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Molecule Transformation (beta)

Indigo extensions for KNIME Workbench version 2.0.0.qualifier by EPAM Systems, Inc.

This node transforms molecules according to reaction-base set of rules. See the examples for more details.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

The node is based on the Indigo cheminformatics toolkit.

Options

Target molecule column
The column that contains molecule structures.
Query Reaction column
The column that contains Indigo query reactions.
Append Column
Appends a new molecule column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Molecule type
Treat input as: a molecule.
Reaction type
Treat input as a query reaction
Treat X as pseudoatom
Treat the "X" atoms in Molfiles as pseudoatoms, not as "any halogen" query atoms.
Ignore stereochemistry errors
Ignore incorrectly specified stereochemistry on input structures, rather than sending the structures with stereochemistry errors to the "invalid molecules" table.
Treat query reaction as SMARTS
Treat input strings for reaction (port 2) as SMARTS.

Input Ports

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Table containing molecules to transform.
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Table containing query reactions describing transformations.

Output Ports

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The transformed molecules table.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Indigo KNIME integration 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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