def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
ComputeGrids_18 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_19 = self.macroNetwork.ipNode
apply(input_Ports_19.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_19 = None
try:
## saving node output Ports ##
output_Ports_20 = self.macroNetwork.opNode
apply(output_Ports_20.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_20.move(217, 471)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_20 = None
try:
## saving node GetComputeGridsInputs ##
from Vision.StandardNodes import Generic
GetComputeGridsInputs_21 = Generic(constrkw={},
name='GetComputeGridsInputs',
library=stdlib)
self.macroNetwork.addNode(GetComputeGridsInputs_21, 217, 79)
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'receptor_pdbqt',
'cast': True,
'datatype': 'receptor_prepared',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#009900',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addInputPort, (), {
'singleConnection': True,
'name': 'gpf_obj',
'cast': True,
'datatype': 'gpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF3333',
'originalDatatype': 'None'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'gpf_template_path',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
GetComputeGridsInputs_21.addOutputPort, (), {
'name': 'prepared_receptor',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, receptor_pdbqt, gpf_obj):
gpf_path = gpf_obj.fullpath
if not(os.path.exists(gpf_path)):
print "ERROR: GPF template " + gpf_path + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
ligand_lib = ligands.loc
prepared_receptor = receptor_pdbqt.path
pass
self.outputData(gpf_template_path=gpf_path, filter_file=filter_file, ligand_lib=ligand_lib, prepared_receptor=prepared_receptor)
## to ouput data on port gpf_template_path use
## self.outputData(gpf_template_path=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port prepared_receptor use
## self.outputData(prepared_receptor=data)
"""
GetComputeGridsInputs_21.configure(function=code)
apply(GetComputeGridsInputs_21.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named GetComputeGridsInputs in network self.macroNetwork"
print_exc()
GetComputeGridsInputs_21 = None
try:
## saving node prepareGPF_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
prepareGPF_kryptonite_nbcr_net_22 = FunctionNode(
functionOrString='prepareGPF_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'singlelib': '',
'r_url': '',
'zpoints': '',
'filter_file_url': '',
'lib': '',
'ypoints': '',
'filter_file': '',
'gpf': '',
'xcenter': 'auto',
'urllib': '',
'p': '',
'r': '',
'o': '',
'zcenter': 'auto',
'v': False,
'userlib': '',
'xpoints': '',
'localRun': False,
'ycenter': 'auto',
'execPath': ''
},
constrkw={
'functionOrString': "'prepareGPF_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'singlelib': '',
'r_url': '',
'zpoints': '',
'filter_file_url': '',
'lib': '',
'ypoints': '',
'filter_file': '',
'gpf': '',
'xcenter': 'auto',
'urllib': '',
'p': '',
'r': '',
'o': '',
'zcenter': 'auto',
'v': False,
'userlib': '',
'xpoints': '',
'localRun': False,
'ycenter': 'auto',
'execPath': ''
}
},
name='prepareGPF_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(prepareGPF_kryptonite_nbcr_net_22, 217,
141)
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['singlelib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r_url'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zpoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.
inputPortByName['filter_file_url'].configure, (),
{'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ypoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.
inputPortByName['filter_file'].configure, (),
{'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['gpf'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xcenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['urllib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['zcenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['userlib'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['xpoints'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['ycenter'].
configure, (), {'defaultValue': None})
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'singlelib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r_url'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'zpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
apply(
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['lib'].
widget.configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2', 'oldNCI',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'lib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'ypoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'filter_file'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'gpf'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'xcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'urllib'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['p'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r'].rebindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['r'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'r'].unbindWidget()
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['o'].widget.set(
r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'zcenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName['v'].widget.set(
0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'userlib'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'xpoints'].widget.set(r"", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'localRun'].widget.set(0, run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'ycenter'].widget.set(r"auto", run=False)
prepareGPF_kryptonite_nbcr_net_22.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(prepareGPF_kryptonite_nbcr_net_22.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named prepareGPF_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
prepareGPF_kryptonite_nbcr_net_22 = None
try:
## saving node autogrid_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autogrid_kryptonite_nbcr_net_23 = FunctionNode(
functionOrString='autogrid_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'p_url': '',
'infile_url': '',
'l': 'output.glg',
'o': False,
'p': '',
'localRun': False,
'inFile': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autogrid_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'p_url': '',
'infile_url': '',
'l': 'output.glg',
'o': False,
'p': '',
'localRun': False,
'inFile': '',
'execPath': ''
}
},
name='autogrid_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autogrid_kryptonite_nbcr_net_23, 251,
292)
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['p_url'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['infile_url'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].configure,
(), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['inFile'].
configure, (), {'defaultValue': None})
apply(
autogrid_kryptonite_nbcr_net_23.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'p_url'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'infile_url'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['l'].widget.set(
r"output.glg", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['o'].widget.set(
0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName['p'].widget.set(
r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'localRun'].widget.set(0, run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].rebindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].widget.set(r"", run=False)
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'inFile'].unbindWidget()
autogrid_kryptonite_nbcr_net_23.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(autogrid_kryptonite_nbcr_net_23.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named autogrid_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autogrid_kryptonite_nbcr_net_23 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_24 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_24, 251, 348)
apply(GetMainURLFromList_24.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_24.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_24 = None
try:
## saving node MakeAutogridResultObj ##
from Vision.StandardNodes import Generic
MakeAutogridResultObj_25 = Generic(constrkw={},
name='MakeAutogridResultObj',
library=stdlib)
self.macroNetwork.addNode(MakeAutogridResultObj_25, 121, 402)
apply(
MakeAutogridResultObj_25.addInputPort, (), {
'singleConnection': True,
'name': 'autogrid_result_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
MakeAutogridResultObj_25.addOutputPort, (), {
'name': 'autogrid_result_obj',
'datatype': 'autogrid_results',
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC'
})
code = """def doit(self, autogrid_result_url):
from AutoDockTools.VisionInterface.Adt.autogrid_results import autogrid_results
agro = autogrid_results(autogrid_result_url, '''url''')
pass
## to ouput data on port autogrid_result_obj use
self.outputData(autogrid_result_obj=agro)
"""
MakeAutogridResultObj_25.configure(function=code)
apply(MakeAutogridResultObj_25.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named MakeAutogridResultObj in network self.macroNetwork"
print_exc()
MakeAutogridResultObj_25 = None
try:
## saving node GetURLFromList ##
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_26 = GetURLFromListNode(constrkw={},
name='GetURLFromList',
library=wslib)
self.macroNetwork.addNode(GetURLFromList_26, 110, 198)
apply(GetURLFromList_26.inputPortByName['urllist'].configure, (),
{'defaultValue': None})
apply(GetURLFromList_26.inputPortByName['ext'].configure, (),
{'defaultValue': None})
GetURLFromList_26.inputPortByName['ext'].widget.set(r"gpf",
run=False)
apply(GetURLFromList_26.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore GetURLFromListNode named GetURLFromList in network self.macroNetwork"
print_exc()
GetURLFromList_26 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network ComputeGrids ##
input_Ports_19 = self.macroNetwork.ipNode
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"ligands",
blocking=True,
splitratio=[0.25038057532685992, 0.40242243717082576])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"receptor_pdbqt",
blocking=True,
splitratio=[0.31642654296910228, 0.49356822236979669])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if input_Ports_19 is not None and GetComputeGridsInputs_21 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_19,
GetComputeGridsInputs_21,
"new",
"gpf_obj",
blocking=True,
splitratio=[0.57570983312901203, 0.33826779179418875])
except:
print "WARNING: failed to restore connection between input_Ports_19 and GetComputeGridsInputs_21 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"gpf_template_path",
"gpf",
blocking=True,
splitratio=[0.37911517364560754, 0.49588454022594075])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.51555458245420727, 0.58910990532612562])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.45378244060628786, 0.49829462092378918])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and prepareGPF_kryptonite_nbcr_net_22 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
prepareGPF_kryptonite_nbcr_net_22,
"prepared_receptor",
"r",
blocking=True,
splitratio=[0.30158184825681655, 0.46256232709378253])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and prepareGPF_kryptonite_nbcr_net_22 in network self.macroNetwork"
if GetComputeGridsInputs_21 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetComputeGridsInputs_21,
autogrid_kryptonite_nbcr_net_23,
"prepared_receptor",
"inFile",
blocking=True,
splitratio=[0.63016045430148715, 0.62091422998177115])
except:
print "WARNING: failed to restore connection between GetComputeGridsInputs_21 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
if autogrid_kryptonite_nbcr_net_23 is not None and GetMainURLFromList_24 is not None:
try:
self.macroNetwork.connectNodes(
autogrid_kryptonite_nbcr_net_23,
GetMainURLFromList_24,
"result",
"urls",
blocking=True,
splitratio=[0.4713453370864038, 0.73699665503637379])
except:
print "WARNING: failed to restore connection between autogrid_kryptonite_nbcr_net_23 and GetMainURLFromList_24 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and MakeAutogridResultObj_25 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24,
MakeAutogridResultObj_25,
"newurl",
"autogrid_result_url",
blocking=True,
splitratio=[0.37530325590010172, 0.67260462300696811])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and MakeAutogridResultObj_25 in network self.macroNetwork"
output_Ports_20 = self.macroNetwork.opNode
if MakeAutogridResultObj_25 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
MakeAutogridResultObj_25,
output_Ports_20,
"autogrid_result_obj",
"new",
blocking=True,
splitratio=[0.54860274312929591, 0.61692487705230459])
except:
print "WARNING: failed to restore connection between MakeAutogridResultObj_25 and output_Ports_20 in network self.macroNetwork"
if GetMainURLFromList_24 is not None and output_Ports_20 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_24,
output_Ports_20,
"newurl",
"new",
blocking=True,
splitratio=[0.56961778623989434, 0.55443680742298707])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_24 and output_Ports_20 in network self.macroNetwork"
if prepareGPF_kryptonite_nbcr_net_22 is not None and GetURLFromList_26 is not None:
try:
self.macroNetwork.connectNodes(
prepareGPF_kryptonite_nbcr_net_22,
GetURLFromList_26,
"result",
"urllist",
blocking=True,
splitratio=[0.38550670487593142, 0.45424125807822219])
except:
print "WARNING: failed to restore connection between prepareGPF_kryptonite_nbcr_net_22 and GetURLFromList_26 in network self.macroNetwork"
if GetURLFromList_26 is not None and autogrid_kryptonite_nbcr_net_23 is not None:
try:
self.macroNetwork.connectNodes(
GetURLFromList_26,
autogrid_kryptonite_nbcr_net_23,
"url",
"p_url",
blocking=True,
splitratio=[0.65566147293832433, 0.57782517914212228])
except:
print "WARNING: failed to restore connection between GetURLFromList_26 and autogrid_kryptonite_nbcr_net_23 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_19 = self.macroNetwork.ipNode
input_Ports_19.outputPorts[1].configure(
name='GetComputeGridsInputs_ligands')
input_Ports_19.outputPorts[2].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
input_Ports_19.outputPorts[3].configure(
name='GetComputeGridsInputs_gpf_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_20 = self.macroNetwork.opNode
output_Ports_20.inputPorts[1].configure(singleConnection='auto')
output_Ports_20.inputPorts[2].configure(singleConnection='auto')
output_Ports_20.inputPorts[1].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
output_Ports_20.inputPorts[2].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
ComputeGrids_18.inputPorts[0].configure(
name='GetComputeGridsInputs_ligands')
ComputeGrids_18.inputPorts[0].configure(datatype='LigandDB')
ComputeGrids_18.inputPorts[1].configure(
name='GetComputeGridsInputs_receptor_pdbqt')
ComputeGrids_18.inputPorts[1].configure(datatype='receptor_prepared')
ComputeGrids_18.inputPorts[2].configure(
name='GetComputeGridsInputs_gpf_obj')
ComputeGrids_18.inputPorts[2].configure(datatype='gpf_template')
## configure MacroNode output ports
ComputeGrids_18.outputPorts[0].configure(
name='MakeAutogridResultObj_autogrid_result_obj')
ComputeGrids_18.outputPorts[0].configure(datatype='autogrid_results')
ComputeGrids_18.outputPorts[1].configure(
name='GetMainURLFromList_newurl')
ComputeGrids_18.outputPorts[1].configure(datatype='string')
ComputeGrids_18.shrink()
## reset modifications ##
ComputeGrids_18.resetTags()
ComputeGrids_18.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
TrajQR_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(183, 405)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node Make_Zip_File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make_Zip_File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 47, 75)
apply(Make_Zip_File_3.inputPortByName['input_directory'].configure,
(), {'defaultValue': None})
apply(
Make_Zip_File_3.inputPortByName['output_directory'].configure,
(), {'defaultValue': None})
apply(Make_Zip_File_3.inputPortByName['output_name'].configure, (),
{'defaultValue': None})
apply(Make_Zip_File_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MakeZipFileNE named Make_Zip_File in network self.macroNetwork"
print_exc()
Make_Zip_File_3 = None
try:
## saving node TrajQR_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
TrajQR_kryptonite_nbcr_net_4 = FunctionNode(
functionOrString='TrajQR_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
},
constrkw={
'functionOrString': "'TrajQR_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'license': False,
'rmsd': '',
'qh_filename': 'qh.tre',
'qr_filename': 'qr.out',
'compressed_pdbs': '',
'localRun': False,
'execPath': ''
}
},
name='TrajQR_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(TrajQR_kryptonite_nbcr_net_4, 279, 135)
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].configure,
(), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qh_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['qr_filename'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.
