructureBrowser import StructureBrowser
StructureBrowser_0 = StructureBrowser(constrkw={}, name='StructureBrowser', library=Adt)
masterNet.addNode(StructureBrowser_0,32,37)
StructureBrowser_0.inputPortByName['receptor_file'].widget.set(r"VinaVSlocal_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
print_exc()
StructureBrowser_0=None
try:
## saving node Vina Config File Browser ##
from Vision.StandardNodes import FileBrowserNE
Vina_Config_File_Browser_1 = FileBrowserNE(constrkw={}, name='Vina Config File Browser', library=stdlib)
masterNet.addNode(Vina_Config_File_Browser_1,849,41)
Vina_Config_File_Browser_1.inputPortByName['filename'].widget.set(r"VinaVSlocal_0.1_input/test.config", run=False)
apply(Vina_Config_File_Browser_1.configure, (), {'paramPanelImmediate': 1})
except:
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 StructureBrowser ##
from Adt.Input.StructureBrowser import StructureBrowser
StructureBrowser_0 = StructureBrowser(constrkw={},
name='StructureBrowser',
library=Adt)
masterNet.addNode(StructureBrowser_0, 32, 37)
StructureBrowser_0.inputPortByName['receptor_file'].widget.set(
r"VinaVSpublic_0.1_input/2HTY_A-2HTY_A.pdb", run=False)
apply(StructureBrowser_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore StructureBrowser named StructureBrowser in network masterNet"
print_exc()
StructureBrowser_0 = None
try:
## saving node PublicServerLigandDB ##
from Adt.Input.PublicServerLigandDB import PublicServerLigandDB
PublicServerLigandDB_1 = PublicServerLigandDB(constrkw={},
name='PublicServerLigandDB',
library=Adt)
masterNet.addNode(PublicServerLigandDB_1, 419, 38)
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://oolite.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
## saving node FileWithCommandOrdering ##
from Vision.StandardNodes import FileBrowserNE
FileWithCommandOrdering_87 = FileBrowserNE(constrkw={}, name='FileWithCommandOrdering', library=stdlib)
masterNet.addNode(FileWithCommandOrdering_87,30,10)
FileWithCommandOrdering_87.inputPortByName['filename'].widget.set(r"NAMDNBCR_0.1_input/order.txt", run=False)
apply(FileWithCommandOrdering_87.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
print_exc()
FileWithCommandOrdering_87=None
try:
## saving node GetOrdering ##
from Vision.StandardNodes import Generic
GetOrdering_88 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
masterNet.addNode(GetOrdering_88,30,107)
apply(GetOrdering_88.addInputPort, (), {'singleConnection': True, 'name': 'order_file', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetOrdering_88.addOutputPort, (), {'name': 'order_list', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
code = """def doit(self, order_file):
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:
## saving node NumProcessors ##
from Vision.StandardNodes import EntryNE
NumProcessors_1 = EntryNE(constrkw={}, name='NumProcessors', library=stdlib)
masterNet.addNode(NumProcessors_1,1043,12)
NumProcessors_1.inputPortByName['entry'].widget.set(r"4", run=False)
code = """def doit(self, entry):
if len(str(entry))!=0:
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(pmvlib,"Pmv.VisionInterface.PmvNodes", "pmvlib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
try:
## saving node AutoDock VS Result Directory ##
from Vision.StandardNodes import DirBrowserNE
AutoDock_VS_Result_Directory_28 = DirBrowserNE(constrkw={}, name='AutoDock VS Result Directory', library=stdlib)
masterNet.addNode(AutoDock_VS_Result_Directory_28,47,27)
AutoDock_VS_Result_Directory_28.inputPortByName['directory'].widget.set(r"visualization_0.1.1_input", run=False)
apply(AutoDock_VS_Result_Directory_28.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore DirBrowserNE named AutoDock VS Result Directory in network masterNet"
print_exc()
AutoDock_VS_Result_Directory_28=None
try:
## saving node GetReceptors ##
from Vision.StandardNodes import Generic
GetReceptors_29 = Generic(constrkw={}, name='GetReceptors', library=stdlib)
masterNet.addNode(GetReceptors_29,47,123)
apply(GetReceptors_29.addInputPort, (), {'singleConnection': True, 'name': 'dir', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetReceptors_29.addOutputPort, (), {'name': 'receptors', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
apply(GetReceptors_29.addOutputPort, (), {'name': 'receptor_paths', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
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:
## saving node GetOrdering ##
from Vision.StandardNodes import Generic
