if_14, rename_stdout_13, "_if", "in_name", blocking=True , splitratio=[0.42861758851787812, 0.59732773543810935]) except: print "WARNING: failed to restore connection between if_14 and rename_stdout_13 in network SaveNAMDResults_5.macroNetwork" SaveNAMDResults_5.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_6.outputPorts[1].configure(name='GetOutURLs_url') input_Ports_6.outputPorts[2].configure(name='GetOutURLs_filename') SaveNAMDResults_5.inputPorts[0].configure(name='GetOutURLs_url') SaveNAMDResults_5.inputPorts[0].configure(datatype='string') SaveNAMDResults_5.inputPorts[1].configure(name='GetOutURLs_filename') SaveNAMDResults_5.inputPorts[1].configure(datatype='string') ## configure MacroNode input ports ## configure MacroNode output ports SaveNAMDResults_5.shrink() apply(SaveNAMDResults_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet" print_exc() SaveNAMDResults_5=None try: ## saving node NamdWS ## from NetworkEditor.macros import MacroNode NamdWS_15 = MacroNode(name='NamdWS') masterNet.addNode(NamdWS_15, 455, 313) output_Ports_17 = NamdWS_15.macroNetwork.opNode apply(output_Ports_17.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) output_Ports_17.move(211, 381) from NetworkEditor.items import FunctionNode
if_101, rename_stdout_100, "_if", "in_name", blocking=True , splitratio=[0.42861758851787812, 0.59732773543810935]) except: print "WARNING: failed to restore connection between if_101 and rename_stdout_100 in network SaveNAMDResults_92.macroNetwork" SaveNAMDResults_92.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_93.outputPorts[1].configure(name='GetOutURLs_url') input_Ports_93.outputPorts[2].configure(name='GetOutURLs_filename') SaveNAMDResults_92.inputPorts[0].configure(name='GetOutURLs_url') SaveNAMDResults_92.inputPorts[0].configure(datatype='string') SaveNAMDResults_92.inputPorts[1].configure(name='GetOutURLs_filename') SaveNAMDResults_92.inputPorts[1].configure(datatype='string') ## configure MacroNode input ports ## configure MacroNode output ports SaveNAMDResults_92.shrink() apply(SaveNAMDResults_92.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet" print_exc() SaveNAMDResults_92=None try: ## saving node NamdWS ## from NetworkEditor.macros import MacroNode NamdWS_102 = MacroNode(name='NamdWS') masterNet.addNode(NamdWS_102, 455, 294) output_Ports_104 = NamdWS_102.macroNetwork.opNode apply(output_Ports_104.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) output_Ports_104.move(211, 381) from NetworkEditor.items import FunctionNode
## modifying MacroInputNode dynamic ports input_Ports_32.outputPorts[1].configure(name='getMolePath_mol') input_Ports_32.outputPorts[2].configure(name='getMolePath_mol_paths') ## modifying MacroOutputNode dynamic ports output_Ports_33.inputPorts[1].configure(singleConnection='auto') output_Ports_33.inputPorts[1].configure(name='getMolePath_mol_path') LoadMolecule_31.inputPorts[0].configure(name='getMolePath_mol') LoadMolecule_31.inputPorts[0].configure(datatype='string') LoadMolecule_31.inputPorts[1].configure(name='getMolePath_mol_paths') LoadMolecule_31.inputPorts[1].configure(datatype='list') ## configure MacroNode input ports LoadMolecule_31.outputPorts[0].configure(name='getMolePath_mol_path') LoadMolecule_31.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports LoadMolecule_31.shrink() apply(LoadMolecule_31.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named LoadMolecule in network masterNet" print_exc() LoadMolecule_31=None try: ## saving node GetLigands ## from Vision.StandardNodes import Generic GetLigands_41 = Generic(constrkw={}, name='GetLigands', library=stdlib) masterNet.addNode(GetLigands_41,332,135) apply(GetLigands_41.addInputPort, (), {'singleConnection': True, 'name': 'rps', 'cast': True, 'datatype': 'list', 'defaultValue': None, 'required': True, 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan', 'originalDatatype': 'None'}) apply(GetLigands_41.addInputPort, (), {'singleConnection': True, 'name': 'r', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'}) apply(GetLigands_41.addOutputPort, (), {'name': 'ligands', 'datatype': 'list', 'height': 12, 'width': 12, 'shape': 'oval', 'color': 'cyan'}) code = """def doit(self, rps, r):
input_Ports_21.outputPorts[3].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config') ## modifying MacroOutputNode dynamic ports output_Ports_22.inputPorts[1].configure(singleConnection='auto') output_Ports_22.inputPorts[1].configure(name='GetMainURLFromList_newurl') Vina_20.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj') Vina_20.inputPorts[0].configure(datatype='receptor_prepared') Vina_20.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj') Vina_20.inputPorts[1].configure(datatype='LigandDB') Vina_20.inputPorts[2].configure(name='AutodockVina_Screening_kryptonite_nbcr_net_config') Vina_20.inputPorts[2].configure(datatype='string') ## configure MacroNode input ports Vina_20.outputPorts[0].configure(name='GetMainURLFromList_newurl') Vina_20.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports Vina_20.shrink() apply(Vina_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named Vina in network masterNet" print_exc() Vina_20=None try: ## saving node DownloadSaveDir ## from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode DownloadSaveDir_26 = DownloadSaveDirNode(constrkw={}, name='DownloadSaveDir', library=wslib) masterNet.addNode(DownloadSaveDir_26,350,411) apply(DownloadSaveDir_26.inputPortByName['url'].configure, (), {'defaultValue': None}) DownloadSaveDir_26.inputPortByName['url'].rebindWidget() DownloadSaveDir_26.inputPortByName['url'].widget.set(r"", run=False) DownloadSaveDir_26.inputPortByName['url'].unbindWidget()
def afterAddingToNetwork(self): masterNet = self.macroNetwork from NetworkEditor.macros import MacroNode MacroNode.afterAddingToNetwork(self) from WebServices.VisionInterface.WSNodes import wslib from Vision.StandardNodes import stdlib ## building macro network ## PrepareReceptor_0 = self from traceback import print_exc from WebServices.VisionInterface.WSNodes import wslib from Vision.StandardNodes import stdlib masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib") from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory try: addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False) except: pass try: ## saving node input Ports ## input_Ports_1 = self.macroNetwork.ipNode input_Ports_1.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) except: print("WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork") print_exc() input_Ports_1=None try: ## saving node output Ports ## output_Ports_2 = self.macroNetwork.opNode output_Ports_2.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) except: print("WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork") print_exc() output_Ports_2=None try: ## saving node Pdb2pqrWS ## from NetworkEditor.macros import MacroNode Pdb2pqrWS_3 = MacroNode(name='Pdb2pqrWS') self.macroNetwork.addNode(Pdb2pqrWS_3, 153, 86) input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode input_Ports_4.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) input_Ports_4.move(65, 10) output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode output_Ports_5.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) output_Ports_5.move(65, 310) from Vision.StandardNodes import Generic CheckFileFormat_6 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib) Pdb2pqrWS_3.macroNetwork.addNode(CheckFileFormat_6,82,62) CheckFileFormat_6.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) CheckFileFormat_6.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) CheckFileFormat_6.addOutputPort(*(), **{'name': 'pqr_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) CheckFileFormat_6.addOutputPort(*(), **{'name': 'pdb_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, value): if value.get_ext_loc('''pqr''') != None or value.get_ext_loc('''pdbqt''') != None: self.outputData(receptor_obj=value) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')]) else: pqr_name = value.get_id() + '''.pqr''' pdb_path = value.get_ext_loc('''pdb''') self.outputData(receptor_obj=value, pqr_name=pqr_name, pdb_path=pdb_path) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''pqr_name'''), self.getOutputPortByName('''pdb_path''')]) """ CheckFileFormat_6.configure(function=code) CheckFileFormat_6.