inputPortByName['compressed_pdbs'].configure, (), {
'defaultValue': None,
'required': True
})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
TrajQR_kryptonite_nbcr_net_4.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
TrajQR_kryptonite_nbcr_net_4.inputPortByName['license'].widget.set(
0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].widget.set(
r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName['rmsd'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qh_filename'].widget.set(r"qh.tre", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'qr_filename'].widget.set(r"qr.out", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].rebindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].widget.set(r"", run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'compressed_pdbs'].unbindWidget()
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'localRun'].widget.set(0, run=False)
TrajQR_kryptonite_nbcr_net_4.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(TrajQR_kryptonite_nbcr_net_4.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named TrajQR_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
TrajQR_kryptonite_nbcr_net_4 = None
try:
## saving node SelectOnExtension ##
from Vision.StandardNodes import SelectOnExtension
SelectOnExtension_5 = SelectOnExtension(constrkw={},
name='SelectOnExtension',
library=stdlib)
self.macroNetwork.addNode(SelectOnExtension_5, 279, 192)
apply(SelectOnExtension_5.inputPortByName['filenames'].configure,
(), {'defaultValue': None})
apply(SelectOnExtension_5.inputPortByName['extension'].configure,
(), {'defaultValue': None})
SelectOnExtension_5.inputPortByName['extension'].widget.set(
r".out", run=False)
apply(SelectOnExtension_5.configure, (),
{'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore SelectOnExtension named SelectOnExtension in network self.macroNetwork"
print_exc()
SelectOnExtension_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 123, 281)
apply(
Index_6.inputPortByName['data'].configure, (), {
'datatype': 'list',
'defaultValue': None,
'originalDatatype': 'None'
})
apply(Index_6.inputPortByName['index'].configure, (),
{'defaultValue': None})
apply(Index_6.outputPortByName['data'].configure, (),
{'datatype': 'string'})
apply(Index_6.inputPortByName['index'].widget.configure, (), {
'max': 0,
'min': -1
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
apply(Index_6.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_6 = None
try:
## saving node GetSelectedPDBs ##
from Vision.StandardNodes import Generic
GetSelectedPDBs_7 = Generic(constrkw={},
name='GetSelectedPDBs',
library=stdlib)
self.macroNetwork.addNode(GetSelectedPDBs_7, 200, 346)
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'trajqr_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_in_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addInputPort, (), {
'singleConnection': True,
'name': 'pdb_out_dir',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
apply(
GetSelectedPDBs_7.addOutputPort, (), {
'name': 'pdb_out_dir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, trajqr_url, pdb_in_dir, pdb_out_dir):
pdb_in_dir = os.path.abspath(pdb_in_dir)
pdb_out_dir = os.path.abspath(pdb_out_dir)
import urllib
import shutil
pdb_list = []
f = urllib.urlopen(trajqr_url)
for i in f.readlines():
pdb_file = i.strip('''
''')+'''.pdb'''
infile = pdb_in_dir + os.sep + pdb_file
outfile = pdb_out_dir + os.sep + pdb_file
shutil.copyfile(infile, outfile)
f.close
pass
## to ouput data on port pdb_list use
self.outputData(pdb_out_dir=pdb_out_dir)
"""
GetSelectedPDBs_7.configure(function=code)
apply(GetSelectedPDBs_7.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named GetSelectedPDBs in network self.macroNetwork"
print_exc()
GetSelectedPDBs_7 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network TrajQR ##
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
Make_Zip_File_3,
"new",
"input_directory",
blocking=True,
splitratio=[0.67469172328672133, 0.50941480178765064])
except:
print "WARNING: failed to restore connection between input_Ports_1 and Make_Zip_File_3 in network self.macroNetwork"
if input_Ports_1 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
TrajQR_kryptonite_nbcr_net_4,
"new",
"rmsd",
blocking=True,
splitratio=[0.45681934134493246, 0.33803410340720857])
except:
print "WARNING: failed to restore connection between input_Ports_1 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if Make_Zip_File_3 is not None and TrajQR_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
TrajQR_kryptonite_nbcr_net_4,
"zipfile",
"compressed_pdbs",
blocking=True,
splitratio=[0.71081093868178202, 0.43908686250860129])
except:
print "WARNING: failed to restore connection between Make_Zip_File_3 and TrajQR_kryptonite_nbcr_net_4 in network self.macroNetwork"
if TrajQR_kryptonite_nbcr_net_4 is not None and SelectOnExtension_5 is not None:
try:
self.macroNetwork.connectNodes(
TrajQR_kryptonite_nbcr_net_4,
SelectOnExtension_5,
"result",
"filenames",
blocking=True,
splitratio=[0.63533198718963335, 0.2560040659014205])
except:
print "WARNING: failed to restore connection between TrajQR_kryptonite_nbcr_net_4 and SelectOnExtension_5 in network self.macroNetwork"
if SelectOnExtension_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
SelectOnExtension_5,
Index_6,
"matching",
"data",
blocking=True,
splitratio=[0.65832290589891362, 0.21624347250969889])
except:
print "WARNING: failed to restore connection between SelectOnExtension_5 and Index_6 in network self.macroNetwork"
if Index_6 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
GetSelectedPDBs_7,
"data",
"trajqr_url",
blocking=True,
splitratio=[0.51754619993986595, 0.63949220525823236])
except:
print "WARNING: failed to restore connection between Index_6 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"Make_Zip_File_input_directory",
"pdb_in_dir",
blocking=True,
splitratio=[0.7121964126696847, 0.42697952864467786])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
if input_Ports_1 is not None and GetSelectedPDBs_7 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
GetSelectedPDBs_7,
"new",
"pdb_out_dir",
blocking=True,
splitratio=[0.62460995639428174, 0.60275185701976297])
except:
print "WARNING: failed to restore connection between input_Ports_1 and GetSelectedPDBs_7 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetSelectedPDBs_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetSelectedPDBs_7,
output_Ports_2,
"pdb_out_dir",
"new",
blocking=True,
splitratio=[0.7431176169343523, 0.73697976585137526])
except:
print "WARNING: failed to restore connection between GetSelectedPDBs_7 and output_Ports_2 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
input_Ports_1.outputPorts[3].configure(
name='GetSelectedPDBs_pdb_out_dir')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='GetSelectedPDBs_pdb_out_dir')
## configure MacroNode input ports
TrajQR_0.inputPorts[0].configure(name='Make_Zip_File_input_directory')
TrajQR_0.inputPorts[0].configure(datatype='string')
TrajQR_0.inputPorts[1].configure(
name='TrajQR_kryptonite_nbcr_net_rmsd')
TrajQR_0.inputPorts[1].configure(datatype='string')
TrajQR_0.inputPorts[2].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
TrajQR_0.outputPorts[0].configure(name='GetSelectedPDBs_pdb_out_dir')
TrajQR_0.outputPorts[0].configure(datatype='string')
TrajQR_0.shrink()
## reset modifications ##
TrajQR_0.resetTags()
TrajQR_0.buildOriginalList()
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
from Vision.StandardNodes import stdlib
## building macro network ##
recluster_11 = self
from traceback import print_exc
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(
molkitlib, "MolKit.VisionInterface.MolKitNodes", "molkitlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(
stdlib, "Vision.StandardNodes", "stdlib")
try:
## saving node input Ports ##
input_Ports_12 = self.macroNetwork.ipNode
input_Ports_12.move(172, 137)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_12 = None
try:
## saving node output Ports ##
output_Ports_13 = self.macroNetwork.opNode
output_Ports_13.move(172, 479)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_13 = None
try:
## saving node Docking ##
from Vision.StandardNodes import Generic
Docking_16 = Generic(constrkw={}, name='Docking', library=stdlib)
self.macroNetwork.addNode(Docking_16, 189, 250)
apply(
Docking_16.addInputPort, (), {
'name': 'docking_logs',
'cast': True,
'datatype': 'list',
'balloon':
'list of docking log files to be read into as a single Docking',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'cyan'
})
apply(
Docking_16.addInputPort, (), {
'name': 'rmsTool',
'cast': True,
'datatype': 'None',
'balloon': 'rmsTool to be used for clustering',
'required': False,
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
apply(
Docking_16.addOutputPort, (), {
'name': 'docking',
'datatype': 'None',
'balloon': 'docking instance',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, docking_logs, rmsTool):
from AutoDockTools.Docking import Docking
d = Docking()
for f in docking_logs:
d.readDlg(f)
d.clusterer.rmsTool = rmsTool
self.outputData(docking = d)
## to ouput data on port docking use
## self.outputData(docking=data)
"""
Docking_16.configure(function=code)
except:
print "WARNING: failed to restore Generic named Docking in network self.macroNetwork"
print_exc()
Docking_16 = None
try:
## saving node rmsTool ##
from Vision.StandardNodes import Generic
rmsTool_17 = Generic(constrkw={}, name='rmsTool', library=stdlib)
self.macroNetwork.addNode(rmsTool_17, 206, 197)
apply(
rmsTool_17.addInputPort, (), {
'name': 'crds',
'cast': True,
'datatype': 'coordinates3D',
'balloon':
'coordinates to use as reference for rms calculation.',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'green'
})
apply(
rmsTool_17.addOutputPort, (), {
'name': 'rmsTool',
'datatype': 'None',
'balloon': 'rmsTool created using crds as reference',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, crds):
from mglutil.math.rmsd import RMSDCalculator
rmsTool = RMSDCalculator(crds)
self.outputData(rmsTool = rmsTool)
"""
rmsTool_17.configure(function=code)
except:
print "WARNING: failed to restore Generic named rmsTool in network self.macroNetwork"
print_exc()
rmsTool_17 = None
try:
## saving node Read Molecule ##
from MolKit.VisionInterface.MolKitNodes import ReadMolecule
Read_Molecule_18 = ReadMolecule(constrkw={},
name='Read Molecule',
library=molkitlib)
self.macroNetwork.addNode(Read_Molecule_18, 243, 16)
apply(Read_Molecule_18.inputPortByName['filename'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Read_Molecule_18.outputPortByName['MolSets'].configure, (), {
'color': '#c64e70',
'shape': 'oval'
})
Read_Molecule_18.inputPortByName['filename'].widget.set(
"ind.pdbqt", run=False)
except:
print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork"
print_exc()
Read_Molecule_18 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_19 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_19, 243, 66)
apply(
Index_19.inputPortByName['data'].configure, (), {
'datatype': 'MoleculeSet',
'cast': True,
'shape': 'oval',
'color': '#c64e70'
})
apply(Index_19.inputPortByName['index'].configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(Index_19.outputPortByName['data'].configure, (), {
'color': 'white',
'shape': 'diamond'
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_19 = None
try:
## saving node Get allAtoms.coords ##
from Vision.StandardNodes import GetAttr
Get_allAtoms_coords_20 = GetAttr(constrkw={},
name='Get allAtoms.coords',
library=stdlib)
self.macroNetwork.addNode(Get_allAtoms_coords_20, 243, 115)
apply(Get_allAtoms_coords_20.inputPortByName['objects'].configure,
(), {
'color': 'white',
'cast': True,
'shape': 'diamond'
})
apply(Get_allAtoms_coords_20.inputPortByName['attr'].configure, (),
{
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Get_allAtoms_coords_20.outputPortByName['attrs'].configure,
(), {
'color': 'cyan',
'shape': 'oval'
})
apply(
Get_allAtoms_coords_20.inputPortByName['attr'].widget.
configure, (), {
'choices':
('AAradii', 'AtomRadiiPatterns', 'NodesFromName', 'ROOT',
'TORSDOF', '_MarkTree', '__cmp__', '__doc__', '__eq__',
'__hash__', '__init__', '__module__', '__ne__',
'__repr__', '__str__', '_atomRadius', '_copyNode',
'_copy_atom_attr', '_fit_atom_into_tree',
'_numberOfDeletedNodes', 'addBond', 'adopt', 'allAtoms',
'assignUniqIndex', 'atmNum', 'attach_nonbonded_fragments',
'bonds', 'bondsflag', 'buildBondsBhtree',
'buildBondsByDistance', 'buildBondsByDistanceOnAtoms',
'buildBrokenBonds', 'chains', 'childByName', 'children',
'childrenName', 'childrenSetClass', 'closerThan',
'compare', 'compiled_patterns', 'configureProgressBar',
'copy', 'defaultRadii', 'deleteSubTree', 'dump',
'elementType', 'findLevels', 'findType', 'full_name',
'get', 'getAtoms', 'getCenter', 'getNext',
'getParentOfType', 'getPrevious', 'getRoot',
'getTypeList', 'hasBonds', 'hasSS', 'isAbove', 'isBelow',
'levels', 'makeNameUniq', 'merge', 'mergeNPH', 'name',
'ndihe', 'p', 'parent', 'parser', 'read', 'remove',
'removeAllHydrogens', 'removeBond', 'secondaryStructure',
'secondaryStructureFromFile',
'secondaryStructureFromStride', 'setClass', 'split',
'subTree', 'top', 'torTree', 'updateProgressBar', 'write')
})
Get_allAtoms_coords_20.inputPortByName['attr'].widget.set(
"allAtoms.coords", run=False)
apply(Get_allAtoms_coords_20.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore GetAttr named Get allAtoms.coords in network self.macroNetwork"
print_exc()
Get_allAtoms_coords_20 = None
try:
## saving node Get clusterer ##
from Vision.StandardNodes import GetAttr
Get_clusterer_21 = GetAttr(constrkw={},
name='Get clusterer',
library=stdlib)
self.macroNetwork.addNode(Get_clusterer_21, 189, 306)
apply(Get_clusterer_21.inputPortByName['objects'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'diamond'
})
apply(Get_clusterer_21.inputPortByName['attr'].configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(Get_clusterer_21.outputPortByName['attrs'].configure, (), {
'color': 'cyan',
'shape': 'oval'
})
apply(
Get_clusterer_21.inputPortByName['attr'].widget.configure, (),
{
'choices':
('__doc__', '__init__', '__module__', 'addConformations',
'ch', 'clusterer', 'clusterer_dict', 'defaultParser',
'dlo_list', 'flex_res', 'ligMol', 'parser', 'readDlg',
'readEntropiaResults', 'readXMLResults', 'set_ligand',
'version', 'warnings', 'writeConformation',
'write_current_conformation')
})
Get_clusterer_21.inputPortByName['attr'].widget.set("clusterer",
run=False)
apply(Get_clusterer_21.configure, (), {'expanded': True})
except:
print "WARNING: failed to restore GetAttr named Get clusterer in network self.macroNetwork"
print_exc()
Get_clusterer_21 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_22 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_22, 188, 383)
apply(Index_22.inputPortByName['data'].configure, (), {
'datatype': 'list',
'cast': True,
'shape': 'oval',
'color': 'cyan'
})
apply(Index_22.inputPortByName['index'].configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(Index_22.outputPortByName['data'].configure, (), {
'color': 'white',
'shape': 'diamond'
})
except:
print "WARNING: failed to restore Index named Index in network self.macroNetwork"
print_exc()
Index_22 = None
try:
## saving node make clustering ##
from Vision.StandardNodes import Generic
make_clustering_23 = Generic(constrkw={},
name='make clustering',
library=stdlib)
self.macroNetwork.addNode(make_clustering_23, 189, 432)
apply(
make_clustering_23.addInputPort, (), {
'name': 'clusterer',
'cast': True,
'datatype': 'None',
'balloon': 'clusterer which will make the new clustering',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
apply(
make_clustering_23.addInputPort, (), {
'name': 'tolerance',
'cast': True,
'datatype': 'float',
'balloon': 'rms tolerance for the new clustering',
'height': 12,
'width': 12,
'shape': 'circle',
'color': 'green'
})
apply(
make_clustering_23.addOutputPort, (), {
'name': 'clustering',
'datatype': 'None',
'balloon': 'clustering at newest rms',
'height': 8,
'width': 12,
'shape': 'diamond',
'color': 'white'
})
code = """def doit(self, clusterer, tolerance):
clusterer.make_clustering(tolerance)
self.outputData(clustering = clusterer.clustering_dict[tolerance])
"""
make_clustering_23.configure(function=code)
except:
print "WARNING: failed to restore Generic named make clustering in network self.macroNetwork"
print_exc()
make_clustering_23 = None
try:
## saving node Dial ##
from Vision.StandardNodes import DialNE
Dial_24 = DialNE(constrkw={}, name='Dial', library=stdlib)
self.macroNetwork.addNode(Dial_24, 233, 380)
apply(Dial_24.inputPortByName['dial'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.inputPortByName['mini'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.inputPortByName['maxi'].configure, (), {
'color': 'green',
'cast': True,
'shape': 'circle'
})
apply(Dial_24.outputPortByName['value'].configure, (), {
'color': 'green',
'shape': 'circle'
})
Dial_24.inputPortByName['dial'].widget.set(3.0, run=False)
apply(Dial_24.configure, (), {'expanded': False})
except:
print "WARNING: failed to restore DialNE named Dial in network self.macroNetwork"
print_exc()
Dial_24 = None
self.macroNetwork.freeze()
## saving connections for network recluster ##
if rmsTool_17 is not None and Docking_16 is not None:
try:
self.macroNetwork.connectNodes(rmsTool_17,
Docking_16,
"rmsTool",
