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Parameter flow variables 1-2

Parameter flow variable use-cases

Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, Shape Screening, MacroModel minimization, Molecule reader, and other nodes.

[Requires (optionally): MacroModel, Phase, LigPrep, Prime] [Keywords: Parameter flow variables, Quick form]

See also the following workflow examples:
- Quantum Mechanical properties
- ESP charges
- Jaguar pKa

Parameter flow variable use-cases:Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the proteinpreparation, Shape Screening, MacroModel minimization, Molecule reader, and other nodes.[Requires (optionally): MacroModel, Phase, LigPrep, Prime] [Keywords: Parameter flow variables, Quick form] See also the following workflow examples:- Quantum Mechanical properties- ESP charges- Jaguar pKa For the node using a Python configuration panel, flow variablescan't be used to control the options in the panel. HoweverParameter flow variables can be used to control the equivalentcommand line options.This is applicable for the following nodes: LigPrep, Glide liganddocking, Shape screening, IFD, Residue scanning, Conformercluster... Similarityhigher than 0.5 -help_classic OPLS 2005 force fieldOutput complexes[configure - Parameter flow variable]Remove waters with less than n H-Bonds to non-waters1bl7 Chains with small molecules mergedif necessaryKNIME wrappersbackend -hUsage messageSome KNIME wrappers (like scripts/mmodCLI.py)utilities/prepwizard(see the backend used in the node description)backend -hUsage messagewith options that can be passed as Parameter flow variablesList1rst structure LigandsUsage messageUsage messageUsage message Usage message(through a Parameter flow variable since the force field is not exposed in the configuration panel)Usage messageUsage message Usage messageMolprint2DMolprint2D/tmp/database.fp Against/tmp/database.fpDescending Similarity NeighborSimilar compoundsMatrixMatrix Hit countNormalizationmodeHit numbers Usage messagePose strainsP38 MAPK (1bl7)FragmentsUsage message Ligand-receptor#atomsReceptor first HTVSUsage message Usage message Usage messageUsage message Usage messageUsage message Docking keywords KNIMEStart-up scriptoptionsKNIME_batch.pyUsagemessageKeep waters,fill loops and minimizeFill side chainsOPLS_2005-merge_ligands_with_chain-merge_waters_with_chainOPLS3Flow variable control(exposed in the control panel)OPLS_2005 increasedscale factorOPLS2005(or OPLS3)-first_occ-all_occ-first_occ-all_occ-epik_metal_bindingusing a Parameter flow variableOld search algorithmandNormalization = "Query structure" ShapeScreen-norm 3Old search algorithmandNormalization = "Query structure" ShapeScreen-norm 3Test each Normalization modeTest each Normalization mode-sort-caprow-filter-ifp-sort-caprow Complexes instead of the protein and ligandsKNIME_batch.py-print_allowedUsagemessagePOSES_PER_LIG 5 Prime MM-GBSA Shape Screening Get Help Table Viewer Glide GridGeneration Java EditVariable (simple) Protein PreparationWizard Extra options Get PDB Split by Structure Table Viewer ChemistryExternal Tool Table Viewer Table Creator Table Creator ChemistryExternal Tool Table Viewer ChemistryExternal Tool Row Filter Extract Properties Run Maestro Molecule Reader(to MAE) Table Viewer Table Viewer Table Viewer Molecule-to-MAE Table Viewer Molecule Reader(to MAE) Prime MM-GBSA Table Viewer Table Viewer Molecule Writer(from MAE) Prime Energy Table Viewer Table Viewer Canvas FingerprintGeneration Canvas FingerprintGeneration Canvas FingerprintWriter GeneratePairwise Matrix Similarity Matrix(from Molecules) Convert Matrixto Table Convert Matrixto Table Generate PairwiseMatrix (2 Inputs) Sorter Column Rename ExtractColumn Header ConstantValue Column Table Viewer Table Viewer Table Viewer Loop End(deprecated) Counting Loop Start(deprecated) Extract Properties Value Counter ConstantValue Column Table Viewer Strain Rescore Table Viewer Table Viewer Glide Grid Reader Molecule Reader(to MAE) Table Viewer Split by Structure Extract Properties Sorter Extract Properties LigPrep Shape Screening Glide LigandDocking Get Help Get Help Get Help Get Help Get Help Get Help Get Help Get Help Get Help Table Viewer Get Help Get Help Table Viewer Get Help Table Viewer Table Viewer Get Help Get Help Table Viewer Table Viewer Get Help Get Help Table Viewer Get Help Table Viewer Protein PreparationWizard String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) Table Row to Variable(deprecated) Table Viewer Get Help Table Viewer String Manipulation(Variable) Parameter flow variable use-cases:Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the proteinpreparation, Shape Screening, MacroModel minimization, Molecule reader, and other nodes.