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) from NetworkEditor.items import FunctionNode Pdb2pqrOpalService_ws_nbcr_net_7 = FunctionNode(functionOrString='Pdb2pqrOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}, constrkw={'functionOrString': "'Pdb2pqrOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}}, name='Pdb2pqrOpalService_ws_nbcr_net', library=wslib) Pdb2pqrWS_3.macroNetwork.addNode(Pdb2pqrOpalService_ws_nbcr_net_7,99,115) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].configure(*(), **{'defaultValue': None, 'required': True}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].configure(*(), **{'defaultValue': None, 'required': True}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].rebindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].unbindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].rebindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].unbindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['clean'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inId'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['apbs_input'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.configure(*(), **{'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['localRun'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['rama'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['execPath'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['assign_only'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) from WebServices.VisionInterface.WSNodes import GetURLFromListNode GetURLFromList_8 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib) Pdb2pqrWS_3.macroNetwork.addNode(GetURLFromList_8,117,169) GetURLFromList_8.inputPortByName['ext'].widget.set(r"pqr", run=False) GetURLFromList_8.configure(*(), **{'paramPanelImmediate': 1}) from Vision.StandardNodes import Generic UpdateReceptor_9 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib) Pdb2pqrWS_3.macroNetwork.addNode(UpdateReceptor_9,82,256) UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) UpdateReceptor_9.addInputPort(*(), **{'singleConnection': True, 'name': 'pqr', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'}) UpdateReceptor_9.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) UpdateReceptor_9.addOutputPort(*(), **{'name': 'pdb2pqr_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, receptor_obj, pqr): if pqr != '''no data yet''': pdb2pqr_result = pqr receptor_obj.set_ext_loc(pqr) else: pdbqt = receptor_obj.get_ext_loc('''pdbqt''') pqr = receptor_obj.get_ext_loc('''pqr''') if pdbqt != None: pdb2pqr_result = pdbqt elif pqr != None: pdb2pqr_result = pqr pass self.outputData(receptor_obj=receptor_obj, pdb2pqr_result=pdb2pqr_result) """ UpdateReceptor_9.configure(function=code) UpdateReceptor_9.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) ## saving connections for network Pdb2pqrWS ## Pdb2pqrWS_3.macroNetwork.freeze() if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pqr_name", "output_file", blocking=True , splitratio=[0.43278717885693868, 0.65281492247209427]) except: print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork") if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pdb_path", "inFile", blocking=True , splitratio=[0.61978340673276544, 0.69977512898866912]) except: print("WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork") if Pdb2pqrOpalService_ws_nbcr_net_7 is not None and GetURLFromList_8 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( Pdb2pqrOpalService_ws_nbcr_net_7, GetURLFromList_8, "result", "urllist", blocking=True , splitratio=[0.73247388879852338, 0.69014271703344965]) except: print("WARNING: failed to restore connection between Pdb2pqrOpalService_ws_nbcr_net_7 and GetURLFromList_8 in network Pdb2pqrWS_3.macroNetwork") if GetURLFromList_8 is not None and UpdateReceptor_9 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( GetURLFromList_8, UpdateReceptor_9, "url", "pqr", blocking=True , splitratio=[0.35224914715245104, 0.47693375858097758]) except: print("WARNING: failed to restore connection between GetURLFromList_8 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork") if CheckFileFormat_6 is not None and UpdateReceptor_9 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, UpdateReceptor_9, "receptor_obj", "receptor_obj", blocking=True , splitratio=[0.57865377076653579, 0.45824116584600394]) except: print("WARNING: failed to restore connection between CheckFileFormat_6 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork") input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode if input_Ports_4 is not None and CheckFileFormat_6 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( input_Ports_4, CheckFileFormat_6, "new", "value", blocking=True , splitratio=[0.28291581858817416, 0.70581213384962171]) except: print("WARNING: failed to restore connection between input_Ports_4 and CheckFileFormat_6 in network Pdb2pqrWS_3.macroNetwork") output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode if UpdateReceptor_9 is not None and output_Ports_5 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( UpdateReceptor_9, output_Ports_5, "receptor_obj", "new", blocking=True , splitratio=[0.24354423773729619, 0.72115604180615911]) except: print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork") if UpdateReceptor_9 is not None and output_Ports_5 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( UpdateReceptor_9, output_Ports_5, "pdb2pqr_result", "new", blocking=True , splitratio=[0.31141907324539131, 0.41794097665671487]) except: print("WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork") Pdb2pqrWS_3.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_4.outputPorts[1].configure(name='CheckFileFormat_value') ## modifying MacroOutputNode dynamic ports output_Ports_5.inputPorts[1].configure(singleConnection='auto') output_Ports_5.inputPorts[2].configure(singleConnection='auto') output_Ports_5.inputPorts[1].configure(name='UpdateReceptor_receptor_obj') output_Ports_5.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result') Pdb2pqrWS_3.inputPorts[0].configure(name='CheckFileFormat_value') Pdb2pqrWS_3.inputPorts[0].configure(datatype='receptor') ## configure MacroNode input ports Pdb2pqrWS_3.outputPorts[0].configure(name='UpdateReceptor_receptor_obj') Pdb2pqrWS_3.outputPorts[0].configure(datatype='receptor') Pdb2pqrWS_3.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result') Pdb2pqrWS_3.outputPorts[1].configure(datatype='string') ## configure MacroNode output ports Pdb2pqrWS_3.shrink() Pdb2pqrWS_3.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) except: print("WARNING: failed to restore MacroNode named Pdb2pqrWS in network self.macroNetwork") print_exc() Pdb2pqrWS_3=None try: ## saving node PrepareReceptorWS ## from NetworkEditor.macros import MacroNode PrepareReceptorWS_10 = MacroNode(name='PrepareReceptorWS') self.macroNetwork.addNode(PrepareReceptorWS_10, 217, 140) input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode input_Ports_11.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) input_Ports_11.move(145, 8) output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode output_Ports_12.