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Bond Replacer

Indigo extensions for KNIME Workbench version 2.0.0.v201603210922 by EPAM Systems, Inc.

This node replaces the structure bond types with a specifed bond type.

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.
Bond order
Bond type to replace by.
Replace only highlighted bonds
Says to replace highlighted bonds as well as other or not.
Input type
Treat input as a molecule or as 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

The same as input, but with bonds replaced

Best Friends (Incoming)

Best Friends (Outgoing)

Update Site

To use this node in KNIME, install Indigo extensions for KNIME Workbench from the following update site:

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