[Requires (optionally): MacroModel, Phase, LigPrep, Prime] [Keywords: Parameter flow variables, Quick form] See also the following workflow examples:- Quantum Mechanical properties- ESP charges- Jaguar pKa For the node using a Python configuration panel, flow variablescan't be used to control the options in the panel. HoweverParameter flow variables can be used to control the equivalentcommand line options.This is applicable for the following nodes: LigPrep, Glide liganddocking, Shape screening, IFD, Residue scanning, Conformercluster... Similarityhigher than 0.5 -help_classic OPLS 2005 force fieldOutput complexes[configure - Parameter flow variable]Remove waters with less than n H-Bonds to non-waters1bl7 Chains with small molecules mergedif necessaryKNIME wrappersbackend -hUsage messageSome KNIME wrappers (like scripts/mmodCLI.py)utilities/prepwizard(see the backend used in the node description)backend -hUsage messagewith options that can be passed as Parameter flow variablesList1rst structure LigandsUsage messageUsage messageUsage message Usage message(through a Parameter flow variable since the force field is not exposed in the configuration panel)Usage messageUsage message Usage messageMolprint2DMolprint2D/tmp/database.fp Against/tmp/database.fpDescending Similarity NeighborSimilar compoundsMatrixMatrix Hit countNormalizationmodeHit numbers Usage messagePose strainsP38 MAPK (1bl7)FragmentsUsage message Ligand-receptor#atomsReceptor first HTVSUsage message Usage message Usage messageUsage message Usage messageUsage message Docking keywords KNIMEStart-up scriptoptionsKNIME_batch.pyUsagemessageKeep waters,fill loops and minimizeFill side chainsOPLS_2005-merge_ligands_with_chain-merge_waters_with_chainOPLS3Flow variable control(exposed in the control panel)OPLS_2005 increasedscale factorOPLS2005(or OPLS3)-first_occ-all_occ-first_occ-all_occ-epik_metal_bindingusing a Parameter flow variableOld search algorithmandNormalization = "Query structure" ShapeScreen-norm 3Old search algorithmandNormalization = "Query structure" ShapeScreen-norm 3Test each Normalization modeTest each Normalization mode-sort-caprow-filter-ifp-sort-caprow Complexes instead of the protein and ligandsKNIME_batch.py-print_allowedUsagemessagePOSES_PER_LIG 5Prime MM-GBSA Shape Screening Get Help Table Viewer Glide GridGeneration Java EditVariable (simple) Protein PreparationWizard Extra options Get PDB Split by Structure Table Viewer ChemistryExternal Tool Table Viewer Table Creator Table Creator ChemistryExternal Tool Table Viewer ChemistryExternal Tool Row Filter Extract Properties Run Maestro Molecule Reader(to MAE) Table Viewer Table Viewer Table Viewer Molecule-to-MAE Table Viewer Molecule Reader(to MAE) Prime MM-GBSA Table Viewer Table Viewer Molecule Writer(from MAE) Prime Energy Table Viewer Table Viewer Canvas FingerprintGeneration Canvas FingerprintGeneration Canvas FingerprintWriter GeneratePairwise Matrix Similarity Matrix(from Molecules) Convert Matrixto Table Convert Matrixto Table Generate PairwiseMatrix (2 Inputs) Sorter Column Rename ExtractColumn Header ConstantValue Column Table Viewer Table Viewer Table Viewer Loop End(deprecated) Counting Loop Start(deprecated) Extract Properties Value Counter ConstantValue Column Table Viewer Strain Rescore Table Viewer Table Viewer Glide Grid Reader Molecule Reader(to MAE) Table Viewer Split by Structure Extract Properties Sorter Extract Properties LigPrep Shape Screening Glide LigandDocking Get Help Get Help Get Help Get Help Get Help Get Help Get Help Get Help Get Help Table Viewer Get Help Get Help Table Viewer Get Help Table Viewer Table Viewer Get Help Get Help Table Viewer Table Viewer Get Help Get Help Table Viewer Get Help Table Viewer Protein PreparationWizard String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) String Manipulation(Variable) Table Row to Variable(deprecated) Table Viewer Get Help Table Viewer String Manipulation(Variable)

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On NodePit since: 2020-08-12
Last update: 2024-11-18
Created with KNIME version: v4.5.1
Tags: LabsMacroModelPhaseLigPrepPrimeParameter flow variablesQuick form

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