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RDKit Substructure Counter

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

This node is used to calculate the number of times a particular query molecule is present in an input molecule. The number of times the query molecule present in the input molecule can be repeated. It is possible to choose the unique number of times the query molecule is present in the input molecule.

Options

Input

RDKit Mol column
The input column with RDKit Molecules.
Input Query Column
The name of the column in second table containing query molecules which will act as substructure for the input molecules

Search

Count Unique Matches Only?
This option is selected if user requires unique matches of the query molecule in an input molecule.

Output

Instead of query molecules use names as result header titles (and tags)
Select this option to allow the node to use names specified in the query table as column title for the resulting count columns and tags. If disabled, it will use the SMILES or SMARTS value as title.
Column with names for header titles
If the last option is enabled the column with the query names must be selected here.
Add total hits count column
Select this option to add a column that contains the accumulated hits count of all hits.
New column name for total hits count
If the last option is enabled the name for the new column must be specified here.
Add column with tags for matching queries
Select this option to add a column that contains a collection of all tags (SMILES, SMARTS values or tags taken from header titles column) for the matching queries. This can be useful for further processing.
New column name for tags
If the last option is enabled the name for the new column must be specified here.

Input Ports

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Table with input molecule column
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Table with input query column

Output Ports

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Input molecule table with one additional column for each row in the query molecule table. The new columns added contain the number of times that a query molecule is found in the molecule.

Views

Interactive Table View
Displays the data in a table view. Has the capability to show chemical structures in the headers of the substructure count columns.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.2

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

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Developers

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