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Substructure Search

Search a list of target molecules against a set of queries, composed of either molecules or partial structures.

Backend implementation

utilities/canvasSearch
canvasSearch is used to implement this node.

Options

Column in first input containing query molecules

Column of query molecules.

Column in second input containing molecules

Column of target molecules.

Column in second input containing title for smiles

If the first column is Smiles, then this selects the string or integer column which represents the molecule titles.

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaces Input - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Minimum number of matches that must be satisfied

Require the target molecules to match at least n queries (n>=0). By default, all the queries have to be matched.

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

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: CanvasSearch
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

Input Ports

: Query molecules in Smiles, Maestro, or Sd format
: Target molecules in Smiles, Maestro, or Sd format

Output Ports

: Target molecules that passed the filter and matched all or the required number of queries in Smiles (default), Maestro, or Sd format
: Target molecules that do not satisfy the required matches in Smiles (default), Maestro, or Sd format

Views

Std output/error of Substructure Search: Std output/error of Substructure Search

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.3.138.v202407300410

On NodePit since: 2023-12-06

Last update: 2024-11-20

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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