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) output_Ports_12.move(29, 412) from Vision.StandardNodes import Generic CheckFileFormat_13 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib) PrepareReceptorWS_10.macroNetwork.addNode(CheckFileFormat_13,46,64) CheckFileFormat_13.addInputPort(*(), **{'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) CheckFileFormat_13.addOutputPort(*(), **{'name': 'receptor_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) CheckFileFormat_13.addOutputPort(*(), **{'name': 'download_loc', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, value): if value.get_ext_loc('''pdbqt''') != None: self.outputData(receptor_obj=value) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')]) else: pqr = value.get_ext_loc('''pqr''') pdb = value.get_ext_loc('''pdb''') download_loc = value.get_workdir() + os.sep + value.get_id() + '''.pdbqt''' if pqr != None: if value.get_ext_type('''pqr''') == '''url''': receptor_url = pqr receptor_local = "" else: receptor_url = "" receptor_local = pqr elif pdb != None: if value.get_ext_type('''pdb''') == '''url''': receptor_url = pdb receptor_local = "" else: receptor_url = "" receptor_local = pdb else: print "*** ERROR: pqr and pqr both missing from receptor object" print receptor_obj.ext_loc return '''stop''' self.outputData(receptor_obj=value, receptor_url=receptor_url, receptor_local=receptor_local, download_loc=download_loc) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''receptor_url'''), self.getOutputPortByName('''receptor_local'''), self.getOutputPortByName('''download_loc''')]) """ CheckFileFormat_13.configure(function=code) CheckFileFormat_13.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) from NetworkEditor.items import FunctionNode PrepareReceptorOpalService_ws_nbcr_net_14 = FunctionNode(functionOrString='PrepareReceptorOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'PrepareReceptorOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}}, name='PrepareReceptorOpalService_ws_nbcr_net', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(PrepareReceptorOpalService_ws_nbcr_net_14,180,128) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].configure(*(), **{'defaultValue': None}) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].configure(*(), **{'defaultValue': None, 'required': True}) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].configure(*(), **{'defaultValue': None, 'required': True}) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['o'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['v'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['localRun'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['execPath'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) from WebServices.VisionInterface.WSNodes import GetURLFromListNode GetURLFromList_15 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(GetURLFromList_15,180,186) GetURLFromList_15.inputPortByName['ext'].widget.set(r"pdbqt", run=False) GetURLFromList_15.configure(*(), **{'paramPanelImmediate': 1}) from WebServices.VisionInterface.WSNodes import DownloadToFileNode DownloadToFile_16 = DownloadToFileNode(constrkw={}, name='DownloadToFile', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(DownloadToFile_16,80,272) DownloadToFile_16.inputPortByName['url'].configure(*(), **{'defaultValue': None}) DownloadToFile_16.inputPortByName['filename'].configure(*(), **{'defaultValue': None}) DownloadToFile_16.inputPortByName['url'].rebindWidget() DownloadToFile_16.inputPortByName['url'].widget.set(r"", run=False) DownloadToFile_16.inputPortByName['url'].unbindWidget() DownloadToFile_16.inputPortByName['filename'].rebindWidget() DownloadToFile_16.inputPortByName['filename'].widget.set(r"", run=False) DownloadToFile_16.inputPortByName['filename'].unbindWidget() DownloadToFile_16.inputPortByName['overwrite'].widget.set(1, run=False) DownloadToFile_16.configure(*(), **{'paramPanelImmediate': 1}) from Vision.StandardNodes import Generic UpdateReceptor_17 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib) PrepareReceptorWS_10.macroNetwork.addNode(UpdateReceptor_17,46,358) UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) UpdateReceptor_17.addInputPort(*(), **{'singleConnection': True, 'name': 'pdbqt', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'}) UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_prepared_obj', 'datatype': 'receptor_prepared', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900'}) UpdateReceptor_17.addOutputPort(*(), **{'name': 'receptor_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, receptor_obj, pdbqt): from AutoDockTools.VisionInterface.Adt.receptor_prepared import receptor_prepared if pdbqt != '''no data yet''': receptor_prepared_obj = receptor_prepared(pdbqt) receptor_obj.set_ext_loc(pdbqt) receptor_result = pdbqt else: pdbqt_org = receptor_obj.get_ext_loc('''pdbqt''') receptor_prepared_obj = receptor_prepared(pdbqt_org) receptor_result = pdbqt_org pass self.outputData(receptor_prepared_obj = receptor_prepared_obj, receptor_result=receptor_result) """ UpdateReceptor_17.configure(function=code) UpdateReceptor_17.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) ## saving connections for network PrepareReceptorWS ## PrepareReceptorWS_10.macroNetwork.freeze() input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode if input_Ports_11 is not None and CheckFileFormat_13 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( input_Ports_11, CheckFileFormat_13, "new", "value", blocking=True , splitratio=[0.64907843562020084, 0.47057253960060474]) except: print("WARNING: failed to restore connection between input_Ports_11 and CheckFileFormat_13 in network PrepareReceptorWS_10.macroNetwork") if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_url", "url", blocking=True , splitratio=[0.6171192646814192, 0.42883431331137822]) except: print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork") if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_local", "r", blocking=True , splitratio=[0.66136144381723583, 0.28482114514549767]) except: print("WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork") if input_Ports_11 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( input_Ports_11, PrepareReceptorOpalService_ws_nbcr_net_14, "new", "C", blocking=True , splitratio=[0.53817543437956172, 0.61119702937572407]) except: print("WARNING: failed to restore connection between input_Ports_11 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork") if PrepareReceptorOpalService_ws_nbcr_net_14 is not None and GetURLFromList_15 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( PrepareReceptorOpalService_ws_nbcr_net_14, GetURLFromList_15, "result", "urllist", blocking=True , splitratio=[0.43369347916867251, 0.26566786648658042]) except: print("WARNING: failed to restore connection between PrepareReceptorOpalService_ws_nbcr_net_14 and GetURLFromList_15 in network PrepareReceptorWS_10.macroNetwork") if GetURLFromList_15 is not None and DownloadToFile_16 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( GetURLFromList_15, DownloadToFile_16, "url", "url", blocking=True , splitratio=[0.70502483723033316, 0.71683158018466053]) except: print("WARNING: failed to restore connection between GetURLFromList_15 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork") if CheckFileFormat_13 is not None and DownloadToFile_16 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, DownloadToFile_16, "download_loc", "filename", blocking=True , splitratio=[0.60455581032885575, 0.35606890231085681]) except: print("WARNING: failed to restore connection between CheckFileFormat_13 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork") if CheckFileFormat_13 is not None and UpdateReceptor_17 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, UpdateReceptor_17, "receptor_obj", "receptor_obj", blocking=True , splitratio=[0.74908230670336207, 0.38226563370205602]) except: print("WARNING: failed to restore connection between CheckFileFormat_13 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork") if DownloadToFile_16 is not None and UpdateReceptor_17 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( DownloadToFile_16, UpdateReceptor_17, "filename", "pdbqt", blocking=True , splitratio=[0.38698393490575966, 0.2874426709930199]) except: print("WARNING: failed to restore connection between DownloadToFile_16 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork") output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode if UpdateReceptor_17 is not None and output_Ports_12 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( UpdateReceptor_17, output_Ports_12, "receptor_prepared_obj", "new", blocking=True , splitratio=[0.69589857263374943, 0.59566078506240416]) except: print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork") if UpdateReceptor_17 is not None and output_Ports_12 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( UpdateReceptor_17, output_Ports_12, "receptor_result", "new", blocking=True , splitratio=[0.44926362052272689, 0.38628711158860896]) except: print("WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork") PrepareReceptorWS_10.