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InChi
Indigo extensions for KNIME Workbench version 2.0.0.qualifier by EPAM Systems, Inc.
This node takes a table containing a column with molecules as a target and append new column with these objects in InChi format and, if required, with InChiKey representation(both column types are String).
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.
- InChi column
- The column that contains molecules in the InChi format.
- Append InChiKey column
- Name for the InChiKey column that contains InChiKey molecule's representation.
- 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
Output Ports
- The same as input, but with a new string column containing InChi representations. One more column with corresponding InChiKey representation can be appended as well.
Best Friends (Incoming)
- RDKit To Molecule (12 %) Streamable
- Molecule Type Cast (8 %) Streamable
- SDF Reader (7 %)
- Standardizer (5 %)
- MolConverter (5 %) Streamable
- Concatenate (5 %) Streamable
- Column Filter (5 %) Streamable
- ChemSpider (3 %)
- Column Rename (3 %) Streamable
- Atom Replacer (2 %)
- Aromatizer (2 %)
- Canonical SMILES (2 %)
- Hydrogen Remover (2 %)
- Molecule Properties (2 %)
PDB Downloader (Source)(2 %) StreamableDeprecated- Advanced MolConverter (2 %) Streamable
- MarvinSketch (2 %)
- File Reader (2 %) Streamable
- Nominal Value Row Filter (2 %) Streamable
- Row Filter (2 %) Streamable
- Reference Row Filter (2 %)
- Reference Row Splitter (2 %)
- GroupBy (2 %)
- Joiner (2 %)
- RowID (2 %) Streamable
- Ungroup (2 %) Streamable
- Rule-based Row Splitter (2 %) Streamable
- OpenBabel (2 %)
Excel Reader (XLS)(2 %) StreamableDeprecated- Molecule to CDK (2 %)
- RDKit Canon SMILES (2 %) Streamable
- RDKit From Molecule (2 %)
- RDKit One Component Reaction (2 %)
- RDKit To InChI (2 %) Streamable
- RDKit Salt Stripper (2 %)
- CIR (2 %)
- ChEMBLdb Connector Input (2 %)
- Show all 37 recommendations
Best Friends (Outgoing)
- Joiner (18 %)
- GroupBy (12 %)
- Reference Row Filter (7 %)
- Canonical SMILES (5 %)
- Rule-based Row Splitter (5 %) Streamable
- Substructure Match Counter (4 %)
- Column Filter (4 %) Streamable
- Row Splitter (4 %) Streamable
- Reference Row Splitter (4 %)
- Rule-based Row Filter (4 %) Streamable
- RDKit From InChI (4 %) Streamable
- CIR (4 %)
- ChemSpider (2 %)
- Table Row To Variable Loop Start (2 %)
- Concatenate (2 %) Streamable
Concatenate (Optional in)(2 %) StreamableDeprecated- Column Aggregator (2 %) Streamable
- Constant Value Column (2 %) Streamable
- Column Rename (2 %) Streamable
- Renderer to Image (2 %)
- Molecule Type Cast (2 %) Streamable
- Math Formula (2 %) Streamable
- Java Snippet (simple) (2 %)
- Java Snippet Row Splitter (2 %) Streamable
- Molecule to CDK (2 %)
- Fingerprints (2 %)
- RDKit Molecule Extractor (2 %)
- RDKit To InChI (2 %) Streamable
- Show all 28 recommendations
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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