"rmsTool",
blocking=True)
except:
print "WARNING: failed to restore connection between rmsTool_17 and Docking_16 in network self.macroNetwork"
if Read_Molecule_18 is not None and Index_19 is not None:
try:
self.macroNetwork.connectNodes(Read_Molecule_18,
Index_19,
"MolSets",
"data",
blocking=True)
except:
print "WARNING: failed to restore connection between Read_Molecule_18 and Index_19 in network self.macroNetwork"
if Index_19 is not None and Get_allAtoms_coords_20 is not None:
try:
self.macroNetwork.connectNodes(Index_19,
Get_allAtoms_coords_20,
"data",
"objects",
blocking=True)
except:
print "WARNING: failed to restore connection between Index_19 and Get_allAtoms_coords_20 in network self.macroNetwork"
if Get_allAtoms_coords_20 is not None and rmsTool_17 is not None:
try:
self.macroNetwork.connectNodes(Get_allAtoms_coords_20,
rmsTool_17,
"attrs",
"crds",
blocking=True)
except:
print "WARNING: failed to restore connection between Get_allAtoms_coords_20 and rmsTool_17 in network self.macroNetwork"
if Docking_16 is not None and Get_clusterer_21 is not None:
try:
self.macroNetwork.connectNodes(Docking_16,
Get_clusterer_21,
"docking",
"objects",
blocking=True)
except:
print "WARNING: failed to restore connection between Docking_16 and Get_clusterer_21 in network self.macroNetwork"
if Get_clusterer_21 is not None and Index_22 is not None:
try:
self.macroNetwork.connectNodes(Get_clusterer_21,
Index_22,
"attrs",
"data",
blocking=True)
except:
print "WARNING: failed to restore connection between Get_clusterer_21 and Index_22 in network self.macroNetwork"
if Index_22 is not None and make_clustering_23 is not None:
try:
self.macroNetwork.connectNodes(Index_22,
make_clustering_23,
"data",
"clusterer",
blocking=True)
except:
print "WARNING: failed to restore connection between Index_22 and make_clustering_23 in network self.macroNetwork"
if Dial_24 is not None and make_clustering_23 is not None:
try:
self.macroNetwork.connectNodes(Dial_24,
make_clustering_23,
"value",
"tolerance",
blocking=True)
except:
print "WARNING: failed to restore connection between Dial_24 and make_clustering_23 in network self.macroNetwork"
output_Ports_13 = self.macroNetwork.opNode
if make_clustering_23 is not None and output_Ports_13 is not None:
try:
self.macroNetwork.connectNodes(make_clustering_23,
output_Ports_13,
"clustering",
"new",
blocking=True)
except:
print "WARNING: failed to restore connection between make_clustering_23 and output_Ports_13 in network self.macroNetwork"
input_Ports_12 = self.macroNetwork.ipNode
if input_Ports_12 is not None and Docking_16 is not None:
try:
self.macroNetwork.connectNodes(input_Ports_12,
Docking_16,
"new",
"docking_logs",
blocking=True)
except:
print "WARNING: failed to restore connection between input_Ports_12 and Docking_16 in network self.macroNetwork"
self.macroNetwork.unfreeze()
recluster_11.shrink()
## reset modifications ##
recluster_11.resetTags()
recluster_11.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
PrepareReceptor_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork")
print_exc()
input_Ports_1=None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork")
print_exc()
output_Ports_2=None
try:
## saving node Pdb2pqrWS ##
from NetworkEditor.macros import MacroNode
Pdb2pqrWS_3 = MacroNode(name='Pdb2pqrWS')
self.macroNetwork.addNode(Pdb2pqrWS_3, 153, 86)
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
input_Ports_4.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
input_Ports_4.move(65, 10)
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
output_Ports_5.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
output_Ports_5.move(65, 310)
from Vision.StandardNodes import Generic
CheckFileFormat_6 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(CheckFileFormat_6,82,62)
CheckFileFormat_6.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'pqr_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_6.addOutputPort(*(), **{'name': 'pdb_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pqr''') != None or value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr_name = value.get_id() + '''.pqr'''
pdb_path = value.get_ext_loc('''pdb''')
self.outputData(receptor_obj=value, pqr_name=pqr_name, pdb_path=pdb_path)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''pqr_name'''), self.getOutputPortByName('''pdb_path''')])
"""
CheckFileFormat_6.configure(function=code)
CheckFileFormat_6.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
Pdb2pqrOpalService_ws_nbcr_net_7 = FunctionNode(functionOrString='Pdb2pqrOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}, constrkw={'functionOrString': "'Pdb2pqrOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}}, name='Pdb2pqrOpalService_ws_nbcr_net', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(Pdb2pqrOpalService_ws_nbcr_net_7,99,115)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].configure(*(), **{'defaultValue': None, 'required': True})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].configure(*(), **{'defaultValue': None, 'required': True})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].rebindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].unbindWidget()
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['clean'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inId'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['apbs_input'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')})
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['localRun'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['rama'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['execPath'].widget.set(r"", run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['assign_only'].widget.set(0, run=False)
Pdb2pqrOpalService_ws_nbcr_net_7.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_8 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
Pdb2pqrWS_3.macroNetwork.addNode(GetURLFromList_8,117,169)
GetURLFromList_8.inputPortByName['ext'].widget.set(r"pqr", run=False)
GetURLFromList_8.configure(*(), **{'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_9 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
Pdb2pqrWS_3.macroNetwork.addNode(UpdateReceptor_9,82,256)
UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'pqr', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
UpdateReceptor_9.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
UpdateReceptor_9.addOutputPort(*(), **{'name': 'pdb2pqr_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pqr):
if pqr != '''no data yet''':
pdb2pqr_result = pqr
receptor_obj.set_ext_loc(pqr)
else:
pdbqt = receptor_obj.get_ext_loc('''pdbqt''')
pqr = receptor_obj.get_ext_loc('''pqr''')
if pdbqt != None:
pdb2pqr_result = pdbqt
elif pqr != None:
pdb2pqr_result = pqr
pass
self.outputData(receptor_obj=receptor_obj, pdb2pqr_result=pdb2pqr_result)
"""
UpdateReceptor_9.configure(function=code)
UpdateReceptor_9.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network Pdb2pqrWS ##
Pdb2pqrWS_3.macroNetwork.freeze()
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pqr_name", "output_file", blocking=True
, splitratio=[0.43278717885693868, 0.65281492247209427])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork")
if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pdb_path", "inFile", blocking=True
, splitratio=[0.61978340673276544, 0.69977512898866912])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork")
if Pdb2pqrOpalService_ws_nbcr_net_7 is not None and GetURLFromList_8 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
Pdb2pqrOpalService_ws_nbcr_net_7, GetURLFromList_8, "result", "urllist", blocking=True
, splitratio=[0.73247388879852338, 0.69014271703344965])
except:
print("WARNING: failed to restore connection between Pdb2pqrOpalService_ws_nbcr_net_7 and GetURLFromList_8 in network Pdb2pqrWS_3.macroNetwork")
if GetURLFromList_8 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
GetURLFromList_8, UpdateReceptor_9, "url", "pqr", blocking=True
, splitratio=[0.35224914715245104, 0.47693375858097758])
except:
print("WARNING: failed to restore connection between GetURLFromList_8 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork")
if CheckFileFormat_6 is not None and UpdateReceptor_9 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
CheckFileFormat_6, UpdateReceptor_9, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.57865377076653579, 0.45824116584600394])
except:
print("WARNING: failed to restore connection between CheckFileFormat_6 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork")
input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode
if input_Ports_4 is not None and CheckFileFormat_6 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
input_Ports_4, CheckFileFormat_6, "new", "value", blocking=True
, splitratio=[0.28291581858817416, 0.70581213384962171])
except:
print("WARNING: failed to restore connection between input_Ports_4 and CheckFileFormat_6 in network Pdb2pqrWS_3.macroNetwork")
output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "receptor_obj", "new", blocking=True
, splitratio=[0.24354423773729619, 0.72115604180615911])
except:
print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork")
if UpdateReceptor_9 is not None and output_Ports_5 is not None:
try:
Pdb2pqrWS_3.macroNetwork.connectNodes(
UpdateReceptor_9, output_Ports_5, "pdb2pqr_result", "new", blocking=True
, splitratio=[0.31141907324539131, 0.41794097665671487])
except:
print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork")
Pdb2pqrWS_3.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_4.outputPorts[1].configure(name='CheckFileFormat_value')
## modifying MacroOutputNode dynamic ports
output_Ports_5.inputPorts[1].configure(singleConnection='auto')
output_Ports_5.inputPorts[2].configure(singleConnection='auto')
output_Ports_5.inputPorts[1].configure(name='UpdateReceptor_receptor_obj')
output_Ports_5.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.inputPorts[0].configure(name='CheckFileFormat_value')
Pdb2pqrWS_3.inputPorts[0].configure(datatype='receptor')
## configure MacroNode input ports
Pdb2pqrWS_3.outputPorts[0].configure(name='UpdateReceptor_receptor_obj')
Pdb2pqrWS_3.outputPorts[0].configure(datatype='receptor')
Pdb2pqrWS_3.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result')
Pdb2pqrWS_3.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
Pdb2pqrWS_3.shrink()
Pdb2pqrWS_3.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroNode named Pdb2pqrWS in network self.macroNetwork")
print_exc()
Pdb2pqrWS_3=None
try:
## saving node PrepareReceptorWS ##
from NetworkEditor.macros import MacroNode
PrepareReceptorWS_10 = MacroNode(name='PrepareReceptorWS')
self.macroNetwork.addNode(PrepareReceptorWS_10, 217, 140)
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
input_Ports_11.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
input_Ports_11.move(145, 8)
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
output_Ports_12.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
output_Ports_12.move(29, 412)
from Vision.StandardNodes import Generic
CheckFileFormat_13 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(CheckFileFormat_13,46,64)
CheckFileFormat_13.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
CheckFileFormat_13.addOutputPort(*(), **{'name': 'download_loc', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, value):
if value.get_ext_loc('''pdbqt''') != None:
self.outputData(receptor_obj=value)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')])
else:
pqr = value.get_ext_loc('''pqr''')
pdb = value.get_ext_loc('''pdb''')
download_loc = value.get_workdir() + os.sep + value.get_id() + '''.pdbqt'''
if pqr != None:
if value.get_ext_type('''pqr''') == '''url''':
receptor_url = pqr
receptor_local = ""
else:
receptor_url = ""
receptor_local = pqr
elif pdb != None:
if value.get_ext_type('''pdb''') == '''url''':
receptor_url = pdb
receptor_local = ""
else:
receptor_url = ""
receptor_local = pdb
else:
print "*** ERROR: pqr and pqr both missing from receptor object"
print receptor_obj.ext_loc
return '''stop'''
self.outputData(receptor_obj=value, receptor_url=receptor_url, receptor_local=receptor_local, download_loc=download_loc)
self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''receptor_url'''), self.getOutputPortByName('''receptor_local'''), self.getOutputPortByName('''download_loc''')])
"""
CheckFileFormat_13.configure(function=code)
CheckFileFormat_13.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from NetworkEditor.items import FunctionNode
PrepareReceptorOpalService_ws_nbcr_net_14 = FunctionNode(functionOrString='PrepareReceptorOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'PrepareReceptorOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}}, name='PrepareReceptorOpalService_ws_nbcr_net', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(PrepareReceptorOpalService_ws_nbcr_net_14,180,128)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].configure(*(), **{'defaultValue': None})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].configure(*(), **{'defaultValue': None, 'required': True})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].configure(*(), **{'defaultValue': None, 'required': True})
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['o'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].rebindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].unbindWidget()
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['v'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['localRun'].widget.set(0, run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['execPath'].widget.set(r"", run=False)
PrepareReceptorOpalService_ws_nbcr_net_14.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
from WebServices.VisionInterface.WSNodes import GetURLFromListNode
GetURLFromList_15 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(GetURLFromList_15,180,186)
GetURLFromList_15.inputPortByName['ext'].widget.set(r"pdbqt", run=False)
GetURLFromList_15.configure(*(), **{'paramPanelImmediate': 1})
from WebServices.VisionInterface.WSNodes import DownloadToFileNode
DownloadToFile_16 = DownloadToFileNode(constrkw={}, name='DownloadToFile', library=wslib)
PrepareReceptorWS_10.macroNetwork.addNode(DownloadToFile_16,80,272)
DownloadToFile_16.inputPortByName['url'].configure(*(), **{'defaultValue': None})
DownloadToFile_16.inputPortByName['filename'].configure(*(), **{'defaultValue': None})
DownloadToFile_16.inputPortByName['url'].rebindWidget()
DownloadToFile_16.inputPortByName['url'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['url'].unbindWidget()
DownloadToFile_16.inputPortByName['filename'].rebindWidget()
DownloadToFile_16.inputPortByName['filename'].widget.set(r"", run=False)
DownloadToFile_16.inputPortByName['filename'].unbindWidget()
DownloadToFile_16.inputPortByName['overwrite'].widget.set(1, run=False)
DownloadToFile_16.configure(*(), **{'paramPanelImmediate': 1})
from Vision.StandardNodes import Generic
UpdateReceptor_17 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib)
PrepareReceptorWS_10.macroNetwork.addNode(UpdateReceptor_17,46,358)
UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'})
UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'pdbqt', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'})
UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_prepared_obj', 'datatype': 'receptor_prepared', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900'})
UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'})
code = """def doit(self, receptor_obj, pdbqt):
from AutoDockTools.VisionInterface.Adt.receptor_prepared import receptor_prepared
if pdbqt != '''no data yet''':
receptor_prepared_obj = receptor_prepared(pdbqt)
receptor_obj.set_ext_loc(pdbqt)
receptor_result = pdbqt
else:
pdbqt_org = receptor_obj.get_ext_loc('''pdbqt''')
receptor_prepared_obj = receptor_prepared(pdbqt_org)
receptor_result = pdbqt_org
pass
self.outputData(receptor_prepared_obj = receptor_prepared_obj, receptor_result=receptor_result)
"""
UpdateReceptor_17.configure(function=code)
UpdateReceptor_17.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
## saving connections for network PrepareReceptorWS ##
PrepareReceptorWS_10.macroNetwork.freeze()
input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode
if input_Ports_11 is not None and CheckFileFormat_13 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, CheckFileFormat_13, "new", "value", blocking=True
, splitratio=[0.64907843562020084, 0.47057253960060474])
except:
print("WARNING: failed to restore connection between input_Ports_11 and CheckFileFormat_13 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_url", "url", blocking=True
, splitratio=[0.6171192646814192, 0.42883431331137822])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_local", "r", blocking=True
, splitratio=[0.66136144381723583, 0.28482114514549767])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if input_Ports_11 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
input_Ports_11, PrepareReceptorOpalService_ws_nbcr_net_14, "new", "C", blocking=True
, splitratio=[0.53817543437956172, 0.61119702937572407])
except:
print("WARNING: failed to restore connection between input_Ports_11 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork")
if PrepareReceptorOpalService_ws_nbcr_net_14 is not None and GetURLFromList_15 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
