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Reaction Automapper

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

Generates reaction atom-to-atom mappings (AAM).

Supported types:

  • Reaction: String, Rxn, Smiles, CML
  • Query reaction: String, Rxn, Smiles, SMARTS

The node is based on the Indigo cheminformatics toolkit.

Options

Target Column
The column that contains the reactions.
Append Column
Appends a new reaction column (with the name as specified in the text field) if checked, replaces the original column otherwise.
Mode
  • discard : discards the existing mapping entirely and considers only the existing reaction centers (the default)
  • keep : keeps the existing mapping and maps unmapped atoms
  • alter : alters the existing mapping, and maps the rest of the reaction but may change the existing mapping
  • clear : removes the mapping from the reaction
Ignore charges
Skips atom charges from input structures.
Ignore isotopes
Skips atom isotopes from input structures.
Ignore radicals
Skips atom radicals from input structures.
Ignore valence
Skips atom valence from input structures.
Input type
Treat input as: a reaction, a query reaction.
Output reaction type
Result reaction column type.
Input type
Treat input as: a reaction, a query 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.
Treat query reaction as SMARTS
Treat string input for reaction as SMARTS.

Input Ports

Table containing reactions to map.

Output Ports

Table with the successfully mapped reactions.
Table with the reactions that mapped with errors.

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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