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_11.outputPorts[1].configure(name='CheckFileFormat_value') input_Ports_11.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C') ## modifying MacroOutputNode dynamic ports output_Ports_12.inputPorts[1].configure(singleConnection='auto') output_Ports_12.inputPorts[2].configure(singleConnection='auto') output_Ports_12.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj') output_Ports_12.inputPorts[2].configure(name='UpdateReceptor_receptor_result') PrepareReceptorWS_10.inputPorts[0].configure(name='CheckFileFormat_value') PrepareReceptorWS_10.inputPorts[0].configure(datatype='receptor') PrepareReceptorWS_10.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C') PrepareReceptorWS_10.inputPorts[1].configure(datatype='boolean') ## configure MacroNode input ports PrepareReceptorWS_10.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj') PrepareReceptorWS_10.outputPorts[0].configure(datatype='receptor_prepared') PrepareReceptorWS_10.outputPorts[1].configure(name='UpdateReceptor_receptor_result') PrepareReceptorWS_10.outputPorts[1].configure(datatype='string') ## configure MacroNode output ports PrepareReceptorWS_10.shrink() PrepareReceptorWS_10.configure(*(), **{'paramPanelImmediate': 1, 'expanded': False}) except: print("WARNING: failed to restore MacroNode named PrepareReceptorWS in network self.macroNetwork") print_exc() PrepareReceptorWS_10=None #self.macroNetwork.run() self.macroNetwork.freeze() ## saving connections for network PrepareReceptor ## input_Ports_1 = self.macroNetwork.ipNode Pdb2pqrWS_3 = self.macroNetwork.nodes[2] if input_Ports_1 is not None and Pdb2pqrWS_3 is not None: try: self.macroNetwork.connectNodes( input_Ports_1, Pdb2pqrWS_3, "new", "CheckFileFormat_value", blocking=True , splitratio=[0.73531020066010289, 0.24042404972613104]) except: print("WARNING: failed to restore connection between input_Ports_1 and Pdb2pqrWS_3 in network self.macroNetwork") PrepareReceptorWS_10 = self.macroNetwork.nodes[3] if Pdb2pqrWS_3 is not None and PrepareReceptorWS_10 is not None: try: self.macroNetwork.connectNodes( Pdb2pqrWS_3, PrepareReceptorWS_10, "UpdateReceptor_receptor_obj", "CheckFileFormat_value", blocking=True , splitratio=[0.54479169827535734, 0.4847384502006486]) except: print("WARNING: failed to restore connection between Pdb2pqrWS_3 and PrepareReceptorWS_10 in network self.macroNetwork") if input_Ports_1 is not None and PrepareReceptorWS_10 is not None: try: self.macroNetwork.connectNodes( input_Ports_1, PrepareReceptorWS_10, "new", "PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True , splitratio=[0.37730151685222141, 0.48897820190498614]) except: print("WARNING: failed to restore connection between input_Ports_1 and PrepareReceptorWS_10 in network self.macroNetwork") output_Ports_2 = self.macroNetwork.opNode if PrepareReceptorWS_10 is not None and output_Ports_2 is not None: try: self.macroNetwork.connectNodes( PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_prepared_obj", "new", blocking=True , splitratio=[0.64110508898616414, 0.45535290355389196]) except: print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork") if PrepareReceptorWS_10 is not None and output_Ports_2 is not None: try: self.macroNetwork.connectNodes( PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_result", "new", blocking=True , splitratio=[0.45846842546122241, 0.44240009354017412]) except: print("WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork") self.macroNetwork.runOnNewData.value = False ## modifying MacroInputNode dynamic ports input_Ports_1 = self.macroNetwork.ipNode input_Ports_1.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value') input_Ports_1.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C') ## modifying MacroOutputNode dynamic ports output_Ports_2 = self.macroNetwork.opNode output_Ports_2.inputPorts[1].configure(singleConnection='auto') output_Ports_2.inputPorts[2].configure(singleConnection='auto') output_Ports_2.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj') output_Ports_2.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result') ## configure MacroNode input ports PrepareReceptor_0.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value') PrepareReceptor_0.inputPorts[0].configure(datatype='receptor') PrepareReceptor_0.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C') PrepareReceptor_0.inputPorts[1].configure(datatype='boolean') ## configure MacroNode output ports PrepareReceptor_0.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj') PrepareReceptor_0.outputPorts[0].configure(datatype='receptor_prepared') PrepareReceptor_0.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result') PrepareReceptor_0.outputPorts[1].configure(datatype='string') PrepareReceptor_0.shrink() ## reset modifications ## PrepareReceptor_0.resetTags() PrepareReceptor_0.buildOriginalList()
input_Ports_5.outputPorts[3].configure(name='NAMD_rocce_ucsd_edu_procs') ## modifying MacroOutputNode dynamic ports output_Ports_6.inputPorts[1].configure(singleConnection='auto') output_Ports_6.inputPorts[1].configure(name='GetMainURLFromList_newurl') AMDws_4.inputPorts[0].configure(name='eval_in1') AMDws_4.inputPorts[0].configure(datatype='string') AMDws_4.inputPorts[1].configure(name='prepareForZip_in1') AMDws_4.inputPorts[1].configure(datatype='string') AMDws_4.inputPorts[2].configure(name='NAMD_rocce_ucsd_edu_procs') AMDws_4.inputPorts[2].configure(datatype='string') ## configure MacroNode input ports AMDws_4.outputPorts[0].configure(name='GetMainURLFromList_newurl') AMDws_4.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports AMDws_4.shrink() apply(AMDws_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named AMDws in network masterNet" print_exc() AMDws_4=None try: ## saving node DownloadDir ## from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode DownloadDir_12 = DownloadSaveDirNode(constrkw={}, name='DownloadDir', library=wslib) masterNet.addNode(DownloadDir_12,494,320) apply(DownloadDir_12.inputPortByName['url'].configure, (), {'defaultValue': None}) DownloadDir_12.inputPortByName['url'].rebindWidget() DownloadDir_12.inputPortByName['url'].widget.set(r"", run=False) DownloadDir_12.inputPortByName['url'].unbindWidget()
blocking=True, splitratio=[0.42861758851787812, 0.59732773543810935]) except: print "WARNING: failed to restore connection between if_14 and rename_stdout_13 in network SaveNAMDResults_5.macroNetwork" SaveNAMDResults_5.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_6.outputPorts[1].configure(name='GetOutURLs_url') input_Ports_6.outputPorts[2].configure(name='GetOutURLs_filename') SaveNAMDResults_5.inputPorts[0].configure(name='GetOutURLs_url') SaveNAMDResults_5.inputPorts[0].configure(datatype='string') SaveNAMDResults_5.inputPorts[1].configure(name='GetOutURLs_filename') SaveNAMDResults_5.inputPorts[1].configure(datatype='string') ## configure MacroNode input ports ## configure MacroNode output ports SaveNAMDResults_5.shrink() apply(SaveNAMDResults_5.configure, (), { 'paramPanelImmediate': 1, 'expanded': False }) except: print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet" print_exc() SaveNAMDResults_5 = None try: ## saving node NamdWS ## from NetworkEditor.macros import MacroNode NamdWS_15 = MacroNode(name='NamdWS') masterNet.addNode(NamdWS_15, 455, 313) output_Ports_17 = NamdWS_15.macroNetwork.opNode