PrepareReceptorOpalService_ws_nbcr_net_14, GetURLFromList_15, "result", "urllist", blocking=True
, splitratio=[0.43369347916867251, 0.26566786648658042])
except:
print("WARNING: failed to restore connection between PrepareReceptorOpalService_ws_nbcr_net_14 and GetURLFromList_15 in network PrepareReceptorWS_10.macroNetwork")
if GetURLFromList_15 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
GetURLFromList_15, DownloadToFile_16, "url", "url", blocking=True
, splitratio=[0.70502483723033316, 0.71683158018466053])
except:
print("WARNING: failed to restore connection between GetURLFromList_15 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and DownloadToFile_16 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, DownloadToFile_16, "download_loc", "filename", blocking=True
, splitratio=[0.60455581032885575, 0.35606890231085681])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork")
if CheckFileFormat_13 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
CheckFileFormat_13, UpdateReceptor_17, "receptor_obj", "receptor_obj", blocking=True
, splitratio=[0.74908230670336207, 0.38226563370205602])
except:
print("WARNING: failed to restore connection between CheckFileFormat_13 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork")
if DownloadToFile_16 is not None and UpdateReceptor_17 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
DownloadToFile_16, UpdateReceptor_17, "filename", "pdbqt", blocking=True
, splitratio=[0.38698393490575966, 0.2874426709930199])
except:
print("WARNING: failed to restore connection between DownloadToFile_16 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork")
output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_prepared_obj", "new", blocking=True
, splitratio=[0.69589857263374943, 0.59566078506240416])
except:
print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork")
if UpdateReceptor_17 is not None and output_Ports_12 is not None:
try:
PrepareReceptorWS_10.macroNetwork.connectNodes(
UpdateReceptor_17, output_Ports_12, "receptor_result", "new", blocking=True
, splitratio=[0.44926362052272689, 0.38628711158860896])
except:
print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork")
PrepareReceptorWS_10.macroNetwork.unfreeze()
## modifying MacroInputNode dynamic ports
input_Ports_11.outputPorts[1].configure(name='CheckFileFormat_value')
input_Ports_11.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_12.inputPorts[1].configure(singleConnection='auto')
output_Ports_12.inputPorts[2].configure(singleConnection='auto')
output_Ports_12.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj')
output_Ports_12.inputPorts[2].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.inputPorts[0].configure(name='CheckFileFormat_value')
PrepareReceptorWS_10.inputPorts[0].configure(datatype='receptor')
PrepareReceptorWS_10.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptorWS_10.inputPorts[1].configure(datatype='boolean')
## configure MacroNode input ports
PrepareReceptorWS_10.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj')
PrepareReceptorWS_10.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptorWS_10.outputPorts[1].configure(name='UpdateReceptor_receptor_result')
PrepareReceptorWS_10.outputPorts[1].configure(datatype='string')
## configure MacroNode output ports
PrepareReceptorWS_10.shrink()
PrepareReceptorWS_10.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False})
except:
print("WARNING: failed to restore MacroNode named PrepareReceptorWS in network self.macroNetwork")
print_exc()
PrepareReceptorWS_10=None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network PrepareReceptor ##
input_Ports_1 = self.macroNetwork.ipNode
Pdb2pqrWS_3 = self.macroNetwork.nodes[2]
if input_Ports_1 is not None and Pdb2pqrWS_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Pdb2pqrWS_3, "new", "CheckFileFormat_value", blocking=True
, splitratio=[0.73531020066010289, 0.24042404972613104])
except:
print("WARNING: failed to restore connection between input_Ports_1 and Pdb2pqrWS_3 in network self.macroNetwork")
PrepareReceptorWS_10 = self.macroNetwork.nodes[3]
if Pdb2pqrWS_3 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
Pdb2pqrWS_3, PrepareReceptorWS_10, "UpdateReceptor_receptor_obj", "CheckFileFormat_value", blocking=True
, splitratio=[0.54479169827535734, 0.4847384502006486])
except:
print("WARNING: failed to restore connection between Pdb2pqrWS_3 and PrepareReceptorWS_10 in network self.macroNetwork")
if input_Ports_1 is not None and PrepareReceptorWS_10 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, PrepareReceptorWS_10, "new", "PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True
, splitratio=[0.37730151685222141, 0.48897820190498614])
except:
print("WARNING: failed to restore connection between input_Ports_1 and PrepareReceptorWS_10 in network self.macroNetwork")
output_Ports_2 = self.macroNetwork.opNode
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_prepared_obj", "new", blocking=True
, splitratio=[0.64110508898616414, 0.45535290355389196])
except:
print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork")
if PrepareReceptorWS_10 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_result", "new", blocking=True
, splitratio=[0.45846842546122241, 0.44240009354017412])
except:
print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork")
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value')
input_Ports_1.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
output_Ports_2.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
## configure MacroNode input ports
PrepareReceptor_0.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value')
PrepareReceptor_0.inputPorts[0].configure(datatype='receptor')
PrepareReceptor_0.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C')
PrepareReceptor_0.inputPorts[1].configure(datatype='boolean')
## configure MacroNode output ports
PrepareReceptor_0.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj')
PrepareReceptor_0.outputPorts[0].configure(datatype='receptor_prepared')
PrepareReceptor_0.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result')
PrepareReceptor_0.outputPorts[1].configure(datatype='string')
PrepareReceptor_0.shrink()
## reset modifications ##
PrepareReceptor_0.resetTags()
PrepareReceptor_0.buildOriginalList()
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'
})
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVsCSF_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory(
"http://oolitevm.calit2.optiputer.net/opal2", replace=False)
except:
pass
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
apply(input_Ports_1.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
apply(output_Ports_2.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(183, 363)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2 = None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_3 = Generic(constrkw={},
name='PrepareADVSInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_3, 217, 76)
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'autogrid_results',
'cast': True,
'datatype': 'autogrid_results',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addInputPort, (), {
'singleConnection': True,
'name': 'dpf_template_obj',
'cast': True,
'datatype': 'dpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#9933FF',
'originalDatatype': 'None'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'dpf_template_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'autogrid_res_url',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(
PrepareADVSInputs_3.addOutputPort, (), {
'name': 'autogrid_res_local',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_3.configure(function=code)
apply(PrepareADVSInputs_3.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
print_exc()
PrepareADVSInputs_3 = None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_4 = FunctionNode(
functionOrString='autodock_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autodock_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
}
},
name='autodock_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_4, 217, 132)
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_run'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.
inputPortByName['filter_file_url'].configure, (),
{'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_num_evals'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['filter_file'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['urllib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.
inputPortByName['ga_num_generations'].configure, (),
{'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].configure,
(), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['userlib'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['ga_pop_size'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['localRun'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['email'].
configure, (), {'defaultValue': None})
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['execPath'].
configure, (), {'defaultValue': None})
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_run'].widget.set(r"", run=False)
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.
configure, (), {
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
autodock_kryptonite_nbcr_net_4.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'filter_file'].unbindWidget()
apply(
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.
configure, (), {'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_4.inputPortByName['sched'].widget.set(
r"CSF", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'urllib'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].rebindWidget(
)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['dpf'].unbindWidget(
)
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['u'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'utar'].rebindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName['utar'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'utar'].unbindWidget()
autodock_kryptonite_nbcr_net_4.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName['email'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_4.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(autodock_kryptonite_nbcr_net_4.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
print_exc()
autodock_kryptonite_nbcr_net_4 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_5 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_5, 217, 188)
apply(GetMainURLFromList_5.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_5.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_5 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_7 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_7, 201, 301)
apply(GetMainURLFromList_7.inputPortByName['urls'].configure, (),
{'defaultValue': None})
apply(GetMainURLFromList_7.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
print_exc()
GetMainURLFromList_7 = None
try:
## saving node AutodockSlice_oolitevm_calit2_optiputer_net ##
from NetworkEditor.items import FunctionNode
AutodockSlice_oolitevm_calit2_optiputer_net_8 = FunctionNode(
functionOrString='AutodockSlice_oolitevm_calit2_optiputer_net',
host="http://oolitevm.calit2.optiputer.net/opal2",
namedArgs={
'execPath': '',
'localRun': False,
'divisor': '',
'lib': '',
'input_url': ''
},
constrkw={
'functionOrString':
"'AutodockSlice_oolitevm_calit2_optiputer_net'",
'host': '"http://oolitevm.calit2.optiputer.net/opal2"',
'namedArgs': {
'execPath': '',
'localRun': False,
'divisor': '',
'lib': '',
'input_url': ''
}
},
name='AutodockSlice_oolitevm_calit2_optiputer_net',
library=wslib)
self.macroNetwork.addNode(
AutodockSlice_oolitevm_calit2_optiputer_net_8, 200, 240)
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['execPath'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['localRun'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['divisor'].configure, (),
{'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['lib'].configure, (), {'defaultValue': None})
apply(
AutodockSlice_oolitevm_calit2_optiputer_net_8.
inputPortByName['input_url'].configure, (),
{'defaultValue': None})
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'localRun'].widget.set(0, run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'divisor'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'lib'].unbindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].rebindWidget()
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].widget.set(r"", run=False)
AutodockSlice_oolitevm_calit2_optiputer_net_8.inputPortByName[
'input_url'].unbindWidget()
apply(AutodockSlice_oolitevm_calit2_optiputer_net_8.configure, (),
{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print "WARNING: failed to restore FunctionNode named AutodockSlice_oolitevm_calit2_optiputer_net in network self.macroNetwork"
print_exc()
AutodockSlice_oolitevm_calit2_optiputer_net_8 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVsCSF ##
if autodock_kryptonite_nbcr_net_4 is not None and GetMainURLFromList_5 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_4,
GetMainURLFromList_5,
"result",
"urls",
blocking=True,
splitratio=[0.36974288957131424, 0.63465596053596318])
except:
print "WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_4 and GetMainURLFromList_5 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.33230642287344903, 0.65770700108889613])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.50680104599665787, 0.51414170500293577])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"dpf_template_file",
"dpf",
blocking=True,
splitratio=[0.51615646597598808, 0.25661305528484007])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"autogrid_res_url",
"u",
blocking=True,
splitratio=[0.5760732944947704, 0.2032376887917188])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and autodock_kryptonite_nbcr_net_4 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
autodock_kryptonite_nbcr_net_4,
"autogrid_res_local",
"utar",
blocking=True,
splitratio=[0.52802808938949819, 0.66978534572736881])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and autodock_kryptonite_nbcr_net_4 in network self.macroNetwork"
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"ligands",
blocking=True,
splitratio=[0.23314258225660414, 0.72184112037432979])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"autogrid_results",
blocking=True,
splitratio=[0.56916626620432731, 0.43089669830392019])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
if input_Ports_1 is not None and PrepareADVSInputs_3 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
PrepareADVSInputs_3,
"new",
"dpf_template_obj",
blocking=True,
splitratio=[0.26502286453989665, 0.3911248444502638])
except:
print "WARNING: failed to restore connection between input_Ports_1 and PrepareADVSInputs_3 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if GetMainURLFromList_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_7,
output_Ports_2,
"newurl",
"new",
blocking=True,
splitratio=[0.2408747073082603, 0.22897876889044461])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_7 and output_Ports_2 in network self.macroNetwork"
if PrepareADVSInputs_3 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_3,
AutodockSlice_oolitevm_calit2_optiputer_net_8,
"ligand_lib",
"lib",
blocking=True,
splitratio=[0.36439875698533941, 0.58443612376117082])
except:
print "WARNING: failed to restore connection between PrepareADVSInputs_3 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if GetMainURLFromList_5 is not None and AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_5,
AutodockSlice_oolitevm_calit2_optiputer_net_8,
"newurl",
"input_url",
blocking=True,
splitratio=[0.32808833199778697, 0.69237553555389719])
except:
print "WARNING: failed to restore connection between GetMainURLFromList_5 and AutodockSlice_oolitevm_calit2_optiputer_net_8 in network self.macroNetwork"
if AutodockSlice_oolitevm_calit2_optiputer_net_8 is not None and GetMainURLFromList_7 is not None:
try:
self.macroNetwork.connectNodes(
AutodockSlice_oolitevm_calit2_optiputer_net_8,
GetMainURLFromList_7,
"result",
"urls",
blocking=True,
splitratio=[0.69930142895840763, 0.2984777644803871])
except:
print "WARNING: failed to restore connection between AutodockSlice_oolitevm_calit2_optiputer_net_8 and GetMainURLFromList_7 in network self.macroNetwork"
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_1.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_1.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
AutodockVsCSF_0.inputPorts[0].configure(
name='PrepareADVSInputs_ligands')
AutodockVsCSF_0.inputPorts[0].configure(datatype='LigandDB')
AutodockVsCSF_0.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVsCSF_0.inputPorts[1].configure(datatype='autogrid_results')
AutodockVsCSF_0.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVsCSF_0.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode output ports
AutodockVsCSF_0.outputPorts[0].configure(
name='GetMainURLFromList_newurl')
AutodockVsCSF_0.outputPorts[0].configure(datatype='string')
AutodockVsCSF_0.shrink()
## reset modifications ##
AutodockVsCSF_0.resetTags()
AutodockVsCSF_0.buildOriginalList()
AutodockVina_Screening_kryptonite_nbcr_net_24.inputPortByName[
'ligand_db'].widget.set(r"", run=False)
apply(
AutodockVina_Screening_kryptonite_nbcr_net_24.inputPortByName['cpu'].
