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3D-e-Chem extension test

A simple and incomplete workflow to test nodes of the 3D-e-chem extension.
Pharmacophore Sygma MolViewer Ligand Viewer1. A 3D representation of 10 molecules is displayed when the Ligand Viewer’s Interactive View isopened.2. Molecules can be rotated in 3D space by holding the left mouse button and moving the pointer.3. Molecules can be translated in 3D space by holding the right mouse button and moving thepointer.4. Zoom in and out using the mouse wheel or equivalent.5. Visualisation of individual molecules can be switched on and off by clicking the button with the"eye" symbol.6. Change the colour of the molecules by clicking the arrow in the Interactive View.7. Automatically centre the molecules by clicking the button with the "target" or "centre" symbol. PROBLEMS/ERRORSUnfortunately it seems that the protein visualization nodes are no longerworking. The same PDB file working in this example (https://github.com/3D-e-Chem/knime-molviewer/tree/master/examples) is currently not working in thisworkflow gifing the following error:ERROR Proteins Viewer 11:24 Execute failed: Column 'PDB' isincompatible, should be column with labels on port proteinsIs it possible that the PDB Loader node changed the way how it parses PDBfiles? It should work with a SMILES as input but it gives thefollowing error:ERROR SyGMa Metabolites 11:66 Execute failed:class org.knime.chem.types.SmilesAdapterCell cannotbe cast to class org.knime.core.data.def.StringCell(org.knime.chem.types.SmilesAdapterCell is in unnamedmodule of loaderorg.eclipse.osgi.internal.loader.EquinoxClassLoader@5f87d15a; org.knime.core.data.def.StringCell is inunnamed module of loaderorg.eclipse.osgi.internal.loader.EquinoxClassLoader@23c05889) visualize ligands(aligned ligands)Node 17Node 18example filesin data dirNode 21select file:3D/10_rand_mol_3D_aligned.sdfNode 23gives errorsNode 25gives errorsselect file:3D/PDB_example.pdbNode 32generatepharmacophoreselect 8th moleculesre-create pharmacophoreselect file:3D/10_rand_mol_3D.sdfNode 41Node 42Node 43Node 44visualize ligands(unaligned ligands)Node 46Node 47extract pharmacophorepointsrepresent pharmacophoreas moleculeNode 51select pharmacophorepoints(remove exclusion spheres)write to a temporarypharmacophore filegeneratepharmacophoreone molecule at at timeotherwise (I don't know why)the Pharmacophore from moleculenode failsNode 60try-catch to avoid possibleproblems in the generationof pharmacophoretry-catch to avoid possibleproblems in the generationof pharmacophorefilter out mols thatfailed to generatea pharmacophoreNode 64read just writtenpharmacophore filegives errorsread a csvfile with SMILESNode 69 Ligands Viewer SDF Reader RowID List Files/Folders Table Rowto Variable Row Filter Path to String(Variable) Proteins Viewer PDB Loader Ligands andProteins Viewer Row Filter Path to String Pharmacophorefrom molecule Row Filter Merge pharmacophorepoints Row Filter Table Rowto Variable Path to String(Variable) RowID SDF Reader Ligands Viewer Alignpharmacophores Table Rowto Variable Extract pharmacophorepoints Pharmacophoreto molecule PharmacophoresViewer Row Filter Pharmacophorewriter Pharmacophorefrom molecule Chunk Loop Start Loop End Try (Data Ports) Catch Errors(Data Ports) Row Filter PharmacophoresViewer Pharmacophorereader SyGMa Metabolites CSV Reader RowID Pharmacophore Sygma MolViewer Ligand Viewer1. A 3D representation of 10 molecules is displayed when the Ligand Viewer’s Interactive View isopened.2. Molecules can be rotated in 3D space by holding the left mouse button and moving the pointer.3. Molecules can be translated in 3D space by holding the right mouse button and moving thepointer.4. Zoom in and out using the mouse wheel or equivalent.5. Visualisation of individual molecules can be switched on and off by clicking the button with the"eye" symbol.6. Change the colour of the molecules by clicking the arrow in the Interactive View.7. Automatically centre the molecules by clicking the button with the "target" or "centre" symbol. PROBLEMS/ERRORSUnfortunately it seems that the protein visualization nodes are no longerworking. The same PDB file working in this example (https://github.com/3D-e-Chem/knime-molviewer/tree/master/examples) is currently not working in thisworkflow gifing the following error:ERROR Proteins Viewer 11:24 Execute failed: Column 'PDB' isincompatible, should be column with labels on port proteinsIs it possible that the PDB Loader node changed the way how it parses PDBfiles? It should work with a SMILES as input but it gives thefollowing error:ERROR SyGMa Metabolites 11:66 Execute failed:class org.knime.chem.types.SmilesAdapterCell cannotbe cast to class org.knime.core.data.def.StringCell(org.knime.chem.types.SmilesAdapterCell is in unnamedmodule of loaderorg.eclipse.osgi.internal.loader.EquinoxClassLoader@5f87d15a; org.knime.core.data.def.StringCell is inunnamed module of loaderorg.eclipse.osgi.internal.loader.EquinoxClassLoader@23c05889) visualize ligands(aligned ligands)Node 17Node 18example filesin data dirNode 21select file:3D/10_rand_mol_3D_aligned.sdfNode 23gives errorsNode 25gives errorsselect file:3D/PDB_example.pdbNode 32generatepharmacophoreselect 8th moleculesre-create pharmacophoreselect file:3D/10_rand_mol_3D.sdfNode 41Node 42Node 43Node 44visualize ligands(unaligned ligands)Node 46Node 47extract pharmacophorepointsrepresent pharmacophoreas moleculeNode 51select pharmacophorepoints(remove exclusion spheres)write to a temporarypharmacophore filegeneratepharmacophoreone molecule at at timeotherwise (I don't know why)the Pharmacophore from moleculenode failsNode 60try-catch to avoid possibleproblems in the generationof pharmacophoretry-catch to avoid possibleproblems in the generationof pharmacophorefilter out mols thatfailed to generatea pharmacophoreNode 64read just writtenpharmacophore filegives errorsread a csvfile with SMILESNode 69 Ligands Viewer SDF Reader RowID List Files/Folders Table Rowto Variable Row Filter Path to String(Variable) Proteins Viewer PDB Loader Ligands andProteins Viewer Row Filter Path to String Pharmacophorefrom molecule Row Filter Merge pharmacophorepoints Row Filter Table Rowto Variable Path to String(Variable) RowID SDF Reader Ligands Viewer Alignpharmacophores Table Rowto Variable Extract pharmacophorepoints Pharmacophoreto molecule PharmacophoresViewer Row Filter Pharmacophorewriter Pharmacophorefrom molecule Chunk Loop Start Loop End Try (Data Ports) Catch Errors(Data Ports) Row Filter PharmacophoresViewer Pharmacophorereader SyGMa Metabolites CSV Reader RowID

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Created by: giovannicincilla
Created at: 2025-07-24
On NodePit since: 2025-07-26
Last update: 2025-07-27
Created with KNIME version: v5.2.6
Tags: test

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