## modifying MacroOutputNode dynamic ports output_Ports_23.inputPorts[1].configure(singleConnection='auto') output_Ports_23.inputPorts[1].configure(name='GetMainURLFromList_newurl') Vina_21.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj') Vina_21.inputPorts[0].configure(datatype='receptor_prepared') Vina_21.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj') Vina_21.inputPorts[1].configure(datatype='LigandDB') Vina_21.inputPorts[2].configure( name='AutodockVina_Screening_kryptonite_nbcr_net_config') Vina_21.inputPorts[2].configure(datatype='string') ## configure MacroNode input ports Vina_21.outputPorts[0].configure(name='GetMainURLFromList_newurl') Vina_21.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports Vina_21.shrink() apply(Vina_21.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named Vina in network masterNet" print_exc() Vina_21 = None try: ## saving node DownloadSaveDir ## from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode DownloadSaveDir_27 = DownloadSaveDirNode(constrkw={}, name='DownloadSaveDir', library=wslib) masterNet.addNode(DownloadSaveDir_27, 402, 366) apply(DownloadSaveDir_27.inputPortByName['url'].configure, (), {'defaultValue': None})
## modifying MacroInputNode dynamic ports input_Ports_4.outputPorts[1].configure(name='FindMolPath_molname') input_Ports_4.outputPorts[2].configure(name='abs_path_in1') ## modifying MacroOutputNode dynamic ports output_Ports_5.inputPorts[1].configure(singleConnection='auto') output_Ports_5.inputPorts[1].configure(name='FindMolPath_molpath') LoadMolecule5_3.inputPorts[0].configure(name='FindMolPath_molname') LoadMolecule5_3.inputPorts[0].configure(datatype='string') LoadMolecule5_3.inputPorts[1].configure(name='abs_path_in1') LoadMolecule5_3.inputPorts[1].configure(datatype='string') ## configure MacroNode input ports LoadMolecule5_3.outputPorts[0].configure(name='FindMolPath_molpath') LoadMolecule5_3.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports LoadMolecule5_3.shrink() apply(LoadMolecule5_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named LoadMolecule5 in network masterNet" print_exc() LoadMolecule5_3=None try: ## saving node ShowConformations6 ## from NetworkEditor.macros import MacroNode ShowConformations6_14 = MacroNode(name='ShowConformations6') masterNet.addNode(ShowConformations6_14, 543, 541) output_Ports_16 = ShowConformations6_14.macroNetwork.opNode apply(output_Ports_16.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) output_Ports_16.move(220, 365) from Vision.StandardNodes import Generic
## modifying MacroOutputNode dynamic ports output_Ports_22.inputPorts[1].configure(singleConnection='auto') output_Ports_22.inputPorts[1].configure(name='GetMainURLFromList_newurl') Vina_20.inputPorts[0].configure(name='PrepareVinaInputs_receptor_obj') Vina_20.inputPorts[0].configure(datatype='receptor_prepared') Vina_20.inputPorts[1].configure(name='PrepareVinaInputs_ligand_obj') Vina_20.inputPorts[1].configure(datatype='LigandDB') Vina_20.inputPorts[2].configure( name='AutodockVina_Screening_kryptonite_nbcr_net_config') Vina_20.inputPorts[2].configure(datatype='string') ## configure MacroNode input ports Vina_20.outputPorts[0].configure(name='GetMainURLFromList_newurl') Vina_20.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports Vina_20.shrink() apply(Vina_20.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named Vina in network masterNet" print_exc() Vina_20 = None try: ## saving node DownloadSaveDir ## from WebServices.VisionInterface.WSNodes import DownloadSaveDirNode DownloadSaveDir_26 = DownloadSaveDirNode(constrkw={}, name='DownloadSaveDir', library=wslib) masterNet.addNode(DownloadSaveDir_26, 350, 411) apply(DownloadSaveDir_26.inputPortByName['url'].configure, (), {'defaultValue': None})
def afterAddingToNetwork(self): masterNet = self.macroNetwork from NetworkEditor.macros import MacroNode MacroNode.afterAddingToNetwork(self) from WebServices.VisionInterface.WSNodes import wslib from Vision.StandardNodes import stdlib ## building macro network ## PrepareReceptor_0 = self from traceback import print_exc from WebServices.VisionInterface.WSNodes import wslib from Vision.StandardNodes import stdlib masterNet.getEditor().addLibraryInstance(wslib,"WebServices.VisionInterface.WSNodes", "wslib") from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory try: addOpalServerAsCategory("http://ws.nbcr.net/opal2", replace=False) except: pass try: ## saving node input Ports ## input_Ports_1 = self.macroNetwork.ipNode apply(input_Ports_1.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork" print_exc() input_Ports_1=None try: ## saving node output Ports ## output_Ports_2 = self.macroNetwork.opNode apply(output_Ports_2.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork" print_exc() output_Ports_2=None try: ## saving node Pdb2pqrWS ## from NetworkEditor.macros import MacroNode Pdb2pqrWS_3 = MacroNode(name='Pdb2pqrWS') self.macroNetwork.addNode(Pdb2pqrWS_3, 153, 86) input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode apply(input_Ports_4.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) input_Ports_4.move(65, 10) output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode apply(output_Ports_5.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) output_Ports_5.move(65, 310) from Vision.StandardNodes import Generic CheckFileFormat_6 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib) Pdb2pqrWS_3.macroNetwork.addNode(CheckFileFormat_6,82,62) apply(CheckFileFormat_6.addInputPort, (), {'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) apply(CheckFileFormat_6.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) apply(CheckFileFormat_6.addOutputPort, (), {'name': 'pqr_name', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) apply(CheckFileFormat_6.addOutputPort, (), {'name': 'pdb_path', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, value): if value.get_ext_loc('''pqr''') != None or value.get_ext_loc('''pdbqt''') != None: self.outputData(receptor_obj=value) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')]) else: pqr_name = value.get_id() + '''.pqr''' pdb_path = value.get_ext_loc('''pdb''') self.outputData(receptor_obj=value, pqr_name=pqr_name, pdb_path=pdb_path) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''pqr_name'''), self.getOutputPortByName('''pdb_path''')]) """ CheckFileFormat_6.configure(function=code) apply(CheckFileFormat_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) from NetworkEditor.items import FunctionNode Pdb2pqrOpalService_ws_nbcr_net_7 = FunctionNode(functionOrString='Pdb2pqrOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}, constrkw={'functionOrString': "'Pdb2pqrOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'noopt': False, 'phi': False, 'psi': False, 'verbose': True, 'chain': False, 'nodebump': False, 'chi': False, 'output_file': '', 'ligand': '', 'hbond': False, 'inFile': '', 'with_ph': '', 'forcefield': 'AMBER', 'clean': False, 'inId': '', 'apbs_input': False, 'ffout': '', 'localRun': False, 'rama': False, 'execPath': '', 'assign_only': False}}, name='Pdb2pqrOpalService_ws_nbcr_net', library=wslib) Pdb2pqrWS_3.macroNetwork.addNode(Pdb2pqrOpalService_ws_nbcr_net_7,99,115) apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].configure, (), {'defaultValue': None, 'required': True}) apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].configure, (), {'defaultValue': None, 'required': True}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['noopt'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['phi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['psi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['verbose'].widget.set(1, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chain'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['nodebump'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['chi'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].rebindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['output_file'].unbindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ligand'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['hbond'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].rebindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inFile'].unbindWidget() Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['with_ph'].widget.set(r"", run=False) apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['forcefield'].widget.set(r"AMBER", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['clean'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['inId'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['apbs_input'].widget.set(0, run=False) apply(Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.configure, (), {'choices': ('AMBER', 'CHARMM', 'PARSE', 'TYL06')}) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['ffout'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['localRun'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['rama'].widget.set(0, run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['execPath'].widget.set(r"", run=False) Pdb2pqrOpalService_ws_nbcr_net_7.inputPortByName['assign_only'].widget.set(0, run=False) apply(Pdb2pqrOpalService_ws_nbcr_net_7.