GromosCluster_0.inputPorts[3].configure(datatype='string') ## configure MacroNode input ports GromosCluster_0.outputPorts[0].configure(name='DownloadSaveDir_output') GromosCluster_0.outputPorts[0].configure(datatype='string') ## configure MacroNode output ports GromosCluster_0.shrink() apply(GromosCluster_0.configure, (), {'paramPanelImmediate': 1, 'expanded': False}) except: print "WARNING: failed to restore GromosCluster named GromosCluster in network masterNet" print_exc() GromosCluster_0=None try: ## saving node TrajectoryPDBFile ## from Vision.StandardNodes import FileBrowserNE TrajectoryPDBFile_7 = FileBrowserNE(constrkw={}, name='TrajectoryPDBFile', library=stdlib) masterNet.addNode(TrajectoryPDBFile_7,88,47) TrajectoryPDBFile_7.inputPortByName['filename'].widget.set(r"GROMOSClustering_0.1_input/trajectory.pdb", run=False) apply(TrajectoryPDBFile_7.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore FileBrowserNE named TrajectoryPDBFile in network masterNet" print_exc() TrajectoryPDBFile_7=None try: ## saving node ActiveResidueFile ## from Vision.StandardNodes import FileBrowserNE ActiveResidueFile_8 = FileBrowserNE(constrkw={}, name='ActiveResidueFile', library=stdlib) masterNet.addNode(ActiveResidueFile_8,412,46) ActiveResidueFile_8.inputPortByName['filename'].widget.set(r"GROMOSClustering_0.1_input/activeSiteResidue.pdb", run=False) apply(ActiveResidueFile_8.configure, (), {'paramPanelImmediate': 1})
def afterAddingToNetwork(self): from NetworkEditor.macros import MacroNode MacroNode.afterAddingToNetwork(self) ## loading libraries ## from AutoDockTools.VisionInterface.AdtNodes import adtlib from MolKit.VisionInterface.MolKitNodes import molkitlib from Vision.StandardNodes import stdlib ## building macro network ## AD3Dpf_6 = self from traceback import print_exc ## loading libraries ## from AutoDockTools.VisionInterface.AdtNodes import adtlib self.macroNetwork.getEditor().addLibraryInstance( adtlib, "AutoDockTools.VisionInterface.AdtNodes", "adtlib") 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_7 = self.macroNetwork.ipNode input_Ports_7.move(158, 4) except: print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork" print_exc() input_Ports_7 = None try: ## saving node output Ports ## output_Ports_8 = self.macroNetwork.opNode output_Ports_8.move(172, 322) except: print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork" print_exc() output_Ports_8 = None try: ## saving node Docking Parameter File Browser ## from AutoDockTools.VisionInterface.AdtNodes import DockingParameterFileBrowserNE Docking_Parameter_File_Browser_9 = DockingParameterFileBrowserNE( constrkw={}, name='Docking Parameter File Browser', library=adtlib) self.macroNetwork.addNode(Docking_Parameter_File_Browser_9, 204, 93) apply( Docking_Parameter_File_Browser_9.inputPortByName['filename']. configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Docking_Parameter_File_Browser_9.outputPortByName['filename']. configure, (), { 'color': 'white', 'shape': 'oval' }) Docking_Parameter_File_Browser_9.inputPortByName[ 'filename'].widget.set("/mgl/work4/rhuey/dev23/NEWTEST.dpf", run=False) except: print "WARNING: failed to restore DockingParameterFileBrowserNE named Docking Parameter File Browser in network self.macroNetwork" print_exc() Docking_Parameter_File_Browser_9 = None try: ## saving node Prepare AD3Dpf ## from AutoDockTools.VisionInterface.AdtNodes import AdtPrepareDpf3 Prepare_AD3Dpf_10 = AdtPrepareDpf3(constrkw={}, name='Prepare AD3Dpf', library=adtlib) self.macroNetwork.addNode(Prepare_AD3Dpf_10, 170, 266) apply( Prepare_AD3Dpf_10.inputPortByName['ligand_filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Dpf_10.inputPortByName['receptor_filename']. configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Prepare_AD3Dpf_10.inputPortByName['dpf_filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Prepare_AD3Dpf_10.inputPortByName['parameters'].configure, (), { 'color': 