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Indigo Fingerprint

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

This node calculates Indigo structural fingerprints for 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.
New column name
Name of the fingerprint column in the output table.
Dense representation
Output cell format is DenseBitVectorCell instead of SparseBitVectorCell.
“Similarity” part size in qwords
Size of “similarity” part of a fingerprint (1 qword = 8 bytes; 8 by default).
“Ordinary” part size in qwords
Size of “ordinary” part of a fingerprint (1 qword = 8 bytes; 0 by default).
“Tautomer” part size in qwords
Size of “tautomer” part of a fingerprint (1 qword = 8 bytes; 0 by default).
“Any” part size in qwords
Size of “any” part of a fingerprint (1 qword = 8 bytes; 0 by default).
Include 3-byte “EXT” part
Sets whether to include or not 3-byte “EXT” part of the fingerprint for substructure search, where each bit corresponds to some property: has changes, has 2 halogens, has isotopes, etc.
Similarity fingerprint
Useful for calculating similarity measures (default value).
Substructure fingerprint
Useful for substructure screening (building “ext”, “sub” and “any” part).
Resonance substructure fingerprint
Useful for resonance substructure screening (building “ext” and “any” part).
Tautomer substructure fingerprint
Useful for tautomer substructure screening (building “ext”, “any” and “tau” part).
Full fingerprint
Has all the mentioned fingerprint types included.
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

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Table containing molecule or reaction structures.

Output Ports

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The same as input, plus the fingerprints.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.3

A zipped version of the software site can be downloaded here.

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Developers

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