Valence Checker

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

: Table containing molecule or reaction structures.

Output Ports

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

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Installation

To use this node in KNIME, install the extension Indigo KNIME integration 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: EPAM Systems, Inc.

Plugin version: 2.1.0.v202404021236

On NodePit since: 2023-12-06

Last update: 2024-04-23

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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