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Atom Replacer

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

This node discards all the labels on structure's atoms and replaces them with the given label. It also discards all stereochemistry from structures.

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.
Append Column
Appends a new structure column (with the name as specified in the text field) if checked, replaces the original column otherwise.
New atom label
The new atom label which will be put on all structure's atoms (default is "*").
Replace only highlighted atoms
With this options only highlighted atoms will be replaced.
Replace specific atom type
With this options only atoms with specified labels will be replaced. Comma-separated list of atoms is supported.
Replace attachment points
With this options only attachment points will be replaced.
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's or reaction's structures as strings or as Indigo objects.

Output Ports

The same as input, with replaced atom labels

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.1
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Developers

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