widget.configure, (), {'choices': ('1', '2')})
AutodockVina_Screening_kryptonite_nbcr_net_24.inputPortByName[
'cpu'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_24.inputPortByName[
'execPath'].widget.set(r"", run=False)
apply(AutodockVina_Screening_kryptonite_nbcr_net_24.configure, (), {
'paramPanelImmediate': 1,
'expanded': False
})
from Vision.StandardNodes import Generic
PrepareVinaInputs_25 = Generic(constrkw={},
name='PrepareVinaInputs',
library=stdlib)
Vina_21.macroNetwork.addNode(PrepareVinaInputs_25, 140, 107)
apply(
PrepareVinaInputs_25.addInputPort, (), {
'singleConnection': True,
'name': 'receptor_obj',
'cast': True,
'datatype': 'receptor_prepared',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#009900',
'originalDatatype': 'None'
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
from DejaVu.VisionInterface.DejaVuNodes import vizlib
from Vision.StandardNodes import stdlib
## building macro network ##
WebMSMS = self
from traceback import print_exc
## loading libraries ##
from MolKit.VisionInterface.MolKitNodes import molkitlib
self.macroNetwork.getEditor().addLibraryInstance(
molkitlib, "MolKit.VisionInterface.MolKitNodes", "molkitlib")
from DejaVu.VisionInterface.DejaVuNodes import vizlib
self.macroNetwork.getEditor().addLibraryInstance(
vizlib, "DejaVu.VisionInterface.DejaVuNodes", "vizlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(
stdlib, "Vision.StandardNodes", "stdlib")
try:
## saving node input Ports ##
input_Ports = self.macroNetwork.ipNode
input_Ports.move(13, 4)
except:
print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
print_exc()
input_Ports = None
try:
## saving node output Ports ##
output_Ports = self.macroNetwork.opNode
output_Ports.move(256, 220)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports = None
try:
## saving node Assign Radii ##
from MolKit.VisionInterface.MolKitNodes import AssignRadii
Assign_Radii = AssignRadii(constrkw={},
name='Assign Radii',
library=molkitlib)
self.macroNetwork.addNode(Assign_Radii, 30, 68)
apply(
Assign_Radii.getInputPortByName('molecules').configure, (), {
'color': '#c64e70',
'cast': True,
'shape': 'oval'
})
apply(
Assign_Radii.getInputPortByName('united').configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(
Assign_Radii.getOutputPortByName('molecules').configure, (), {
'color': '#c64e70',
'shape': 'oval'
})
apply(
Assign_Radii.getOutputPortByName('radii').configure, (), {
'color': 'cyan',
'shape': 'oval'
})
except:
print "WARNING: failed to restore AssignRadii named Assign Radii in network self.macroNetwork"
print_exc()
Assign_Radii = None
try:
## saving node Select Nodes ##
from MolKit.VisionInterface.MolKitNodes import NodeSelector
Select_Nodes = NodeSelector(constrkw={},
name='Select Nodes',
library=molkitlib)
self.macroNetwork.addNode(Select_Nodes, 29, 135)
apply(
Select_Nodes.getInputPortByName('nodes').configure, (), {
'color': '#c64e70',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getInputPortByName('nodeType').configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getInputPortByName('selectionString').configure,
(), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
Select_Nodes.getOutputPortByName('nodes').configure, (), {
'color': '#fe92a0',
'shape': 'oval'
})
Select_Nodes.getInputPortByName("selectionString").widget.set(".*")
except:
print "WARNING: failed to restore NodeSelector named Select Nodes in network self.macroNetwork"
print_exc()
Select_Nodes = None
try:
## saving node Get xyzr ##
from Vision.StandardNodes import Generic
Get_xyzr = Generic(constrkw={}, name='Get xyzr', library=stdlib)
self.macroNetwork.addNode(Get_xyzr, 30, 194)
apply(
Get_xyzr.addInputPort, (), {
'name': 'atoms',
'cast': True,
'datatype': 'AtomSet',
'height': 8,
'width': 12,
'shape': 'oval',
'color': '#fe92a0'
})
apply(
Get_xyzr.addOutputPort, (), {
'name': 'output',
'datatype': 'string',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, atoms):
lines = ''
for atom in atoms:
lines += str(atom.coords[0]) + ' ' + str(atom.coords[1]) + ' ' + str(atom.coords[2]) + ' '+ str(atom.radius)
lines += "\\n"
self.outputData(output=lines)
"""
Get_xyzr.configure(function=code)
except:
print "WARNING: failed to restore Generic named Get xyzr in network self.macroNetwork"
print_exc()
Get_xyzr = None
try:
## saving node IndexedPolygons ##
from DejaVu.VisionInterface.GeometryNode import IndexedPolygonsNE
IndexedPolygons = IndexedPolygonsNE(constrkw={},
name='IndexedPolygons',
library=vizlib)
self.macroNetwork.addNode(IndexedPolygons, 273, 147)
apply(
IndexedPolygons.getInputPortByName('coords').configure, (), {
'color': 'purple',
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('indices').configure, (), {
'color': 'yellow',
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('vnormals').configure, (), {
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('colors').configure, (), {
'cast': True,
'shape': 'circle'
})
apply(
IndexedPolygons.getInputPortByName('name').configure, (), {
'color': 'white',
'cast': True,
'shape': 'oval'
})
apply(
IndexedPolygons.getInputPortByName(
'instanceMatrices').configure, (), {'cast': True})
apply(
IndexedPolygons.getInputPortByName('geomOptions').configure,
(), {
'color': 'cyan',
'cast': True,
'shape': 'oval'
})
apply(
IndexedPolygons.getInputPortByName('parent').configure, (), {
'color': 'red',
'cast': True,
'shape': 'rect'
})
apply(
IndexedPolygons.getOutputPortByName(
'indexedPolygons').configure, (), {
'color': 'red',
'shape': 'rect'
})
apply(
IndexedPolygons.getOutputPortByName('allGeometries').configure,
(), {
'color': 'red',
'shape': 'rect'
})
except:
print "WARNING: failed to restore IndexedPolygonsNE named IndexedPolygons in network self.macroNetwork"
print_exc()
IndexedPolygons = None
try:
## saving node MSMS WS ##
from Vision.StandardNodes import Generic
MSMS_WS = Generic(constrkw={}, name='MSMS WS', library=stdlib)
self.macroNetwork.addNode(MSMS_WS, 273, 37)
apply(
MSMS_WS.addInputPort, (), {
'name': 'input_str',
'cast': True,
'datatype': 'string',
'height': 12,
'width': 12,
'shape': 'oval',
'color': 'white'
})
apply(MSMS_WS.addInputPort, (), {
'name': 'density',
'datatype': 'float',
'required': False
})
apply(
MSMS_WS.getInputPortByName('density').createWidget, (), {
'descr': {
'initialValue': 1.0,
'increment': 0.1,
'type': 'float',
'master': 'ParamPanel',
'oneTurn': 10,
'min': 1.0,
'labelCfg': {
'text': 'density'
},
'class': 'NEDial'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'probe_radius',
'datatype': 'float',
'required': False
})
apply(
MSMS_WS.getInputPortByName('probe_radius').createWidget, (), {
'descr': {
'initialValue': 1.5,
'increment': 0.1,
'type': 'float',
'master': 'ParamPanel',
'oneTurn': 10,
'min': 0.5,
'labelCfg': {
'text': 'probe radius'
},
'class': 'NEDial'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'allComp',
'datatype': 'int',
'required': False
})
apply(
MSMS_WS.getInputPortByName('allComp').createWidget, (), {
'descr': {
'initialValue': 0,
'master': 'ParamPanel',
'labelCfg': {
'text': 'all components'
},
'class': 'NECheckButton'
}
})
apply(MSMS_WS.addInputPort, (), {
'name': 'getfile',
'datatype': 'boolean'
})
apply(
MSMS_WS.getInputPortByName('getfile').createWidget, (), {
'descr': {
'master': 'ParamPanel',
'labelCfg': {
'text': 'upload output'
},
'class': 'NECheckButton',
'initialValue': True
}
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'vertices',
'datatype': 'coordinates3D',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'green'
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'indices',
'datatype': 'faceIndices',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'purple'
})
apply(
MSMS_WS.addOutputPort, (), {
'name': 'vnormals',
'datatype': 'normals3D',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'blue'
})
MSMS_WS.host = self.host
MSMS_WS.opal_service = self.opal_service
code = """def doit(self, input_str, probe_radius, density, allComp, getfile):
self.opal_service.inputFile.Set_name('msms.xyzr')
self.opal_service.inputFile.Set_contents(input_str)
options = '-if msms.xyzr -of ws_out '
options += '-probe_radius ' + str(probe_radius)
options += ' -density ' + str(density)
if allComp:
options += ' -all_components'
self.opal_service.req._argList = options
inputFiles = []
inputFiles.append(self.opal_service.inputFile)
self.opal_service.req._inputFile = inputFiles
resp = self.opal_service.run('msmsServicePort')
if resp:
for files in resp._outputFile:
if files._url.split('/')[-1] == 'ws_out.face':
face_file = files._url
if files._url.split('/')[-1] == 'ws_out.vert':
vert_file = files._url
if getfile:
from Pmv.msmsParser import MSMSParser
msmsParser = MSMSParser()
import urllib
opener = urllib.FancyURLopener({})
in_file = opener.open(face_file)
msmsParser.getFaces(in_file.readlines())
in_file = opener.open(vert_file)
msmsParser.getVert(in_file.readlines())
self.outputData(vertices = msmsParser.vertices, indices = msmsParser.faces,
vnormals = msmsParser.normals)
else:
self.outputData(vertices = vert_file, indices = face_file,
vnormals = None)
"""
MSMS_WS.configure(function=code)
except:
print "WARNING: failed to restore Generic named MSMS WS in network self.macroNetwork"
print_exc()
MSMS_WS = None
self.macroNetwork.freeze()
## saving connections for network WebMSMS ##
if Assign_Radii is not None and Select_Nodes is not None:
self.macroNetwork.connectNodes(Assign_Radii,
Select_Nodes,
"molecules",
"nodes",
blocking=True)
if Select_Nodes is not None and Get_xyzr is not None:
self.macroNetwork.connectNodes(Select_Nodes,
Get_xyzr,
"nodes",
"atoms",
blocking=True)
if Get_xyzr is not None and MSMS_WS is not None:
self.macroNetwork.connectNodes(Get_xyzr,
MSMS_WS,
"output",
"input_str",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"vertices",
"coords",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"indices",
"indices",
blocking=True)
if MSMS_WS is not None and IndexedPolygons is not None:
self.macroNetwork.connectNodes(MSMS_WS,
IndexedPolygons,
"vnormals",
"vnormals",
blocking=True)
output_Ports = self.macroNetwork.opNode
if IndexedPolygons is not None and output_Ports is not None:
self.macroNetwork.connectNodes(IndexedPolygons,
output_Ports,
"indexedPolygons",
"new",
blocking=True)
input_Ports = self.macroNetwork.ipNode
if input_Ports is not None and Assign_Radii is not None:
self.macroNetwork.connectNodes(input_Ports,
Assign_Radii,
"new",
"molecules",
blocking=True)
self.macroNetwork.unfreeze()
WebMSMS.shrink()
## reset modifications ##
WebMSMS.resetTags()
WebMSMS.buildOriginalList()
from Vision.StandardNodes import CheckButtonNE
Preserve_charges__19 = CheckButtonNE(constrkw={},
name='Preserve charges?',
library=stdlib)
masterNet.addNode(Preserve_charges__19, 458, 43)
Preserve_charges__19.inputPortByName['button'].widget.set(0, run=False)
apply(Preserve_charges__19.configure, (), {'paramPanelImmediate': 1})
except:
print "WARNING: failed to restore CheckButtonNE named Preserve charges? in network masterNet"
print_exc()
Preserve_charges__19 = None
try:
## saving node SaveReceptor ##
from Vision.StandardNodes import Generic
SaveReceptor_20 = Generic(constrkw={}, name='SaveReceptor', library=stdlib)
masterNet.addNode(SaveReceptor_20, 424, 278)
apply(
SaveReceptor_20.addInputPort, (), {
'singleConnection': True,
'name': 'r',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
## building macro network ##
Vina_30 = self
from traceback import print_exc
from Vision.StandardNodes import stdlib
from WebServices.VisionInterface.WSNodes import wslib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_31 = self.macroNetwork.ipNode
input_Ports_31.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_31 = None
try:
## saving node output Ports ##
output_Ports_32 = self.macroNetwork.opNode
output_Ports_32.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_32 = None
try:
## saving node AutodockVina_Screening_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
AutodockVina_Screening_kryptonite_nbcr_net_33 = FunctionNode(
functionOrString='AutodockVina_Screening_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'num_modes': '',
'energy_range': '',
'seed': '',
'receptor': '',
'size_y': '',
'size_z': '',
'out': '',
'log': '',
'urllib': '',
'exhaustiveness': '',
'localRun': False,
'flex': '',
'center_z': '',
'center_x': '',
'center_y': '',
'userlib': '',
'size_x': '',
'config': '',
'filter': '',
'ligand_db': '',
'cpu': '',
'execPath': ''
},
constrkw={
'functionOrString':
"'AutodockVina_Screening_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'num_modes': '',
'energy_range': '',
'seed': '',
'receptor': '',
'size_y': '',
'size_z': '',
'out': '',
'log': '',
'urllib': '',
'exhaustiveness': '',
'localRun': False,
'flex': '',
'center_z': '',
'center_x': '',
'center_y': '',
'userlib': '',
'size_x': '',
'config': '',
'filter': '',
'ligand_db': '',
'cpu': '',
'execPath': ''
}
},
name='AutodockVina_Screening_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(
AutodockVina_Screening_kryptonite_nbcr_net_33, 217, 185)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'seed'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_y'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_z'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'out'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'log'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'flex'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_z'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_x'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_y'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_x'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].configure(*(), **{
'defaultValue': None,
'required': True
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].widget.configure(
*(), **{
'choices':
('1', '2', '3', '4', '5', '6', '7', '8', '9', '10')
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'num_modes'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].widget.configure(
*(), **{'choices': ('1', '2', '3')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'energy_range'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'seed'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'receptor'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'out'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'log'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'urllib'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].widget.configure(
*(),
**{'choices': ('1', '2', '3', '4', '5', '6', '7', '8')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'exhaustiveness'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'localRun'].widget.set(0, run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'flex'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_z'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'center_y'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'userlib'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'size_x'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'config'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].rebindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'filter'].unbindWidget()
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].widget.configure(
*(), **{
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'asinex', 'fda_approved', 'otava',
'zinc_natural_products')
})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'ligand_db'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].widget.configure(*(), **{'choices': ('1', '2')})
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'cpu'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.inputPortByName[