'cyan', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Dpf_10.inputPortByName['outputfilename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Dpf_10.outputPortByName['ad3_parameter_file']. configure, (), { 'color': 'white', 'shape': 'oval' }) except: print "WARNING: failed to restore AdtPrepareDpf3 named Prepare AD3Dpf in network self.macroNetwork" print_exc() Prepare_AD3Dpf_10 = None try: ## saving node Read Molecule ## from MolKit.VisionInterface.MolKitNodes import ReadMolecule Read_Molecule_11 = ReadMolecule(constrkw={}, name='Read Molecule', library=molkitlib) self.macroNetwork.addNode(Read_Molecule_11, 94, 51) apply(Read_Molecule_11.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Read_Molecule_11.outputPortByName['MolSets'].configure, (), { 'color': '#c64e70', 'shape': 'oval' }) except: print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork" print_exc() Read_Molecule_11 = None try: ## saving node Read Molecule ## from MolKit.VisionInterface.MolKitNodes import ReadMolecule Read_Molecule_12 = ReadMolecule(constrkw={}, name='Read Molecule', library=molkitlib) self.macroNetwork.addNode(Read_Molecule_12, 187, 47) apply(Read_Molecule_12.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Read_Molecule_12.outputPortByName['MolSets'].configure, (), { 'color': '#c64e70', 'shape': 'oval' }) except: print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork" print_exc() Read_Molecule_12 = None try: ## saving node File Browser ## from Vision.StandardNodes import FileBrowserNE File_Browser_13 = FileBrowserNE(constrkw={}, name='File Browser', library=stdlib) self.macroNetwork.addNode(File_Browser_13, 286, 143) apply(File_Browser_13.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(File_Browser_13.outputPortByName['filename'].configure, (), { 'color': 'white', 'shape': 'oval' }) except: print "WARNING: failed to restore FileBrowserNE named File Browser in network self.macroNetwork" print_exc() File_Browser_13 = None self.macroNetwork.freeze() ## saving connections for network AD3Dpf ## if Docking_Parameter_File_Browser_9 is not None and Prepare_AD3Dpf_10 is not None: try: self.macroNetwork.connectNodes( Docking_Parameter_File_Browser_9, Prepare_AD3Dpf_10, "filename", "dpf_filename", blocking=True) except: print "WARNING: failed to restore connection between Docking_Parameter_File_Browser_9 and Prepare_AD3Dpf_10 in network self.macroNetwork" if Read_Molecule_11 is not None and Prepare_AD3Dpf_10 is not None: try: self.macroNetwork.connectNodes(Read_Molecule_11, Prepare_AD3Dpf_10, "MolSets", "ligand_filename", blocking=True) except: print "WARNING: failed to restore connection between Read_Molecule_11 and Prepare_AD3Dpf_10 in network self.macroNetwork" if Read_Molecule_12 is not None and Prepare_AD3Dpf_10 is not None: try: self.macroNetwork.connectNodes(Read_Molecule_12, Prepare_AD3Dpf_10, "MolSets", "receptor_filename", blocking=True) except: print "WARNING: failed to restore connection between Read_Molecule_12 and Prepare_AD3Dpf_10 in network self.macroNetwork" if File_Browser_13 is not None and Prepare_AD3Dpf_10 is not None: try: self.macroNetwork.connectNodes(File_Browser_13, Prepare_AD3Dpf_10, "filename", "outputfilename", blocking=True) except: print "WARNING: failed to restore connection between File_Browser_13 and Prepare_AD3Dpf_10 in network self.macroNetwork" output_Ports_8 = self.macroNetwork.opNode if Prepare_AD3Dpf_10 is not None and output_Ports_8 is not None: try: self.macroNetwork.connectNodes(Prepare_AD3Dpf_10, output_Ports_8, "ad3_parameter_file", "new", blocking=True) except: print "WARNING: failed to restore connection between Prepare_AD3Dpf_10 and output_Ports_8 in network self.macroNetwork" self.macroNetwork.unfreeze() AD3Dpf_6.shrink() ## reset modifications ## AD3Dpf_6.resetTags() AD3Dpf_6.buildOriginalList()