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) from WebServices.VisionInterface.WSNodes import GetURLFromListNode GetURLFromList_8 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib) Pdb2pqrWS_3.macroNetwork.addNode(GetURLFromList_8,117,169) GetURLFromList_8.inputPortByName['ext'].widget.set(r"pqr", run=False) apply(GetURLFromList_8.configure, (), {'paramPanelImmediate': 1}) from Vision.StandardNodes import Generic UpdateReceptor_9 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib) Pdb2pqrWS_3.macroNetwork.addNode(UpdateReceptor_9,82,256) apply(UpdateReceptor_9.addInputPort, (), {'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) apply(UpdateReceptor_9.addInputPort, (), {'singleConnection': True, 'name': 'pqr', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'}) apply(UpdateReceptor_9.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) apply(UpdateReceptor_9.addOutputPort, (), {'name': 'pdb2pqr_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, receptor_obj, pqr): if pqr != '''no data yet''': pdb2pqr_result = pqr receptor_obj.set_ext_loc(pqr) else: pdbqt = receptor_obj.get_ext_loc('''pdbqt''') pqr = receptor_obj.get_ext_loc('''pqr''') if pdbqt != None: pdb2pqr_result = pdbqt elif pqr != None: pdb2pqr_result = pqr pass self.outputData(receptor_obj=receptor_obj, pdb2pqr_result=pdb2pqr_result) """ UpdateReceptor_9.configure(function=code) apply(UpdateReceptor_9.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) ## saving connections for network Pdb2pqrWS ## Pdb2pqrWS_3.macroNetwork.freeze() if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pqr_name", "output_file", blocking=True , splitratio=[0.43278717885693868, 0.65281492247209427]) except: print "WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork" if CheckFileFormat_6 is not None and Pdb2pqrOpalService_ws_nbcr_net_7 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, Pdb2pqrOpalService_ws_nbcr_net_7, "pdb_path", "inFile", blocking=True , splitratio=[0.61978340673276544, 0.69977512898866912]) except: print "WARNING: failed to restore connection between CheckFileFormat_6 and Pdb2pqrOpalService_ws_nbcr_net_7 in network Pdb2pqrWS_3.macroNetwork" if Pdb2pqrOpalService_ws_nbcr_net_7 is not None and GetURLFromList_8 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( Pdb2pqrOpalService_ws_nbcr_net_7, GetURLFromList_8, "result", "urllist", blocking=True , splitratio=[0.73247388879852338, 0.69014271703344965]) except: print "WARNING: failed to restore connection between Pdb2pqrOpalService_ws_nbcr_net_7 and GetURLFromList_8 in network Pdb2pqrWS_3.macroNetwork" if GetURLFromList_8 is not None and UpdateReceptor_9 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( GetURLFromList_8, UpdateReceptor_9, "url", "pqr", blocking=True , splitratio=[0.35224914715245104, 0.47693375858097758]) except: print "WARNING: failed to restore connection between GetURLFromList_8 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork" if CheckFileFormat_6 is not None and UpdateReceptor_9 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( CheckFileFormat_6, UpdateReceptor_9, "receptor_obj", "receptor_obj", blocking=True , splitratio=[0.57865377076653579, 0.45824116584600394]) except: print "WARNING: failed to restore connection between CheckFileFormat_6 and UpdateReceptor_9 in network Pdb2pqrWS_3.macroNetwork" input_Ports_4 = Pdb2pqrWS_3.macroNetwork.ipNode if input_Ports_4 is not None and CheckFileFormat_6 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( input_Ports_4, CheckFileFormat_6, "new", "value", blocking=True , splitratio=[0.28291581858817416, 0.70581213384962171]) except: print "WARNING: failed to restore connection between input_Ports_4 and CheckFileFormat_6 in network Pdb2pqrWS_3.macroNetwork" output_Ports_5 = Pdb2pqrWS_3.macroNetwork.opNode if UpdateReceptor_9 is not None and output_Ports_5 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( UpdateReceptor_9, output_Ports_5, "receptor_obj", "new", blocking=True , splitratio=[0.24354423773729619, 0.72115604180615911]) except: print "WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork" if UpdateReceptor_9 is not None and output_Ports_5 is not None: try: Pdb2pqrWS_3.macroNetwork.connectNodes( UpdateReceptor_9, output_Ports_5, "pdb2pqr_result", "new", blocking=True , splitratio=[0.31141907324539131, 0.41794097665671487]) except: print "WARNING: failed to restore connection between UpdateReceptor_9 and output_Ports_5 in network Pdb2pqrWS_3.macroNetwork" Pdb2pqrWS_3.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_4.outputPorts[1].configure(name='CheckFileFormat_value') ## modifying MacroOutputNode dynamic ports output_Ports_5.inputPorts[1].configure(singleConnection='auto') output_Ports_5.inputPorts[2].configure(singleConnection='auto') output_Ports_5.inputPorts[1].configure(name='UpdateReceptor_receptor_obj') output_Ports_5.inputPorts[2].configure(name='UpdateReceptor_pdb2pqr_result') Pdb2pqrWS_3.inputPorts[0].configure(name='CheckFileFormat_value') Pdb2pqrWS_3.inputPorts[0].configure(datatype='receptor') ## configure MacroNode input ports Pdb2pqrWS_3.outputPorts[0].configure(name='UpdateReceptor_receptor_obj') Pdb2pqrWS_3.outputPorts[0].configure(datatype='receptor') Pdb2pqrWS_3.outputPorts[1].configure(name='UpdateReceptor_pdb2pqr_result') Pdb2pqrWS_3.outputPorts[1].configure(datatype='string') ## configure MacroNode output ports Pdb2pqrWS_3.shrink() apply(Pdb2pqrWS_3.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named Pdb2pqrWS in network self.macroNetwork" print_exc() Pdb2pqrWS_3=None try: ## saving node PrepareReceptorWS ## from NetworkEditor.macros import MacroNode PrepareReceptorWS_10 = MacroNode(name='PrepareReceptorWS') self.macroNetwork.addNode(PrepareReceptorWS_10, 217, 140) input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode apply(input_Ports_11.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) input_Ports_11.move(145, 8) output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode apply(output_Ports_12.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) output_Ports_12.move(29, 412) from Vision.StandardNodes import Generic CheckFileFormat_13 = Generic(constrkw={}, name='CheckFileFormat', library=stdlib) PrepareReceptorWS_10.macroNetwork.addNode(CheckFileFormat_13,46,64) apply(CheckFileFormat_13.addInputPort, (), {'singleConnection': True, 'name': 'value', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_obj', 'datatype': 'receptor', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33'}) apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_url', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) apply(CheckFileFormat_13.addOutputPort, (), {'name': 'receptor_local', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) apply(CheckFileFormat_13.addOutputPort, (), {'name': 'download_loc', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, value): if value.get_ext_loc('''pdbqt''') != None: self.outputData(receptor_obj=value) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj''')]) else: pqr = value.get_ext_loc('''pqr''') pdb = value.get_ext_loc('''pdb''') download_loc = value.get_workdir() + os.sep + value.get_id() + '''.pdbqt''' if pqr != None: if value.get_ext_type('''pqr''') == '''url''': receptor_url = pqr receptor_local = "" else: receptor_url = "" receptor_local = pqr elif pdb != None: if value.get_ext_type('''pdb''') == '''url''': receptor_url = pdb receptor_local = "" else: receptor_url = "" receptor_local = pdb else: print "*** ERROR: pqr and pqr both missing from receptor object" print receptor_obj.ext_loc return '''stop''' self.outputData(receptor_obj=value, receptor_url=receptor_url, receptor_local=receptor_local, download_loc=download_loc) self.scheduleChildren(portList=[self.getOutputPortByName('''receptor_obj'''), self.getOutputPortByName('''receptor_url'''), self.getOutputPortByName('''receptor_local'''), self.getOutputPortByName('''download_loc''')]) """ CheckFileFormat_13.configure(function=code) apply(CheckFileFormat_13.