'execPath'].widget.set(r"", run=False)
AutodockVina_Screening_kryptonite_nbcr_net_33.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named AutodockVina_Screening_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
AutodockVina_Screening_kryptonite_nbcr_net_33 = None
try:
## saving node PrepareVinaInputs ##
from Vision.StandardNodes import Generic
PrepareVinaInputs_34 = Generic(constrkw={},
name='PrepareVinaInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareVinaInputs_34, 140, 107)
PrepareVinaInputs_34.addInputPort(
*(), **{
'singleConnection': True,
'name': 'receptor_obj',
'cast': True,
'datatype': 'receptor_prepared',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#009900',
'originalDatatype': 'None'
})
PrepareVinaInputs_34.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligand_obj',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'receptor_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareVinaInputs_34.addOutputPort(
*(), **{
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, receptor_obj, ligand_obj):
receptor_file = receptor_obj.path
filter_file = ligand_obj.filter_file
ligand_lib = ligand_obj.loc
if receptor_obj.type == "local":
if not(os.path.exists(receptor_file)):
print "ERROR: receptor_file " + receptor_file + " does not exist"
return '''stop'''
pass
self.outputData(receptor_file=receptor_file, ligand_lib=ligand_lib, filter_file=filter_file)
## to ouput data on port receptor_file use
## self.outputData(receptor_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
"""
PrepareVinaInputs_34.configure(function=code)
PrepareVinaInputs_34.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named PrepareVinaInputs in network self.macroNetwork"
)
print_exc()
PrepareVinaInputs_34 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_35 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_35, 217, 248)
GetMainURLFromList_35.inputPortByName['urls'].configure(
*(), **{'defaultValue': None})
GetMainURLFromList_35.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
)
print_exc()
GetMainURLFromList_35 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network Vina ##
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"receptor_file",
"receptor",
blocking=True,
splitratio=[0.48630431331124768, 0.72717758735716731])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.61963739449043087, 0.74955133389937689])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if PrepareVinaInputs_34 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
PrepareVinaInputs_34,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"filter_file",
"filter",
blocking=True,
splitratio=[0.32670226336274166, 0.25123642944789149])
except:
print(
"WARNING: failed to restore connection between PrepareVinaInputs_34 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
if AutodockVina_Screening_kryptonite_nbcr_net_33 is not None and GetMainURLFromList_35 is not None:
try:
self.macroNetwork.connectNodes(
AutodockVina_Screening_kryptonite_nbcr_net_33,
GetMainURLFromList_35,
"result",
"urls",
blocking=True,
splitratio=[0.23401196873379349, 0.68593608346615742])
except:
print(
"WARNING: failed to restore connection between AutodockVina_Screening_kryptonite_nbcr_net_33 and GetMainURLFromList_35 in network self.macroNetwork"
)
output_Ports_32 = self.macroNetwork.opNode
if GetMainURLFromList_35 is not None and output_Ports_32 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_35,
output_Ports_32,
"newurl",
"new",
blocking=True,
splitratio=[0.26588001265563421, 0.34355863787969732])
except:
print(
"WARNING: failed to restore connection between GetMainURLFromList_35 and output_Ports_32 in network self.macroNetwork"
)
input_Ports_31 = self.macroNetwork.ipNode
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
PrepareVinaInputs_34,
"new",
"receptor_obj",
blocking=True,
splitratio=[0.59193136382656331, 0.41134942510734418])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
)
if input_Ports_31 is not None and PrepareVinaInputs_34 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
PrepareVinaInputs_34,
"new",
"ligand_obj",
blocking=True,
splitratio=[0.29092159940560591, 0.60619808825531374])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and PrepareVinaInputs_34 in network self.macroNetwork"
)
if input_Ports_31 is not None and AutodockVina_Screening_kryptonite_nbcr_net_33 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_31,
AutodockVina_Screening_kryptonite_nbcr_net_33,
"new",
"config",
blocking=True,
splitratio=[0.24239548372031838, 0.55842775396640953])
except:
print(
"WARNING: failed to restore connection between input_Ports_31 and AutodockVina_Screening_kryptonite_nbcr_net_33 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = True
## modifying MacroInputNode dynamic ports
input_Ports_31 = self.macroNetwork.ipNode
input_Ports_31.outputPorts[1].configure(
name='PrepareVinaInputs_receptor_obj')
input_Ports_31.outputPorts[2].configure(
name='PrepareVinaInputs_ligand_obj')
input_Ports_31.outputPorts[3].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
## modifying MacroOutputNode dynamic ports
output_Ports_32 = self.macroNetwork.opNode
output_Ports_32.inputPorts[1].configure(singleConnection='auto')
output_Ports_32.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
Vina_30.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj')
Vina_30.inputPorts[0].configure(datatype='receptor_prepared')
Vina_30.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj')
Vina_30.inputPorts[1].configure(datatype='LigandDB')
Vina_30.inputPorts[2].configure(
name='AutodockVina_Screening_kryptonite_nbcr_net_config')
Vina_30.inputPorts[2].configure(datatype='string')
## configure MacroNode output ports
Vina_30.outputPorts[0].configure(name='GetMainURLFromList_newurl')
Vina_30.outputPorts[0].configure(datatype='string')
Vina_30.shrink()
## reset modifications ##
Vina_30.resetTags()
Vina_30.buildOriginalList()
def afterAddingToNetwork(self):
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
## loading libraries ##
from symserv.VisionInterface.SymservNodes import symlib
from Vision.StandardNodes import stdlib
from DejaVu.VisionInterface.DejaVuNodes import vizlib
## building macro network ##
RotateScene_0 = self
from traceback import print_exc
## loading libraries ##
from symserv.VisionInterface.SymservNodes import symlib
self.macroNetwork.getEditor().addLibraryInstance(symlib,"symserv.VisionInterface.SymservNodes", "symlib")
from Vision.StandardNodes import stdlib
self.macroNetwork.getEditor().addLibraryInstance(stdlib,"Vision.StandardNodes", "stdlib")
from DejaVu.VisionInterface.DejaVuNodes import vizlib
self.macroNetwork.getEditor().addLibraryInstance(vizlib,"DejaVu.VisionInterface.DejaVuNodes", "vizlib")
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.move(45, 17)
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.move(228, 460)
except:
print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
print_exc()
output_Ports_2=None
try:
## saving node Rotate ##
from symserv.VisionInterface.SymservNodes import SymRotNE
Rotate_3 = SymRotNE(constrkw = {}, name='Rotate', library=symlib)
self.macroNetwork.addNode(Rotate_3,543,101)
apply(Rotate_3.inputPortByName['matrices'].configure, (), {'color': 'cyan', 'cast': True, 'shape': 'rect'})
apply(Rotate_3.inputPortByName['vector'].configure, (), {'datatype': 'list', 'cast': True, 'shape': 'oval', 'color': 'cyan', 'height': 8})
apply(Rotate_3.inputPortByName['point'].configure, (), {'color': 'white', 'cast': True, 'shape': 'diamond'})
apply(Rotate_3.inputPortByName['angle'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'})
apply(Rotate_3.inputPortByName['identity'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(Rotate_3.outputPortByName['outMatrices'].configure, (), {'color': 'cyan', 'shape': 'rect'})
Rotate_3.inputPortByName['vector'].unbindWidget()
Rotate_3.inputPortByName['angle'].widget.set(0.0, run=False)
Rotate_3.inputPortByName['angle'].unbindWidget()
except:
print "WARNING: failed to restore SymRotNE named Rotate in network self.macroNetwork"
print_exc()
Rotate_3=None
try:
## saving node One Redraw ##
from DejaVu.VisionInterface.DejaVuNodes import OneRedraw
One_Redraw_4 = OneRedraw(constrkw = {}, name='One Redraw', library=vizlib)
self.macroNetwork.addNode(One_Redraw_4,22,452)
apply(One_Redraw_4.inputPortByName['viewer'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'rect'})
apply(One_Redraw_4.inputPortByName['trigger'].configure, (), {'color': 'white', 'cast': True, 'shape': 'diamond'})
except:
print "WARNING: failed to restore OneRedraw named One Redraw in network self.macroNetwork"
print_exc()
One_Redraw_4=None
try:
## saving node Choose Geom ##
from DejaVu.VisionInterface.DejaVuNodes import SelectGeometry
Choose_Geom_5 = SelectGeometry(constrkw = {}, name='Choose Geom', library=vizlib)
self.macroNetwork.addNode(Choose_Geom_5,412,220)
apply(Choose_Geom_5.inputPortByName['viewer'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'rect'})
apply(Choose_Geom_5.inputPortByName['geomName'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(Choose_Geom_5.outputPortByName['geometry'].configure, (), {'color': 'red', 'shape': 'rect'})
apply(Choose_Geom_5.inputPortByName['geomName'].widget.configure, (), {'autoList': False, 'choices': ('root',)})
Choose_Geom_5.inputPortByName['geomName'].widget.set("root", run=False)
except:
print "WARNING: failed to restore SelectGeometry named Choose Geom in network self.macroNetwork"
print_exc()
Choose_Geom_5=None
try:
## saving node range ##
from Vision.StandardNodes import Range
range_6 = Range(constrkw = {}, name='range', library=stdlib)
self.macroNetwork.addNode(range_6,246,147)
apply(range_6.inputPortByName['fromInd'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(range_6.inputPortByName['toInd'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(range_6.inputPortByName['step'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'circle'})
apply(range_6.outputPortByName['data'].configure, (), {'color': 'cyan', 'shape': 'oval'})
range_6.inputPortByName['toInd'].unbindWidget()
except:
print "WARNING: failed to restore Range named range in network self.macroNetwork"
print_exc()
range_6=None
try:
## saving node iterate ##
from Vision.StandardNodes import Iterate
iterate_7 = Iterate(constrkw = {}, name='iterate', library=stdlib)
self.macroNetwork.addNode(iterate_7,283,204)
apply(iterate_7.inputPortByName['listToLoopOver'].configure, (), {'color': 'cyan', 'cast': True, 'shape': 'oval'})
apply(iterate_7.outputPortByName['oneItem'].configure, (), {'color': 'white', 'shape': 'diamond'})
apply(iterate_7.outputPortByName['iter'].configure, (), {'color': 'yellow', 'shape': 'circle'})
apply(iterate_7.outputPortByName['begin'].configure, (), {'color': 'yellow', 'shape': 'rect'})
apply(iterate_7.outputPortByName['end'].configure, (), {'color': 'yellow', 'shape': 'rect'})
apply(iterate_7.outputPortByName['maxIter'].configure, (), {'color': 'yellow', 'shape': 'circle'})
except:
print "WARNING: failed to restore Iterate named iterate in network self.macroNetwork"
print_exc()
iterate_7=None
try:
## saving node flattenRotation ##
from Vision.StandardNodes import Generic
flattenRotation_8 = Generic(constrkw = {}, name='flattenRotation', library=stdlib)
self.macroNetwork.addNode(flattenRotation_8,560,200)
apply(flattenRotation_8.addInputPort, (), {'name': 'in0', 'cast': True, 'datatype': 'instancemat(0)', 'height': 8, 'width': 12, 'shape': 'rect', 'color': 'cyan'})
apply(flattenRotation_8.addOutputPort, (), {'name': 'out0', 'datatype': 'float(16)', 'height': 10, 'width': 10, 'shape': 'rect', 'color': 'white'})
code = """def doit(self, in0):
self.outputData(out0=in0[0].ravel())
"""
flattenRotation_8.configure(function=code)
except:
print "WARNING: failed to restore Generic named flattenRotation in network self.macroNetwork"
print_exc()
flattenRotation_8=None
try:
## saving node Pass ##
from Vision.StandardNodes import Pass
Pass_9 = Pass(constrkw = {}, name='Pass', library=stdlib)
self.macroNetwork.addNode(Pass_9,333,339)
apply(Pass_9.inputPortByName['in1'].configure, (), {'color': 'white', 'cast': True, 'shape': 'diamond'})
apply(Pass_9.outputPortByName['out1'].configure, (), {'color': 'white', 'shape': 'diamond'})
apply(Pass_9.configure, (), {'specialPortsVisible': True})
except:
print "WARNING: failed to restore Pass named Pass in network self.macroNetwork"
print_exc()
Pass_9=None
try:
## saving node angle ##
from Vision.StandardNodes import DialNE
angle_10 = DialNE(constrkw = {}, name='angle', library=stdlib)
self.macroNetwork.addNode(angle_10,244,5)
apply(angle_10.inputPortByName['dial'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'})
apply(angle_10.inputPortByName['mini'].configure, (), {'datatype': 'int', 'cast': True, 'shape': 'circle', 'color': 'yellow'})
apply(angle_10.inputPortByName['maxi'].configure, (), {'datatype': 'int', 'cast': True, 'shape': 'circle', 'color': 'yellow'})
apply(angle_10.outputPortByName['value'].configure, (), {'datatype': 'int', 'color': 'yellow', 'shape': 'circle'})
apply(angle_10.inputPortByName['dial'].widget.configure, (), {'type': 'int', 'oneTurn': 100.0})
angle_10.inputPortByName['dial'].widget.set(360, run=False)
except:
print "WARNING: failed to restore DialNE named angle in network self.macroNetwork"
print_exc()
angle_10=None
try:
## saving node nbSteps ##
from Vision.StandardNodes import DialNE
nbSteps_11 = DialNE(constrkw = {}, name='nbSteps', library=stdlib)
self.macroNetwork.addNode(nbSteps_11,634,7)
apply(nbSteps_11.inputPortByName['dial'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'})
apply(nbSteps_11.inputPortByName['mini'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'})
apply(nbSteps_11.inputPortByName['maxi'].configure, (), {'color': 'green', 'cast': True, 'shape': 'circle'})
apply(nbSteps_11.outputPortByName['value'].configure, (), {'color': 'green', 'shape': 'circle'})
apply(nbSteps_11.inputPortByName['dial'].widget.configure, (), {'oneTurn': 10.0})
nbSteps_11.inputPortByName['dial'].widget.set(1.0, run=False)
except:
print "WARNING: failed to restore DialNE named nbSteps in network self.macroNetwork"
print_exc()
nbSteps_11=None
try:
## saving node select axis ##
from DejaVu.VisionInterface.DejaVuNodes import SelectAxis
select_axis_12 = SelectAxis(constrkw = {}, name='select axis', library=stdlib)
self.macroNetwork.addNode(select_axis_12,528,40)
apply(select_axis_12.inputPortByName['x-axis'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'rect'})
apply(select_axis_12.inputPortByName['y-axis'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'rect'})
apply(select_axis_12.inputPortByName['z-axis'].configure, (), {'color': 'yellow', 'cast': True, 'shape': 'rect'})
apply(select_axis_12.outputPortByName['rotationAxis'].configure, (), {'color': 'cyan', 'shape': 'oval'})
except:
print "WARNING: failed to restore SelectAxis named select axis in network self.macroNetwork"
print_exc()
select_axis_12=None
try:
## saving node call method ##
from Vision.StandardNodes import CallMethod
call_method_13 = CallMethod(constrkw = {}, name='call method', library=stdlib)
self.macroNetwork.addNode(call_method_13,412,339)
apply(call_method_13.inputPortByName['objects'].configure, (), {'datatype': 'geom', 'cast': True, 'shape': 'rect', 'color': 'red'})
apply(call_method_13.inputPortByName['signature'].configure, (), {'color': 'white', 'cast': True, 'shape': 'oval'})
apply(call_method_13.addInputPort, (), {'name': 'mat', 'cast': True, 'datatype': 'None', 'height': 8, 'width': 12, 'shape': 'diamond', 'color': 'white'})
