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Organic Splitter

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

This node accepts a table with Indigo molecules and splits it into three sets, one with all organic rows, the second with all the rest, the last one gather all the rows with invalid data (with data which cannot be translated into indigo object for some reasons).

Supported types:

  • Molecule: String, SDF, Smiles, CML, Mol, InChI

The node is based on the Indigo cheminformatics toolkit.

Options

Target column
The column that contains molecules.
Interpret alkali metal salts as inorganic molecules
Conditions defining whether consider alkali metal salts as an organic or not. Yes, by default.
Interpret molecules containing d-block elements as inorganic molecules
Conditions defining whether consider molecules containing d-block elements as an organic or not. Yes, by default.
Input type
Treat input as: a molecule.
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 molecules.

Output Ports

Rows with organic molecules.
Rows with inorganic molecules.
Rows with invalid data: data cannot be translated into Indigo object

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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