def afterAddingToNetwork(self): from NetworkEditor.macros import MacroNode MacroNode.afterAddingToNetwork(self) ## loading libraries ## from AutoDockTools.VisionInterface.AdtNodes import adtlib from MolKit.VisionInterface.MolKitNodes import molkitlib from Vision.StandardNodes import stdlib ## building macro network ## AD3Gpf_15 = self from traceback import print_exc ## loading libraries ## from AutoDockTools.VisionInterface.AdtNodes import adtlib self.macroNetwork.getEditor().addLibraryInstance( adtlib, "AutoDockTools.VisionInterface.AdtNodes", "adtlib") 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_16 = self.macroNetwork.ipNode except: print "WARNING: failed to restore MacroInputNode named input Ports in network self.macroNetwork" print_exc() input_Ports_16 = None try: ## saving node output Ports ## output_Ports_17 = self.macroNetwork.opNode except: print "WARNING: failed to restore MacroOutputNode named output Ports in network self.macroNetwork" print_exc() output_Ports_17 = None try: ## saving node Grid Parameter File Browser ## from AutoDockTools.VisionInterface.AdtNodes import GridParameterFileBrowserNE Grid_Parameter_File_Browser_18 = GridParameterFileBrowserNE( constrkw={}, name='Grid Parameter File Browser', library=adtlib) self.macroNetwork.addNode(Grid_Parameter_File_Browser_18, 310, 99) apply( Grid_Parameter_File_Browser_18.inputPortByName['filename']. configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Grid_Parameter_File_Browser_18.outputPortByName['filename']. configure, (), { 'color': 'white', 'shape': 'oval' }) Grid_Parameter_File_Browser_18.inputPortByName[ 'filename'].widget.set("/mgl/work4/rhuey/dev23/fri2.gpf", run=False) except: print "WARNING: failed to restore GridParameterFileBrowserNE named Grid Parameter File Browser in network self.macroNetwork" print_exc() Grid_Parameter_File_Browser_18 = None try: ## saving node Read Molecule ## from MolKit.VisionInterface.MolKitNodes import ReadMolecule Read_Molecule_19 = ReadMolecule(constrkw={}, name='Read Molecule', library=molkitlib) self.macroNetwork.addNode(Read_Molecule_19, 156, 96) apply(Read_Molecule_19.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Read_Molecule_19.outputPortByName['MolSets'].configure, (), { 'color': '#c64e70', 'shape': 'oval' }) except: print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork" print_exc() Read_Molecule_19 = None try: ## saving node Read Molecule ## from MolKit.VisionInterface.MolKitNodes import ReadMolecule Read_Molecule_20 = ReadMolecule(constrkw={}, name='Read Molecule', library=molkitlib) self.macroNetwork.addNode(Read_Molecule_20, 234, 98) apply(Read_Molecule_20.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Read_Molecule_20.outputPortByName['MolSets'].configure, (), { 'color': '#c64e70', 'shape': 'oval' }) except: print "WARNING: failed to restore ReadMolecule named Read Molecule in network self.macroNetwork" print_exc() Read_Molecule_20 = None try: ## saving node File Browser ## from Vision.StandardNodes import FileBrowserNE File_Browser_21 = FileBrowserNE(constrkw={}, name='File Browser', library=stdlib) self.macroNetwork.addNode(File_Browser_21, 332, 163) apply(File_Browser_21.inputPortByName['filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(File_Browser_21.outputPortByName['filename'].configure, (), { 'color': 'white', 'shape': 'oval' }) except: print "WARNING: failed to restore FileBrowserNE named File Browser in network self.macroNetwork" print_exc() File_Browser_21 = None try: ## saving node Prepare AD3Gpf ## from AutoDockTools.VisionInterface.AdtNodes import AdtPrepareGpf3 Prepare_AD3Gpf_22 = AdtPrepareGpf3(constrkw={}, name='Prepare AD3Gpf', library=adtlib) self.macroNetwork.addNode(Prepare_AD3Gpf_22, 217, 216) apply( Prepare_AD3Gpf_22.inputPortByName['ligand_filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Gpf_22.inputPortByName['receptor_filename']. configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Prepare_AD3Gpf_22.inputPortByName['gpf_filename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply(Prepare_AD3Gpf_22.inputPortByName['parameters'].configure, (), { 