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) from NetworkEditor.items import FunctionNode PrepareReceptorOpalService_ws_nbcr_net_14 = FunctionNode(functionOrString='PrepareReceptorOpalService_ws_nbcr_net', host="http://ws.nbcr.net/opal2", namedArgs={'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}, constrkw={'functionOrString': "'PrepareReceptorOpalService_ws_nbcr_net'", 'host': '"http://ws.nbcr.net/opal2"', 'namedArgs': {'C': False, 'url': '', 'o': '', 'r': '', 'v': False, 'localRun': False, 'execPath': ''}}, name='PrepareReceptorOpalService_ws_nbcr_net', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(PrepareReceptorOpalService_ws_nbcr_net_14,180,128) apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].configure, (), {'defaultValue': None}) apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].configure, (), {'defaultValue': None, 'required': True}) apply(PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].configure, (), {'defaultValue': None, 'required': True}) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['C'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['url'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['o'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].rebindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].widget.set(r"", run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['r'].unbindWidget() PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['v'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['localRun'].widget.set(0, run=False) PrepareReceptorOpalService_ws_nbcr_net_14.inputPortByName['execPath'].widget.set(r"", run=False) apply(PrepareReceptorOpalService_ws_nbcr_net_14.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) from WebServices.VisionInterface.WSNodes import GetURLFromListNode GetURLFromList_15 = GetURLFromListNode(constrkw={}, name='GetURLFromList', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(GetURLFromList_15,180,186) GetURLFromList_15.inputPortByName['ext'].widget.set(r"pdbqt", run=False) apply(GetURLFromList_15.configure, (), {'paramPanelImmediate': 1}) from WebServices.VisionInterface.WSNodes import DownloadToFileNode DownloadToFile_16 = DownloadToFileNode(constrkw={}, name='DownloadToFile', library=wslib) PrepareReceptorWS_10.macroNetwork.addNode(DownloadToFile_16,80,272) apply(DownloadToFile_16.inputPortByName['url'].configure, (), {'defaultValue': None}) apply(DownloadToFile_16.inputPortByName['filename'].configure, (), {'defaultValue': None}) DownloadToFile_16.inputPortByName['url'].rebindWidget() DownloadToFile_16.inputPortByName['url'].widget.set(r"", run=False) DownloadToFile_16.inputPortByName['url'].unbindWidget() DownloadToFile_16.inputPortByName['filename'].rebindWidget() DownloadToFile_16.inputPortByName['filename'].widget.set(r"", run=False) DownloadToFile_16.inputPortByName['filename'].unbindWidget() DownloadToFile_16.inputPortByName['overwrite'].widget.set(1, run=False) apply(DownloadToFile_16.configure, (), {'paramPanelImmediate': 1}) from Vision.StandardNodes import Generic UpdateReceptor_17 = Generic(constrkw={}, name='UpdateReceptor', library=stdlib) PrepareReceptorWS_10.macroNetwork.addNode(UpdateReceptor_17,46,358) apply(UpdateReceptor_17.addInputPort, (), {'singleConnection': True, 'name': 'receptor_obj', 'cast': True, 'datatype': 'receptor', 'defaultValue': None, 'required': True, 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#99FF33', 'originalDatatype': 'None'}) apply(UpdateReceptor_17.addInputPort, (), {'singleConnection': True, 'name': 'pdbqt', 'cast': True, 'datatype': 'string', 'defaultValue': None, 'required': False, 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white', 'originalDatatype': 'None'}) apply(UpdateReceptor_17.addOutputPort, (), {'name': 'receptor_prepared_obj', 'datatype': 'receptor_prepared', 'height': 8, 'width': 12, 'shape': 'triangle', 'color': '#009900'}) apply(UpdateReceptor_17.addOutputPort, (), {'name': 'receptor_result', 'datatype': 'string', 'height': 8, 'width': 12, 'shape': 'oval', 'color': 'white'}) code = """def doit(self, receptor_obj, pdbqt): from AutoDockTools.VisionInterface.Adt.receptor_prepared import receptor_prepared if pdbqt != '''no data yet''': receptor_prepared_obj = receptor_prepared(pdbqt) receptor_obj.set_ext_loc(pdbqt) receptor_result = pdbqt else: pdbqt_org = receptor_obj.get_ext_loc('''pdbqt''') receptor_prepared_obj = receptor_prepared(pdbqt_org) receptor_result = pdbqt_org pass self.outputData(receptor_prepared_obj = receptor_prepared_obj, receptor_result=receptor_result) """ UpdateReceptor_17.configure(function=code) apply(UpdateReceptor_17.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) ## saving connections for network PrepareReceptorWS ## PrepareReceptorWS_10.macroNetwork.freeze() input_Ports_11 = PrepareReceptorWS_10.macroNetwork.ipNode if input_Ports_11 is not None and CheckFileFormat_13 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( input_Ports_11, CheckFileFormat_13, "new", "value", blocking=True , splitratio=[0.64907843562020084, 0.47057253960060474]) except: print "WARNING: failed to restore connection between input_Ports_11 and CheckFileFormat_13 in network PrepareReceptorWS_10.macroNetwork" if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_url", "url", blocking=True , splitratio=[0.6171192646814192, 0.42883431331137822]) except: print "WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork" if CheckFileFormat_13 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, PrepareReceptorOpalService_ws_nbcr_net_14, "receptor_local", "r", blocking=True , splitratio=[0.66136144381723583, 0.28482114514549767]) except: print "WARNING: failed to restore connection between CheckFileFormat_13 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork" if input_Ports_11 is not None and PrepareReceptorOpalService_ws_nbcr_net_14 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( input_Ports_11, PrepareReceptorOpalService_ws_nbcr_net_14, "new", "C", blocking=True , splitratio=[0.53817543437956172, 0.61119702937572407]) except: print "WARNING: failed to restore connection between input_Ports_11 and PrepareReceptorOpalService_ws_nbcr_net_14 in network PrepareReceptorWS_10.macroNetwork" if PrepareReceptorOpalService_ws_nbcr_net_14 is not None and GetURLFromList_15 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( PrepareReceptorOpalService_ws_nbcr_net_14, GetURLFromList_15, "result", "urllist", blocking=True , splitratio=[0.43369347916867251, 0.26566786648658042]) except: print "WARNING: failed to restore connection between PrepareReceptorOpalService_ws_nbcr_net_14 and GetURLFromList_15 in network PrepareReceptorWS_10.macroNetwork" if GetURLFromList_15 is not None and DownloadToFile_16 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( GetURLFromList_15, DownloadToFile_16, "url", "url", blocking=True , splitratio=[0.70502483723033316, 0.71683158018466053]) except: print "WARNING: failed to restore connection between GetURLFromList_15 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork" if CheckFileFormat_13 is not None and DownloadToFile_16 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, DownloadToFile_16, "download_loc", "filename", blocking=True , splitratio=[0.60455581032885575, 0.35606890231085681]) except: print "WARNING: failed to restore connection between CheckFileFormat_13 and DownloadToFile_16 in network PrepareReceptorWS_10.macroNetwork" if CheckFileFormat_13 is not None and UpdateReceptor_17 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( CheckFileFormat_13, UpdateReceptor_17, "receptor_obj", "receptor_obj", blocking=True , splitratio=[0.74908230670336207, 0.38226563370205602]) except: print "WARNING: failed to restore connection between CheckFileFormat_13 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork" if DownloadToFile_16 is not None and UpdateReceptor_17 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( DownloadToFile_16, UpdateReceptor_17, "filename", "pdbqt", blocking=True , splitratio=[0.38698393490575966, 0.2874426709930199]) except: print "WARNING: failed to restore connection between DownloadToFile_16 and UpdateReceptor_17 in network PrepareReceptorWS_10.macroNetwork" output_Ports_12 = PrepareReceptorWS_10.macroNetwork.opNode if UpdateReceptor_17 is not None and output_Ports_12 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( UpdateReceptor_17, output_Ports_12, "receptor_prepared_obj", "new", blocking=True , splitratio=[0.69589857263374943, 0.59566078506240416]) except: print "WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork" if UpdateReceptor_17 is not None and output_Ports_12 is not None: try: PrepareReceptorWS_10.macroNetwork.connectNodes( UpdateReceptor_17, output_Ports_12, "receptor_result", "new", blocking=True , splitratio=[0.44926362052272689, 0.38628711158860896]) except: print "WARNING: failed to restore connection between UpdateReceptor_17 and output_Ports_12 in network PrepareReceptorWS_10.macroNetwork" PrepareReceptorWS_10.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_11.outputPorts[1].configure(name='CheckFileFormat_value') input_Ports_11.outputPorts[2].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C') ## modifying MacroOutputNode dynamic ports output_Ports_12.inputPorts[1].configure(singleConnection='auto') output_Ports_12.inputPorts[2].configure(singleConnection='auto') output_Ports_12.inputPorts[1].configure(name='UpdateReceptor_receptor_prepared_obj') output_Ports_12.inputPorts[2].configure(name='UpdateReceptor_receptor_result') PrepareReceptorWS_10.inputPorts[0].configure(name='CheckFileFormat_value') PrepareReceptorWS_10.inputPorts[0].configure(datatype='receptor') PrepareReceptorWS_10.inputPorts[1].configure(name='PrepareReceptorOpalService_ws_nbcr_net_C') PrepareReceptorWS_10.inputPorts[1].configure(datatype='boolean') ## configure MacroNode input ports PrepareReceptorWS_10.outputPorts[0].configure(name='UpdateReceptor_receptor_prepared_obj') PrepareReceptorWS_10.outputPorts[0].configure(datatype='receptor_prepared') PrepareReceptorWS_10.outputPorts[1].configure(name='UpdateReceptor_receptor_result') PrepareReceptorWS_10.outputPorts[1].configure(datatype='string') ## configure MacroNode output ports PrepareReceptorWS_10.shrink() apply(PrepareReceptorWS_10.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore MacroNode named PrepareReceptorWS in network self.macroNetwork" print_exc() PrepareReceptorWS_10=None #self.macroNetwork.run() self.macroNetwork.freeze() ## saving connections for network PrepareReceptor ## input_Ports_1 = self.macroNetwork.ipNode Pdb2pqrWS_3 = self.macroNetwork.nodes[2] if input_Ports_1 is not None and Pdb2pqrWS_3 is not None: try: self.macroNetwork.connectNodes( input_Ports_1, Pdb2pqrWS_3, "new", "CheckFileFormat_value", blocking=True , splitratio=[0.73531020066010289, 0.24042404972613104]) except: print "WARNING: failed to restore connection between input_Ports_1 and Pdb2pqrWS_3 in network self.macroNetwork" PrepareReceptorWS_10 = self.macroNetwork.nodes[3] if Pdb2pqrWS_3 is not None and PrepareReceptorWS_10 is not None: try: self.macroNetwork.connectNodes( Pdb2pqrWS_3, PrepareReceptorWS_10, "UpdateReceptor_receptor_obj", "CheckFileFormat_value", blocking=True , splitratio=[0.54479169827535734, 0.4847384502006486]) except: print "WARNING: failed to restore connection between Pdb2pqrWS_3 and PrepareReceptorWS_10 in network self.macroNetwork" if input_Ports_1 is not None and PrepareReceptorWS_10 is not None: try: self.macroNetwork.connectNodes( input_Ports_1, PrepareReceptorWS_10, "new", "PrepareReceptorOpalService_ws_nbcr_net_C", blocking=True , splitratio=[0.37730151685222141, 0.48897820190498614]) except: print "WARNING: failed to restore connection between input_Ports_1 and PrepareReceptorWS_10 in network self.macroNetwork" output_Ports_2 = self.macroNetwork.opNode if PrepareReceptorWS_10 is not None and output_Ports_2 is not None: try: self.macroNetwork.connectNodes( PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_prepared_obj", "new", blocking=True , splitratio=[0.64110508898616414, 0.45535290355389196]) except: print "WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork" if PrepareReceptorWS_10 is not None and output_Ports_2 is not None: try: self.macroNetwork.connectNodes( PrepareReceptorWS_10, output_Ports_2, "UpdateReceptor_receptor_result", "new", blocking=True , splitratio=[0.45846842546122241, 0.44240009354017412]) except: print "WARNING: failed to restore connection between PrepareReceptorWS_10 and output_Ports_2 in network self.macroNetwork" self.macroNetwork.runOnNewData.value = False ## modifying MacroInputNode dynamic ports input_Ports_1 = self.macroNetwork.ipNode input_Ports_1.outputPorts[1].configure(name='Pdb2pqrWS_CheckFileFormat_value') input_Ports_1.outputPorts[2].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C') ## modifying MacroOutputNode dynamic ports output_Ports_2 = self.macroNetwork.opNode output_Ports_2.inputPorts[1].configure(singleConnection='auto') output_Ports_2.inputPorts[2].configure(singleConnection='auto') output_Ports_2.inputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj') output_Ports_2.inputPorts[2].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result') ## configure MacroNode input ports PrepareReceptor_0.inputPorts[0].configure(name='Pdb2pqrWS_CheckFileFormat_value') PrepareReceptor_0.inputPorts[0].configure(datatype='receptor') PrepareReceptor_0.inputPorts[1].configure(name='PrepareReceptorWS_PrepareReceptorOpalService_ws_nbcr_net_C') PrepareReceptor_0.inputPorts[1].configure(datatype='boolean') ## configure MacroNode output ports PrepareReceptor_0.outputPorts[0].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_prepared_obj') PrepareReceptor_0.outputPorts[0].configure(datatype='receptor_prepared') PrepareReceptor_0.outputPorts[1].configure(name='PrepareReceptorWS_UpdateReceptor_receptor_result') PrepareReceptor_0.outputPorts[1].configure(datatype='string') PrepareReceptor_0.shrink() ## reset modifications ## PrepareReceptor_0.resetTags() PrepareReceptor_0.buildOriginalList()
blocking=True, splitratio=[0.42861758851787812, 0.59732773543810935]) except: print "WARNING: failed to restore connection between if_101 and rename_stdout_100 in network SaveNAMDResults_92.macroNetwork" SaveNAMDResults_92.macroNetwork.unfreeze() ## modifying MacroInputNode dynamic ports input_Ports_93.outputPorts[1].configure(name='GetOutURLs_url') input_Ports_93.outputPorts[2].configure(name='GetOutURLs_filename') SaveNAMDResults_92.inputPorts[0].configure(name='GetOutURLs_url') SaveNAMDResults_92.inputPorts[0].configure(datatype='string') SaveNAMDResults_92.inputPorts[1].configure(name='GetOutURLs_filename') SaveNAMDResults_92.inputPorts[1].configure(datatype='string') ## configure MacroNode input ports ## configure MacroNode output ports SaveNAMDResults_92.shrink() apply(SaveNAMDResults_92.configure, (), { 'paramPanelImmediate': 1, 'expanded': False }) except: print "WARNING: failed to restore MacroNode named SaveNAMDResults in network masterNet" print_exc() SaveNAMDResults_92 = None try: ## saving node NamdWS ## from NetworkEditor.macros import MacroNode NamdWS_102 = MacroNode(name='NamdWS') masterNet.addNode(NamdWS_102, 455, 294) output_Ports_104 = NamdWS_102.macroNetwork.opNode