GetOrdering_1 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
masterNet.addNode(GetOrdering_1, 30, 107)
apply(
GetOrdering_1.addInputPort, (), {
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:
## saving node GetOrdering ##
from Vision.StandardNodes import Generic
GetOrdering_1 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
masterNet.addNode(GetOrdering_1,30,107)
apply(GetOrdering_1.addInputPort, (), {'singleConnection': True, 'name': 'order_file', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
apply(GetOrdering_1.addOutputPort, (), {'name': 'order_list', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'})
code = """def doit(self, order_file):
"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"
print_exc()
iterate_0 = None
try:
## saving node VirtualScreening ##
from Adt.Macro.VirtualScreening import VirtualScreening
VirtualScreening_1 = VirtualScreening(constrkw={},
name='VirtualScreening',
library=Adt)
masterNet.addNode(VirtualScreening_1, 216, 497)
apply(VirtualScreening_1.configure, (), {
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(matplotliblib,"Vision.matplotlibNodes", "matplotliblib")
masterNet.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
try:
## saving node ReadTable ##
from Vision.StandardNodes import ReadTable
ReadTable_0 = ReadTable(constrkw={}, name='ReadTable', library=stdlib)
masterNet.addNode(ReadTable_0,71,7)
ReadTable_0.inputPortByName['filename'].widget.set(r"Data/axes_data.dat", run=False)
ReadTable_0.inputPortByName['numOfTopLinesToJump'].widget.set(0, run=False)
apply(ReadTable_0.inputPortByName['numOfBottomLinesToJump'].widget.configure, (), {'oneTurn': 10.0})
ReadTable_0.inputPortByName['numOfBottomLinesToJump'].widget.set(2, run=False)
ReadTable_0.inputPortByName['sep'].widget.set(r",", run=False)
ReadTable_0.inputPortByName['datatype'].widget.set(r"float", run=False)
apply(ReadTable_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
except:
print "WARNING: failed to restore ReadTable named ReadTable in network masterNet"
print_exc()
ReadTable_0=None
try:
## saving node Index ##
from Vision.StandardNodes import Index
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://kryptonite.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node Directory_Containing_Input_PDB_Files ##
from Vision.StandardNodes import DirBrowserNE
Directory_Containing_Input_PDB_Files_0 = DirBrowserNE(constrkw={}, name='Directory_Containing_Input_PDB_Files', library=stdlib)
masterNet.addNode(Directory_Containing_Input_PDB_Files_0,45,40)
Directory_Containing_Input_PDB_Files_0.inputPortByName['directory'].widget.set(r"TrajQRClustering_0.1_input", run=False)
apply(Directory_Containing_Input_PDB_Files_0.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore DirBrowserNE named Directory_Containing_Input_PDB_Files in network masterNet"
print_exc()
Directory_Containing_Input_PDB_Files_0=None
try:
## saving node RMSD ##
from Vision.StandardNodes import EntryNE
RMSD_1 = EntryNE(constrkw={}, name='RMSD', library=stdlib)
masterNet.addNode(RMSD_1,379,44)
RMSD_1.inputPortByName['entry'].widget.set(r"0.5", run=False)
apply(RMSD_1.configure, (), {'paramPanelImmediate': 1})
except:
"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"
print_exc()
iterate_0 = None
try:
## saving node VirtualScreening ##
from Adt.Macro.VirtualScreening import VirtualScreening
VirtualScreening_1 = VirtualScreening(constrkw={},
name='VirtualScreening',
library=Adt)
masterNet.addNode(VirtualScreening_1, 216, 497)
apply(VirtualScreening_1.configure, (), {
masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes",
"stdlib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://oolite.calit2.optiputer.net/opal2",
replace=False)
except:
pass
try:
## saving node FileWithCommandOrdering ##
from Vision.StandardNodes import FileBrowserNE
FileWithCommandOrdering_87 = FileBrowserNE(constrkw={},
name='FileWithCommandOrdering',
library=stdlib)
masterNet.addNode(FileWithCommandOrdering_87, 30, 10)
FileWithCommandOrdering_87.inputPortByName['filename'].widget.set(
r"NAMDNBCR_0.1_input/order.txt", run=False)
apply(FileWithCommandOrdering_87.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet"
print_exc()
FileWithCommandOrdering_87 = None
try:
## saving node GetOrdering ##
from Vision.StandardNodes import Generic
GetOrdering_88 = Generic(constrkw={}, name='GetOrdering', library=stdlib)
masterNet.addNode(GetOrdering_88, 30, 107)
apply(
GetOrdering_88.addInputPort, (), {