'color': 'cyan', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Gpf_22.inputPortByName['outputfilename'].configure, (), { 'color': 'white', 'cast': True, 'shape': 'oval' }) apply( Prepare_AD3Gpf_22.outputPortByName['ag3_parameter_file']. configure, (), { 'color': 'white', 'shape': 'oval' }) except: print "WARNING: failed to restore AdtPrepareGpf3 named Prepare AD3Gpf in network self.macroNetwork" print_exc() Prepare_AD3Gpf_22 = None self.macroNetwork.freeze() ## saving connections for network AD3Gpf ## if Read_Molecule_19 is not None and Prepare_AD3Gpf_22 is not None: try: self.macroNetwork.connectNodes(Read_Molecule_19, Prepare_AD3Gpf_22, "MolSets", "ligand_filename", blocking=True) except: print "WARNING: failed to restore connection between Read_Molecule_19 and Prepare_AD3Gpf_22 in network self.macroNetwork" if Read_Molecule_20 is not None and Prepare_AD3Gpf_22 is not None: try: self.macroNetwork.connectNodes(Read_Molecule_20, Prepare_AD3Gpf_22, "MolSets", "receptor_filename", blocking=True) except: print "WARNING: failed to restore connection between Read_Molecule_20 and Prepare_AD3Gpf_22 in network self.macroNetwork" if Grid_Parameter_File_Browser_18 is not None and Prepare_AD3Gpf_22 is not None: try: self.macroNetwork.connectNodes(Grid_Parameter_File_Browser_18, Prepare_AD3Gpf_22, "filename", "gpf_filename", blocking=True) except: print "WARNING: failed to restore connection between Grid_Parameter_File_Browser_18 and Prepare_AD3Gpf_22 in network self.macroNetwork" if File_Browser_21 is not None and Prepare_AD3Gpf_22 is not None: try: self.macroNetwork.connectNodes(File_Browser_21, Prepare_AD3Gpf_22, "filename", "outputfilename", blocking=True) except: print "WARNING: failed to restore connection between File_Browser_21 and Prepare_AD3Gpf_22 in network self.macroNetwork" output_Ports_17 = self.macroNetwork.opNode if Prepare_AD3Gpf_22 is not None and output_Ports_17 is not None: try: self.macroNetwork.connectNodes(Prepare_AD3Gpf_22, output_Ports_17, "ag3_parameter_file", "new", blocking=True) except: print "WARNING: failed to restore connection between Prepare_AD3Gpf_22 and output_Ports_17 in network self.macroNetwork" self.macroNetwork.unfreeze() AD3Gpf_15.shrink() ## reset modifications ## AD3Gpf_15.resetTags() AD3Gpf_15.buildOriginalList()
AutodockOpalService_kryptonite_nbcr_net_0.inputPortByName[ 'execPath'].widget.set(r"", run=False) apply(AutodockOpalService_kryptonite_nbcr_net_0.configure, (), { 'paramPanelImmediate': 1, 'expanded': False }) except: print "WARNING: failed to restore FunctionNode named AutodockOpalService_kryptonite_nbcr_net in network masterNet" print_exc() AutodockOpalService_kryptonite_nbcr_net_0 = None try: ## saving node Ligand File Browser ## from Vision.StandardNodes import FileBrowserNE Ligand_File_Browser_1 = FileBrowserNE(constrkw={}, name='Ligand File Browser', library=stdlib) masterNet.addNode(Ligand_File_Browser_1, 191, 22) Ligand_File_Browser_1.inputPortByName['filename'].widget.set( r"AutoDockSL_0.1_input/diversity0001.pdbqt", run=False) apply(Ligand_File_Browser_1.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore FileBrowserNE named Ligand File Browser in network masterNet" print_exc() Ligand_File_Browser_1 = None try: ## saving node DLG output name ## from Vision.StandardNodes import EntryNE DLG_output_name_2 = EntryNE(constrkw={}, name='DLG output name',
wslib, "WebServices.VisionInterface.WSNodes", "wslib") masterNet.getEditor().addLibraryInstance(stdlib, "Vision.StandardNodes", "stdlib") from WebServices.VisionInterface.WSNodes import addOpalServerAsCategory try: addOpalServerAsCategory("http://oolitevm.calit2.optiputer.net/opal2", replace=False) except: pass try: ## saving node FileWithCommandOrdering ## from Vision.StandardNodes import FileBrowserNE FileWithCommandOrdering_0 = FileBrowserNE(constrkw={}, name='FileWithCommandOrdering', library=stdlib) masterNet.addNode(FileWithCommandOrdering_0, 30, 10) FileWithCommandOrdering_0.inputPortByName['filename'].widget.set( r"NAMDTeragridGPU_0.1_input/order.txt", run=False) apply(FileWithCommandOrdering_0.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore FileBrowserNE named FileWithCommandOrdering in network masterNet" print_exc() FileWithCommandOrdering_0 = None try: ## saving node GetOrdering ## from Vision.StandardNodes import Generic GetOrdering_1 = Generic(constrkw={}, name='GetOrdering', library=stdlib) masterNet.addNode(GetOrdering_1, 30, 107)
