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Indigo-pains-recursive

Based on simple sub-structure workflow by James Davidson

and recursive-loop filter workflow by Iris
http://tech.knime.org/forum/knime-users/row-filter-with-mulitple-criteria-question#post-27527

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)

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2.80GHz single CPU
KNIME 2.7.4
Indigo nodes 1.1.13.201306111153

time, PAINS/OK
multimatch 33m04s, 697/9303
recursive 29m30s, 697/9303

saving: 10.8%

Top half: various ways to input structures Bottom half: input of PAINS query strings manual entryNode 5use number of rows as iterationsNode 11Node 12Node 14read PAINS fileclean upclean upread smiles fileget structureswrite PAINSView resultsfilter PAINSNode 30write goodNode 32Node 33Node 34Node 35Node 36insert Iterationread SD fileclean uploop startloop endTable Creator Molecule Type Cast Extract TableDimension JPython Function Joiner Column Filter File Reader String Replacer String Replacer File Reader Database Reader CSV Writer Interactive Table ReferenceRow Filter Column Filter CSV Writer Molecule to Indigo SubstructureMatcher Query Moleculeto Indigo Molecule Type Cast Row Filter String Manipulation SDF Reader Column Resorter RecursiveLoop Start Recursive Loop End Top half: various ways to input structures Bottom half: input of PAINS query strings manual entryNode 5use number of rows as iterationsNode 11Node 12Node 14read PAINS fileclean upclean upread smiles fileget structureswrite PAINSView resultsfilter PAINSNode 30write goodNode 32Node 33Node 34Node 35Node 36insert Iterationread SD fileclean uploop startloop endTable Creator Molecule Type Cast Extract TableDimension JPython Function Joiner Column Filter File Reader String Replacer String Replacer File Reader Database Reader CSV Writer Interactive Table ReferenceRow Filter Column Filter CSV Writer Molecule to Indigo SubstructureMatcher Query Moleculeto Indigo Molecule Type Cast Row Filter String Manipulation SDF Reader Column Resorter RecursiveLoop Start Recursive Loop End

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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: 2026-04-03
Created with KNIME version: v3.0.1.0049657
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