apply(call_method_13.outputPortByName['objects'].configure, (), {'color': 'white', 'shape': 'diamond'})
apply(call_method_13.outputPortByName['results'].configure, (), {'color': 'white', 'shape': 'diamond'})
call_method_13.inputPortByName['signature'].widget.set("ConcatRotation %mat", run=False)
apply(call_method_13.configure, (), {'specialPortsVisible': True})
except:
print "WARNING: failed to restore CallMethod named call method in network self.macroNetwork"
print_exc()
call_method_13=None
self.macroNetwork.freeze()
## saving connections for network RotateScene ##
if range_6 is not None and iterate_7 is not None:
try:
self.macroNetwork.connectNodes(
range_6, iterate_7, "data", "listToLoopOver", blocking=True)
except:
print "WARNING: failed to restore connection between range_6 and iterate_7 in network self.macroNetwork"
if Rotate_3 is not None and flattenRotation_8 is not None:
try:
self.macroNetwork.connectNodes(
Rotate_3, flattenRotation_8, "outMatrices", "in0", blocking=True)
except:
print "WARNING: failed to restore connection between Rotate_3 and flattenRotation_8 in network self.macroNetwork"
if iterate_7 is not None and Pass_9 is not None:
try:
self.macroNetwork.connectNodes(
iterate_7, Pass_9, "oneItem", "in1", blocking=True)
except:
print "WARNING: failed to restore connection between iterate_7 and Pass_9 in network self.macroNetwork"
if angle_10 is not None and range_6 is not None:
try:
self.macroNetwork.connectNodes(
angle_10, range_6, "value", "toInd", blocking=True)
except:
print "WARNING: failed to restore connection between angle_10 and range_6 in network self.macroNetwork"
if nbSteps_11 is not None and Rotate_3 is not None:
try:
self.macroNetwork.connectNodes(
nbSteps_11, Rotate_3, "value", "angle", blocking=True)
except:
print "WARNING: failed to restore connection between nbSteps_11 and Rotate_3 in network self.macroNetwork"
if select_axis_12 is not None and Rotate_3 is not None:
try:
self.macroNetwork.connectNodes(
select_axis_12, Rotate_3, "rotationAxis", "vector", blocking=True)
except:
print "WARNING: failed to restore connection between select_axis_12 and Rotate_3 in network self.macroNetwork"
output_Ports_2 = self.macroNetwork.opNode
if iterate_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
iterate_7, output_Ports_2, "oneItem", "new", blocking=True)
except:
print "WARNING: failed to restore connection between iterate_7 and output_Ports_2 in network self.macroNetwork"
if Choose_Geom_5 is not None and call_method_13 is not None:
try:
self.macroNetwork.connectNodes(
Choose_Geom_5, call_method_13, "geometry", "objects", blocking=True)
except:
print "WARNING: failed to restore connection between Choose_Geom_5 and call_method_13 in network self.macroNetwork"
if Pass_9 is not None and call_method_13 is not None:
try:
self.macroNetwork.specialConnectNodes(
Pass_9, call_method_13, "trigger", "runNode", blocking=True)
except:
print "WARNING: failed to restore connection between Pass_9 and call_method_13 in network self.macroNetwork"
if flattenRotation_8 is not None and call_method_13 is not None:
try:
self.macroNetwork.connectNodes(
flattenRotation_8, call_method_13, "out0", "mat", blocking=True)
except:
print "WARNING: failed to restore connection between flattenRotation_8 and call_method_13 in network self.macroNetwork"
if call_method_13 is not None and One_Redraw_4 is not None:
try:
self.macroNetwork.connectNodes(
call_method_13, One_Redraw_4, "objects", "trigger", blocking=True)
except:
print "WARNING: failed to restore connection between call_method_13 and One_Redraw_4 in network self.macroNetwork"
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and One_Redraw_4 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, One_Redraw_4, "new", "viewer", blocking=True)
except:
print "WARNING: failed to restore connection between input_Ports_1 and One_Redraw_4 in network self.macroNetwork"
if input_Ports_1 is not None and Choose_Geom_5 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1, Choose_Geom_5, "One Redraw_viewer", "viewer", blocking=True)
except:
print "WARNING: failed to restore connection between input_Ports_1 and Choose_Geom_5 in network self.macroNetwork"
self.macroNetwork.unfreeze()
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection=True)
RotateScene_0.shrink()
## reset modifications ##
RotateScene_0.resetTags()
RotateScene_0.buildOriginalList()
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
AutodockVS_9 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_10 = self.macroNetwork.ipNode
input_Ports_10.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_10 = None
try:
## saving node output Ports ##
output_Ports_11 = self.macroNetwork.opNode
output_Ports_11.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_11 = None
try:
## saving node PrepareADVSInputs ##
from Vision.StandardNodes import Generic
PrepareADVSInputs_12 = Generic(constrkw={},
name='PrepareADVSInputs',
library=stdlib)
self.macroNetwork.addNode(PrepareADVSInputs_12, 217, 76)
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligands',
'cast': True,
'datatype': 'LigandDB',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'autogrid_results',
'cast': True,
'datatype': 'autogrid_results',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#FF33CC',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addInputPort(
*(), **{
'singleConnection': True,
'name': 'dpf_template_obj',
'cast': True,
'datatype': 'dpf_template',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'triangle',
'color': '#9933FF',
'originalDatatype': 'None'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'filter_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'ligand_lib',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'dpf_template_file',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'autogrid_res_url',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
PrepareADVSInputs_12.addOutputPort(
*(), **{
'name': 'autogrid_res_local',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, ligands, autogrid_results, dpf_template_obj):
dpf = dpf_template_obj.fullpath
if not(os.path.exists(dpf)):
print "ERROR: DPF template " + dpf + " does not exist!"
return '''stop'''
filter_file = ligands.filter_file
if autogrid_results.type == '''url''':
autogrid_result_url = autogrid_results.path
autogrid_result_local = ""
else:
autogrid_result_url = ""
autogrid_result_local = autogrid_results.path
ligand_lib = ligands.loc
pass
self.outputData(filter_file=filter_file, ligand_lib=ligand_lib, dpf_template_file=dpf, autogrid_res_url=autogrid_result_url, autogrid_res_local=autogrid_result_local)
## to ouput data on port filter_file use
## self.outputData(filter_file=data)
## to ouput data on port ligand_lib use
## self.outputData(ligand_lib=data)
## to ouput data on port dpf_template_file use
## self.outputData(dpf_template_file=data)
## to ouput data on port autogrid_res_url use
## self.outputData(autogrid_res_url=data)
## to ouput data on port autogrid_res_local use
## self.outputData(autogrid_res_local=data)
"""
PrepareADVSInputs_12.configure(function=code)
PrepareADVSInputs_12.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named PrepareADVSInputs in network self.macroNetwork"
)
print_exc()
PrepareADVSInputs_12 = None
try:
## saving node autodock_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
autodock_kryptonite_nbcr_net_13 = FunctionNode(
functionOrString='autodock_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
},
constrkw={
'functionOrString': "'autodock_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'ga_run': '',
'lib': '',
'filter_file_url': '',
'ga_num_evals': '',
'filter_file': '',
'sched': 'SGE',
'urllib': '',
'ga_num_generations': '',
'dpf': '',
'u': '',
'utar': '',
'userlib': '',
'ga_pop_size': '',
'localRun': False,
'email': '',
'execPath': ''
}
},
name='autodock_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(autodock_kryptonite_nbcr_net_13, 217,
132)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_run'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['lib'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file_url'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_evals'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['sched'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_generations'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['dpf'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['utar'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_pop_size'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName['email'].configure(
*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_run'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'lib'].widget.configure(
*(), **{
'choices':
('sample', 'NCIDS_SC', 'NCI_DS1', 'NCI_DS2',
'human_metabolome', 'chembridge_building_blocks',
'drugbank_nutraceutics', 'drugbank_smallmol',
'fda_approved')
})
autodock_kryptonite_nbcr_net_13.inputPortByName['lib'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file_url'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_evals'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'filter_file'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'sched'].widget.configure(*(), **{'choices': ('SGE', 'CSF')})
autodock_kryptonite_nbcr_net_13.inputPortByName[
'sched'].widget.set(r"SGE", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'urllib'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_num_generations'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'dpf'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['dpf'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'dpf'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName['u'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'utar'].rebindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName['utar'].widget.set(
r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'utar'].unbindWidget()
autodock_kryptonite_nbcr_net_13.inputPortByName[
'userlib'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'ga_pop_size'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'localRun'].widget.set(0, run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'email'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.inputPortByName[
'execPath'].widget.set(r"", run=False)
autodock_kryptonite_nbcr_net_13.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named autodock_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
autodock_kryptonite_nbcr_net_13 = None
try:
## saving node GetMainURLFromList ##
from WebServices.VisionInterface.WSNodes import GetMainURLFromListNode
GetMainURLFromList_14 = GetMainURLFromListNode(
constrkw={}, name='GetMainURLFromList', library=wslib)
self.macroNetwork.addNode(GetMainURLFromList_14, 217, 188)
GetMainURLFromList_14.inputPortByName['urls'].configure(
*(), **{'defaultValue': None})
GetMainURLFromList_14.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore GetMainURLFromListNode named GetMainURLFromList in network self.macroNetwork"
)
print_exc()
GetMainURLFromList_14 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network AutodockVS ##
input_Ports_10 = self.macroNetwork.ipNode
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"ligands",
blocking=True,
splitratio=[0.60597534741634829, 0.41083180453223428])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"autogrid_results",
blocking=True,
splitratio=[0.64561658610430228, 0.21974682015753622])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if input_Ports_10 is not None and PrepareADVSInputs_12 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_10,
PrepareADVSInputs_12,
"new",
"dpf_template_obj",
blocking=True,
splitratio=[0.52491295380143521, 0.32751034461281114])
except:
print(
"WARNING: failed to restore connection between input_Ports_10 and PrepareADVSInputs_12 in network self.macroNetwork"
)
if autodock_kryptonite_nbcr_net_13 is not None and GetMainURLFromList_14 is not None:
try:
self.macroNetwork.connectNodes(
autodock_kryptonite_nbcr_net_13,
GetMainURLFromList_14,
"result",
"urls",
blocking=True,
splitratio=[0.36974288957131424, 0.63465596053596318])
except:
print(
"WARNING: failed to restore connection between autodock_kryptonite_nbcr_net_13 and GetMainURLFromList_14 in network self.macroNetwork"
)
output_Ports_11 = self.macroNetwork.opNode
if GetMainURLFromList_14 is not None and output_Ports_11 is not None:
try:
self.macroNetwork.connectNodes(
GetMainURLFromList_14,
output_Ports_11,
"newurl",
"new",
blocking=True,
splitratio=[0.34850477186787743, 0.35637513198385085])
except:
print(
"WARNING: failed to restore connection between GetMainURLFromList_14 and output_Ports_11 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"filter_file",
"filter_file",
blocking=True,
splitratio=[0.33230642287344903, 0.65770700108889613])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"ligand_lib",
"urllib",
blocking=True,
splitratio=[0.50680104599665787, 0.51414170500293577])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"dpf_template_file",
"dpf",
blocking=True,
splitratio=[0.51615646597598808, 0.25661305528484007])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_url",
"u",
blocking=True,
splitratio=[0.5760732944947704, 0.2032376887917188])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
if PrepareADVSInputs_12 is not None and autodock_kryptonite_nbcr_net_13 is not None:
try:
self.macroNetwork.connectNodes(
PrepareADVSInputs_12,
autodock_kryptonite_nbcr_net_13,
"autogrid_res_local",
"utar",
blocking=True,
splitratio=[0.52802808938949819, 0.66978534572736881])
except:
print(
"WARNING: failed to restore connection between PrepareADVSInputs_12 and autodock_kryptonite_nbcr_net_13 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_10 = self.macroNetwork.ipNode
input_Ports_10.outputPorts[1].configure(
name='PrepareADVSInputs_ligands')
input_Ports_10.outputPorts[2].configure(
name='PrepareADVSInputs_autogrid_results')
input_Ports_10.outputPorts[3].configure(
name='PrepareADVSInputs_dpf_template_obj')
## modifying MacroOutputNode dynamic ports
output_Ports_11 = self.macroNetwork.opNode
output_Ports_11.inputPorts[1].configure(singleConnection='auto')
output_Ports_11.inputPorts[1].configure(
name='GetMainURLFromList_newurl')
## configure MacroNode input ports
AutodockVS_9.inputPorts[0].configure(name='PrepareADVSInputs_ligands')
AutodockVS_9.inputPorts[0].configure(datatype='LigandDB')
AutodockVS_9.inputPorts[1].configure(
name='PrepareADVSInputs_autogrid_results')
AutodockVS_9.inputPorts[1].configure(datatype='autogrid_results')
AutodockVS_9.inputPorts[2].configure(
name='PrepareADVSInputs_dpf_template_obj')
AutodockVS_9.inputPorts[2].configure(datatype='dpf_template')
## configure MacroNode output ports
AutodockVS_9.outputPorts[0].configure(name='GetMainURLFromList_newurl')
AutodockVS_9.outputPorts[0].configure(datatype='string')
AutodockVS_9.shrink()
## reset modifications ##
AutodockVS_9.resetTags()
AutodockVS_9.buildOriginalList()
name='Map Pot On Geom',
library=vizlib)
masterNet.addNode(Map_Pot_On_Geom_4, 250, 181)
Offset_9 = Map_Pot_On_Geom_4.macroNetwork.nodes[4]
Offset_9.inputPortByName['dial'].widget.set(1.0, run=False)
call_method_13 = Map_Pot_On_Geom_4.macroNetwork.nodes[8]
call_method_13.inputPortByName['signature'].widget.set(
"Set materials inheritMaterial", run=False)
Get_viewer_17 = Map_Pot_On_Geom_4.macroNetwork.nodes[12]
apply(Get_viewer_17.inputPortByName['attr'].widget.configure, (),
{'choices': ('viewer', )})
Get_viewer_17.inputPortByName['attr'].widget.set("viewer", run=False)
Slice_Data_18 = Map_Pot_On_Geom_4.macroNetwork.nodes[13]
Slice_Data_18.inputPortByName['_slice'].widget.set("[0]", run=False)
