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04.1 Flow Variables 1

Flow Variables

"Flow Variable" exercise for advanced Life Science User Training
- Filtering rows by an attribute value
- Filtering rows by an attribute value that fulfils a condition and that is updated automatically
- substructure search based on a drawn reference molecule

Activity II: Using Flow Variable for Substructure SearchThe goal of this exercise is to find all compounds from the dataset that match a certain substurcture and prepare thedataset within an interactive view including molecule highlighting. The RDKit Substructure Filter node expects a SMARTS to be entered to do thesearch. Use the Table Row to Variable node to pass the the chemical structure drawn inthe Marvin Sketch node to the RDKit Substructure Filter node as a variableSMARTS. To do so, go to the Flow Variable Tab in the RDKit Substructure Filternode and select as smarts value your variable SMARTS. Step 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 2Pass the Flow Variable"SMARTS" to the"smarts_value" in theFlow Variable Tab Step 1.2Use the GroupBy node to group allthe assay for each compound.Groupby "molecule_chembl_id" andcount the "assay_chembl_id".Use the Sorter node to sort bycount of assays in a descendingorder. Step 1.4Use the Row Filter nodewith Column to Test set to"molecule_chembl_id" andselect the Flow Variable"molecule_chembl_id" to useas pattern matching. Step 2.3Use the Row Filter node and connect theFlow Variable port from the ValueSelection Configuration node with theFlow Variable port of the Row Filter node. - Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1Use the Table Reader node toload theChEMBLID228_SERT_ligands.table Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 2.2Use the Value SelectionConfiguration node and set theDefault Column to "assay_chembl_id" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. Activity I: Flow Variables - Filter the compound data to 1. contain the compounds that were tested in the highest number of assays2. contain only compounds tested for AssayID "CHEMBL853187" Step 1.3Use the Table Row toVariable node convert thefirst row of the table to FlowVariables Action needed: Select some compounds!Draw a referencemolecule for the similaritysearch.You can also paste the following sequence:CC(=O)N1CCNCC1Add SMARTS to create a substructuresearchdata/CHEMBLID228_SERT_ligands.table RDKit Canon SMILES RDKit DescriptorCalculation Tile View(JavaScript) MarvinSketch Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader Activity II: Using Flow Variable for Substructure SearchThe goal of this exercise is to find all compounds from the dataset that match a certain substurcture and prepare thedataset within an interactive view including molecule highlighting. The RDKit Substructure Filter node expects a SMARTS to be entered to do thesearch. Use the Table Row to Variable node to pass the the chemical structure drawn inthe Marvin Sketch node to the RDKit Substructure Filter node as a variableSMARTS. To do so, go to the Flow Variable Tab in the RDKit Substructure Filternode and select as smarts value your variable SMARTS. Step 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 2Pass the Flow Variable"SMARTS" to the"smarts_value" in theFlow Variable Tab Step 1.2Use the GroupBy node to group allthe assay for each compound.Groupby "molecule_chembl_id" andcount the "assay_chembl_id".Use the Sorter node to sort bycount of assays in a descendingorder. Step 1.4Use the Row Filter nodewith Column to Test set to"molecule_chembl_id" andselect the Flow Variable"molecule_chembl_id" to useas pattern matching. Step 2.3Use the Row Filter node and connect theFlow Variable port from the ValueSelection Configuration node with theFlow Variable port of the Row Filter node. - Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1Use the Table Reader node toload theChEMBLID228_SERT_ligands.table Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 2.2Use the Value SelectionConfiguration node and set theDefault Column to "assay_chembl_id" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. Activity I: Flow Variables - Filter the compound data to 1. contain the compounds that were tested in the highest number of assays2. contain only compounds tested for AssayID "CHEMBL853187" Step 1.3Use the Table Row toVariable node convert thefirst row of the table to FlowVariables Action needed: Select some compounds!Draw a referencemolecule for the similaritysearch.You can also paste the following sequence:CC(=O)N1CCNCC1Add SMARTS to create a substructuresearchdata/CHEMBLID228_SERT_ligands.table RDKit Canon SMILES RDKit DescriptorCalculation Tile View(JavaScript) MarvinSketch Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader

Nodes

Extensions

Links

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Created by: glandrum
Created at: 2015-02-07
On NodePit since: 2024-03-15
Last update: 2024-11-21
Created with KNIME version: v5.2.2

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