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RDKIT-pains

Based on simple sub-structure workflow by James Davidson

Modified to use SD file as input, and PAINS strings in SMARTS format from

Rajarshi Guha. "PAINS Substructure Filters as SMARTS. 2010-11-14." http://blog.rguha.net/?p=850. Accessed: 2010-11-14. (Archived by WebCite® at http://www.webcitation.org/5uF4wHEpB)

Top half: various ways to input structures Bottom half: input of PAINS query strings(updated from rdkit.org 20150826) Node 2manual entryNode 5Node 7Node 9Node 10Node 11Node 12Node 13Node 14read PAINS fileclean upclean upread smiles fileget structureswrite PAINSremove duplicatesView resultsfilter PAINSNode 30write goodread SD fileclean upRDKit SubstructureFilter Table Creator Molecule Type Cast RDKit From Molecule Table Row ToVariable Loop Start Loop End JPython Function Joiner Column Rename Column Filter File Reader String Replacer String Replacer File Reader Database Reader CSV Writer GroupBy Interactive Table ReferenceRow Filter Column Filter CSV Writer SDF Reader Column Resorter Top half: various ways to input structures Bottom half: input of PAINS query strings(updated from rdkit.org 20150826) Node 2manual entryNode 5Node 7Node 9Node 10Node 11Node 12Node 13Node 14read PAINS fileclean upclean upread smiles fileget structureswrite PAINSremove duplicatesView resultsfilter PAINSNode 30write goodread SD fileclean upRDKit SubstructureFilter Table Creator Molecule Type Cast RDKit From Molecule Table Row ToVariable Loop Start Loop End JPython Function Joiner Column Rename Column Filter File Reader String Replacer String Replacer File Reader Database Reader CSV Writer GroupBy Interactive Table ReferenceRow Filter Column Filter CSV Writer SDF Reader Column Resorter

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: sauberns
On NodePit since: 2019-06-17
Last update: 2024-04-20
Created with KNIME version: v3.0.1.0049657
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