from Vision.StandardNodes import Generic
Generic_22 = Generic(constrkw={}, name='Generic', library=stdlib)
Map_Pot_On_Geom_4.macroNetwork.addNode(Generic_22, 510, 484)
apply(
Generic_22.addInputPort, (), {
'name': 'surf',
'cast': True,
'datatype': 'geom',
'height': 8,
'width': 12,
'shape': 'rect',
'color': 'red'
})
apply(
Generic_22.addInputPort, (), {
'name': 'colors',
'cast': True,
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'})
code = """def doit(self, dir):
import glob, os
match_str = '''*'''
if dir is not None:
cwd = os.getcwd()
os.chdir(dir)
try:
pdirs = glob.glob(match_str)
receptors = []
for i in pdirs:
try:
## saving node VolumeStats ##
from Volume.VisionInterface.VolumeNodes import VolumeStats
VolumeStats_1 = VolumeStats(constrkw={},
name='VolumeStats',
library=vollib)
masterNet.addNode(VolumeStats_1, 271, 173)
except:
print "WARNING: failed to restore VolumeStats named VolumeStats in network masterNet"
print_exc()
VolumeStats_1 = None
try:
## saving node GenSurf ##
from Vision.StandardNodes import Generic
GenSurf_2 = Generic(constrkw={}, name='GenSurf', library=stdlib)
masterNet.addNode(GenSurf_2, 411, 235)
apply(
GenSurf_2.addInputPort, (), {
'name': 'value',
'cast': True,
'datatype': 'float',
'height': 12,
'width': 12,
'shape': 'circle',
'color': 'green'
})
apply(
GenSurf_2.addInputPort, (), {
'name': 'geom1',
'cast': True,
def afterAddingToNetwork(self):
masterNet = self.macroNetwork
from NetworkEditor.macros import MacroNode
MacroNode.afterAddingToNetwork(self)
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
## building macro network ##
LocalLigandDirectory_0 = self
from traceback import print_exc
from WebServices.VisionInterface.WSNodes import wslib
from Vision.StandardNodes import stdlib
masterNet.getEditor().addLibraryInstance(
wslib, "WebServices.VisionInterface.WSNodes", "wslib")
from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory
try:
addOpalServerAsCategory("http://kryptonite.nbcr.net/opal2",
replace=False)
except:
pass
try:
## saving node input Ports ##
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork"
)
print_exc()
input_Ports_1 = None
try:
## saving node output Ports ##
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
output_Ports_2.move(294, 448)
except:
print(
"WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork"
)
print_exc()
output_Ports_2 = None
try:
## saving node Make Zip File ##
from Vision.StandardNodes import MakeZipFileNE
Make_Zip_File_3 = MakeZipFileNE(constrkw={},
name='Make Zip File',
library=stdlib)
self.macroNetwork.addNode(Make_Zip_File_3, 136, 158)
Make_Zip_File_3.inputPortByName['input_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_directory'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.inputPortByName['output_name'].configure(
*(), **{'defaultValue': None})
Make_Zip_File_3.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore MakeZipFileNE named Make Zip File in network self.macroNetwork"
)
print_exc()
Make_Zip_File_3 = None
try:
## saving node Entry ##
from Vision.StandardNodes import EntryNE
Entry_4 = EntryNE(constrkw={}, name='Entry', library=stdlib)
self.macroNetwork.addNode(Entry_4, 312, 18)
Entry_4.inputPortByName['entry'].configure(
*(), **{'defaultValue': None})
Entry_4.inputPortByName['entry'].widget.set(r"my_ligands.zip",
run=False)
Entry_4.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore EntryNE named Entry in network self.macroNetwork"
)
print_exc()
Entry_4 = None
try:
## saving node LigandDBUpload_kryptonite_nbcr_net ##
from NetworkEditor.items import FunctionNode
LigandDBUpload_kryptonite_nbcr_net_5 = FunctionNode(
functionOrString='LigandDBUpload_kryptonite_nbcr_net',
host="http://kryptonite.nbcr.net/opal2",
namedArgs={
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
},
constrkw={
'functionOrString': "'LigandDBUpload_kryptonite_nbcr_net'",
'host': '"http://kryptonite.nbcr.net/opal2"',
'namedArgs': {
'username': '',
'userlib': '',
'password': '',
'localRun': False,
'execPath': '',
'desc': ''
}
},
name='LigandDBUpload_kryptonite_nbcr_net',
library=wslib)
self.macroNetwork.addNode(LigandDBUpload_kryptonite_nbcr_net_5,
136, 216)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].configure(*(), **{'defaultValue': None})
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'username'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].rebindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'userlib'].unbindWidget()
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'password'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'localRun'].widget.set(0, run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'execPath'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.inputPortByName[
'desc'].widget.set(r"", run=False)
LigandDBUpload_kryptonite_nbcr_net_5.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore FunctionNode named LigandDBUpload_kryptonite_nbcr_net in network self.macroNetwork"
)
print_exc()
LigandDBUpload_kryptonite_nbcr_net_5 = None
try:
## saving node Index ##
from Vision.StandardNodes import Index
Index_6 = Index(constrkw={}, name='Index', library=stdlib)
self.macroNetwork.addNode(Index_6, 136, 273)
Index_6.inputPortByName['data'].configure(*(),
**{'defaultValue': None})
Index_6.inputPortByName['index'].configure(
*(), **{'defaultValue': None})
Index_6.outputPortByName['data'].configure(
*(), **{'datatype': 'string'})
Index_6.inputPortByName['index'].widget.configure(
*(), **{
'max': 7,
'min': -8
})
Index_6.inputPortByName['index'].widget.set(0, run=False)
Index_6.configure(*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Index named Index in network self.macroNetwork"
)
print_exc()
Index_6 = None
try:
## saving node ReplaceURL ##
from WebServices.VisionInterface.WSNodes import ReplaceURLNode
ReplaceURL_7 = ReplaceURLNode(constrkw={},
name='ReplaceURL',
library=wslib)
self.macroNetwork.addNode(ReplaceURL_7, 328, 327)
ReplaceURL_7.inputPortByName['url'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['newfilename'].configure(
*(), **{'defaultValue': None})
ReplaceURL_7.inputPortByName['url'].rebindWidget()
ReplaceURL_7.inputPortByName['url'].widget.set(r"", run=False)
ReplaceURL_7.inputPortByName['url'].unbindWidget()
ReplaceURL_7.configure(*(), **{'paramPanelImmediate': 1})
except:
print(
"WARNING: failed to restore ReplaceURLNode named ReplaceURL in network self.macroNetwork"
)
print_exc()
ReplaceURL_7 = None
try:
## saving node CreateLigandDBObj ##
from Vision.StandardNodes import Generic
CreateLigandDBObj_8 = Generic(constrkw={},
name='CreateLigandDBObj',
library=stdlib)
self.macroNetwork.addNode(CreateLigandDBObj_8, 217, 385)
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'ligand_lib_url',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addInputPort(
*(), **{
'singleConnection': True,
'name': 'log_file',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': False,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
CreateLigandDBObj_8.addOutputPort(
*(), **{
'name': 'ligand_db_obj',
'datatype': 'LigandDB',
'height': 8,
'width': 12,
'shape': 'rect',
'color': '#FFCCFF'
})
code = """def doit(self, ligand_lib_url, log_file):
if log_file == None:
log_file = "ligand_lib_uploads.log"
log_file = os.path.abspath(log_file)
if log_file != None:
from time import strftime
now = strftime("%Y-%m-%d %H:%M:%S")
log_str = '''On ''' + now + ''', you uploaded a ligand library to: \n'''
log_str = log_str + ligand_lib_url + '''\n\n'''
f = open(log_file, '''a''')
f.write(log_str)
print "This ligand library upload has been recorded in " + log_file
from AutoDockTools.VisionInterface.Adt.LigandDB import LigandDB
ligand_db_obj = LigandDB(url_lib=ligand_lib_url)
pass
## to ouput data on port ligand_db_obj use
self.outputData(ligand_db_obj=ligand_db_obj)
"""
CreateLigandDBObj_8.configure(function=code)
CreateLigandDBObj_8.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named CreateLigandDBObj in network self.macroNetwork"
)
print_exc()
CreateLigandDBObj_8 = None
try:
## saving node get_paths ##
from Vision.StandardNodes import Generic
get_paths_9 = Generic(constrkw={},
name='get_paths',
library=stdlib)
self.macroNetwork.addNode(get_paths_9, 136, 105)
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'directory',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addInputPort(
*(), **{
'singleConnection': True,
'name': 'zip_name',
'cast': True,
'datatype': 'string',
'defaultValue': None,
'required': True,
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white',
'originalDatatype': 'None'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'input_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_directory',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_name',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
get_paths_9.addOutputPort(
*(), **{
'name': 'output_basedir',
'datatype': 'string',
'height': 8,
'width': 12,
'shape': 'oval',
'color': 'white'
})
code = """def doit(self, directory, zip_name):
input_directory = os.path.abspath(directory)
if not(os.path.exists(input_directory)):
print "ERROR: ligand input directory " + input_directory + " does not exist"
return '''stop'''
output_directory = os.path.abspath('''.''')
output_name = zip_name
output_basedir = zip_name.rstrip('''.zip''')
pass
self.outputData(input_directory=input_directory, output_directory=output_directory, output_name=zip_name, output_basedir=output_basedir)
## to ouput data on port input_directory use
## self.outputData(input_directory=data)
## to ouput data on port output_directory use
## self.outputData(output_directory=data)
## to ouput data on port output_name use
## self.outputData(output_name=data)
## to ouput data on port output_basedir use
## self.outputData(output_basedir=data)
"""
get_paths_9.configure(function=code)
get_paths_9.configure(
*(), **{
'paramPanelImmediate': 1,
'expanded': False
})
except:
print(
"WARNING: failed to restore Generic named get_paths in network self.macroNetwork"
)
print_exc()
get_paths_9 = None
#self.macroNetwork.run()
self.macroNetwork.freeze()
## saving connections for network LocalLigandDirectory ##
if Make_Zip_File_3 is not None and LigandDBUpload_kryptonite_nbcr_net_5 is not None:
try:
self.macroNetwork.connectNodes(
Make_Zip_File_3,
LigandDBUpload_kryptonite_nbcr_net_5,
"zipfile",
"userlib",
blocking=True,
splitratio=[0.67700056401206909, 0.41786522052018427])
except:
print(
"WARNING: failed to restore connection between Make_Zip_File_3 and LigandDBUpload_kryptonite_nbcr_net_5 in network self.macroNetwork"
)
if LigandDBUpload_kryptonite_nbcr_net_5 is not None and Index_6 is not None:
try:
self.macroNetwork.connectNodes(
LigandDBUpload_kryptonite_nbcr_net_5,
Index_6,
"result",
"data",
blocking=True,
splitratio=[0.27868065815947218, 0.69101010116597561])
except:
print(
"WARNING: failed to restore connection between LigandDBUpload_kryptonite_nbcr_net_5 and Index_6 in network self.macroNetwork"
)
if Index_6 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
Index_6,
ReplaceURL_7,
"data",
"url",
blocking=True,
splitratio=[0.0, 0.50910496731074983])
except:
print(
"WARNING: failed to restore connection between Index_6 and ReplaceURL_7 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
CreateLigandDBObj_8,
"newurl",
"ligand_lib_url",
blocking=True,
splitratio=[0.7375258387145982, 0.34433018843468416])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and CreateLigandDBObj_8 in network self.macroNetwork"
)
output_Ports_2 = self.macroNetwork.opNode
if CreateLigandDBObj_8 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
CreateLigandDBObj_8,
output_Ports_2,
"ligand_db_obj",
"new",
blocking=True,
splitratio=[0.25450332220506922, 0.49254602433654382])
except:
print(
"WARNING: failed to restore connection between CreateLigandDBObj_8 and output_Ports_2 in network self.macroNetwork"
)
input_Ports_1 = self.macroNetwork.ipNode
if input_Ports_1 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
get_paths_9,
"new",
"directory",
blocking=True,
splitratio=[0.73592256661833422, 0.40050624233195609])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and get_paths_9 in network self.macroNetwork"
)
if Entry_4 is not None and get_paths_9 is not None:
try:
self.macroNetwork.connectNodes(
Entry_4,
get_paths_9,
"string",
"zip_name",
blocking=True,
splitratio=[0.74641701362897139, 0.56047721560743557])
except:
print(
"WARNING: failed to restore connection between Entry_4 and get_paths_9 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"input_directory",
"input_directory",
blocking=True,
splitratio=[0.24975092021298884, 0.59053364249853169])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_name",
"output_name",
blocking=True,
splitratio=[0.44934886807300634, 0.5145630699734256])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and Make_Zip_File_3 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
Make_Zip_File_3,
"output_directory",
"output_directory",
blocking=True,
splitratio=[0.65054191214838031, 0.31030412383438832])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and Make_Zip_File_3 in network self.macroNetwork"
)
if get_paths_9 is not None and ReplaceURL_7 is not None:
try:
self.macroNetwork.connectNodes(
get_paths_9,
ReplaceURL_7,
"output_basedir",
"newfilename",
blocking=True,
splitratio=[0.5380996717918376, 0.39023381726820411])
except:
print(
"WARNING: failed to restore connection between get_paths_9 and ReplaceURL_7 in network self.macroNetwork"
)
if input_Ports_1 is not None and CreateLigandDBObj_8 is not None:
try:
self.macroNetwork.connectNodes(
input_Ports_1,
CreateLigandDBObj_8,
"new",
"log_file",
blocking=True,
splitratio=[0.49268182912115838, 0.67412763774649975])
except:
print(
"WARNING: failed to restore connection between input_Ports_1 and CreateLigandDBObj_8 in network self.macroNetwork"
)
if ReplaceURL_7 is not None and output_Ports_2 is not None:
try:
self.macroNetwork.connectNodes(
ReplaceURL_7,
output_Ports_2,
"newurl",
"new",
blocking=True,
splitratio=[0.67446600768034171, 0.74989471765767979])
except:
print(
"WARNING: failed to restore connection between ReplaceURL_7 and output_Ports_2 in network self.macroNetwork"
)
self.macroNetwork.runOnNewData.value = False
## modifying MacroInputNode dynamic ports
input_Ports_1 = self.macroNetwork.ipNode
input_Ports_1.outputPorts[1].configure(
name='Make_Zip_File_input_directory')
input_Ports_1.outputPorts[2].configure(
name='CreateLigandDBObj_log_file')
## modifying MacroOutputNode dynamic ports
output_Ports_2 = self.macroNetwork.opNode
output_Ports_2.inputPorts[1].configure(singleConnection='auto')
output_Ports_2.inputPorts[2].configure(singleConnection='auto')
output_Ports_2.inputPorts[1].configure(
name='CreateLigandDBObj_ligand_db_obj')
output_Ports_2.inputPorts[2].configure(name='ReplaceURL_newurl')
## configure MacroNode input ports
LocalLigandDirectory_0.inputPorts[0].configure(
name='Make_Zip_File_input_directory')
LocalLigandDirectory_0.inputPorts[0].configure(datatype='string')
LocalLigandDirectory_0.inputPorts[1].configure(
name='CreateLigandDBObj_log_file')
LocalLigandDirectory_0.inputPorts[1].configure(datatype='string')
## configure MacroNode output ports
LocalLigandDirectory_0.outputPorts[0].configure(
name='CreateLigandDBObj_ligand_db_obj')
LocalLigandDirectory_0.outputPorts[0].configure(datatype='LigandDB')
LocalLigandDirectory_0.outputPorts[1].configure(
name='ReplaceURL_newurl')
LocalLigandDirectory_0.outputPorts[1].configure(datatype='string')
LocalLigandDirectory_0.shrink()
## reset modifications ##
LocalLigandDirectory_0.resetTags()
LocalLigandDirectory_0.buildOriginalList()
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'
})