try: ## saving node Output Directory Browser ## from Vision.StandardNodes import DirBrowserNE Output_Directory_Browser_2 = DirBrowserNE(constrkw={}, name='Output Directory Browser', library=stdlib) masterNet.addNode(Output_Directory_Browser_2,715,9) Output_Directory_Browser_2.inputPortByName['directory'].widget.set(r"AMDNBCR_0.2_output", run=False) apply(Output_Directory_Browser_2.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore DirBrowserNE named Output Directory Browser in network masterNet" print_exc() Output_Directory_Browser_2=None try: ## saving node Config File Browser ## from Vision.StandardNodes import FileBrowserNE Config_File_Browser_3 = FileBrowserNE(constrkw={}, name='Config File Browser', library=stdlib) masterNet.addNode(Config_File_Browser_3,67,22) Config_File_Browser_3.inputPortByName['filename'].widget.set(r"AMDNBCR_0.2_input/sample-aMD.conf", run=False) apply(Config_File_Browser_3.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore FileBrowserNE named Config File Browser in network masterNet" print_exc() Config_File_Browser_3=None try: ## saving node AMDws ## from NetworkEditor.macros import MacroNode AMDws_4 = MacroNode(name='AMDws') masterNet.addNode(AMDws_4, 357, 184) output_Ports_6 = AMDws_4.macroNetwork.opNode apply(output_Ports_6.configure, (), {'paramPanelImmediate': 1, 'expanded': False})
name='PublicServerLigandDB', library=Adt) masterNet.addNode(PublicServerLigandDB_1, 419, 38) PublicServerLigandDB_1.inputPortByName['server_lib'].widget.set(r"sample", run=False) apply(PublicServerLigandDB_1.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore PublicServerLigandDB named PublicServerLigandDB in network masterNet" print_exc() PublicServerLigandDB_1 = None try: ## saving node Vina Config File Browser ## from Vision.StandardNodes import FileBrowserNE Vina_Config_File_Browser_2 = FileBrowserNE(constrkw={}, name='Vina Config File Browser', library=stdlib) masterNet.addNode(Vina_Config_File_Browser_2, 798, 32) Vina_Config_File_Browser_2.inputPortByName['filename'].widget.set( r"VinaVSpublic_0.1_input/test.config", run=False) apply(Vina_Config_File_Browser_2.configure, (), {'paramPanelImmediate': 1}) except: print "WARNING: failed to restore FileBrowserNE named Vina Config File Browser in network masterNet" print_exc() Vina_Config_File_Browser_2 = None try: ## saving node PrepareReceptor ## from Adt.Macro.PrepareReceptor import PrepareReceptor PrepareReceptor_3 = PrepareReceptor(constrkw={}, name='PrepareReceptor',
# in1 is known in the scope of the eval function result = eval(command) self.outputData(result=result) """ Image_open_in1__44.configure(function=code) apply(Image_open_in1__44.configure, (), {'expanded': True}) except: print "WARNING: failed to restore Eval named Image.open(in1) in network masterNet" print_exc() Image_open_in1__44 = None try: ## saving node File Browser ## from Vision.StandardNodes import FileBrowserNE File_Browser_45 = FileBrowserNE(constrkw={}, name='File Browser', library=stdlib) masterNet.addNode(File_Browser_45, 55, 17) File_Browser_45.inputPortByName['filename'].widget.set("Data/lena.jpg", run=False) apply(File_Browser_45.configure, (), {'expanded': True}) except: print "WARNING: failed to restore FileBrowserNE named File Browser in network masterNet" print_exc() File_Browser_45 = None try: ## saving node Cast ## from Vision.StandardNodes import Cast Cast_46 = Cast(constrkw={}, name='Cast', library=stdlib) masterNet.addNode(Cast_46, 79, 120)