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Valence Checker

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

This node accepts a table with structures and divides it into two sets, one with structures that have correct valencies on atoms, and the other with valence errors.

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI
  • Reaction: String, RXN, SMILES

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column
The column that contains molecule or reaction structures.
Input type
Treat input as: a molecule, a 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.

Input Ports

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Table containing molecule or reaction structures.

Output Ports

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Valid structures are copied as is.
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Invalid structures are supplied with an error message.
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Invalid input data (like missing cells or unconvertible into indigo data). Rows are exactly the same as input.

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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