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Molecule Properties

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

Create new columns holding molecular properties, computed for each structure. The computations are based on the Indigo toolkit and include number of heavy atoms, molecular weight, number of aromatic atoms, and others.

Supported types:

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

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column
Column containing the molecular structures.
Properties
Move the available properties into the INCLUDE (right) list.
Input type
Treat input as: a molecule.
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.

Input Ports

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Table containing molecule structures.

Output Ports

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As input but with additional columns (one for each calculated property).
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Rows with invalid data: data cannot be translated into Indigo object.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Indigo KNIME integration from the following update site:

KNIME 4.3

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

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Developers

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