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Structure Filter

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Filter a list of target molecules using a user-defined file containing SMILES queries and minimum and maximum number of times a query should be matched.

Backend implementation

utilities/canvasSearch
canvasSearch is used to implement this node.

Options

Column in first input containing molecules
Column of target molecules.
Column in first input containing title for smiles
If the first column is Smiles, then this selects the string or integer column which represents the molecule titles.
Select a smiles/smart filter file
User supplied rule file to use. The file must be of the following format: Each line contains one SMARTS/SMILES string, followed by the minimum and maximum number of allowed counts and optional comment surrounded by double-quotes.
File can be an URL like:
knime://LOCAL/path/to/file - knime://LOCAL refers to the current workspace
knime://knime.workflow/path/to/file - knime://knime.workspace refers to the current workflow
Filter file delimiter
Delimiter used to separate each field in filter file.
Maximum number of violations allowed
Maximum number of violations allowed for the rules. By default, this is set to 0.
Output type that contains matches
Type of the first output: Smiles (default), Maestro, or Sd
Output type that contains non-matches
Type of the second output: Smiles (default), Maestro, or Sd

Input Ports

Icon
Target molecules in Smiles (default), Maestro, or Sd format

Output Ports

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Target molecules that passed the filter in Smiles (default), Maestro, or Sd format
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Target molecules filtered out in smiles, Maestro, or Sd format

Views

Std output/error of Structure Filter
Std output/error of Structure Filter

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Schrödinger Extensions for KNIME from the following update site:

KNIME 4.2
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Developers

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