CIR

This node uses the network service CIR (Chemical Identifier Resolver) by the CADD Group at the NCI/NIH as a resolver for different chemical structure identifiers and allows to convert a given structure identifier into another representation or structure identifier.

Options

Select chemical structure identifier column

The column in the input data table that contains the molecule representation.

The input structure identifier type can be one of the following:
- stdinchi - Standard InChI (input must be 'InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H');
- stdinchikey - Standard InChIKey;
- smiles - SMILES of the Structure;
- ficts - NCI/CADD FICTS Identifier;
- ficus - NCI/CADD FICuS Identifier;
- uuuuu - NCI/CADD uuuuu Identifier;
- hashisy - CACTVS HASHISY Hashcode;
- name - Chemical Name for the Structure;
- iupac_name - IUPAC Name;
- cas - CAS Registry Number.

Output format

New structure representation.

The output structure identifier type can be one of the following:
- stdinchi - Standard InChI;
- stdinchikey - Standard InChIKey;
- smiles - SMILES of the Structure;
- ficts - NCI/CADD FICTS Identifier;
- ficus - NCI/CADD FICuS Identifier;
- uuuuu - NCI/CADD uuuuu Identifier;
- hashisy - CACTVS HASHISY Hashcode;
- sdf - SD File of the Structure;
- names - List of Chemical Names for the Structure;
- iupac_name - IUPAC Name;
- cas - CAS Registry Number;
- mw - Molecular Weight;
- formula - Chemical Formula;
- h_bond_donor_count - Number of Hydrogen Bond Donors;
- h_bond_acceptor_count - Number of Hydrogen Bond Acceptors;
- h_bond_center_count - Number of Hydrogen Bond Acceptors and Donors;
- rule_of_5_violation_count - Number of Rule of 5 Violations;
- rotor_count - Number of Freely Rotatable Bonds;
- effective_rotor_count - Number of Effectively Rotatable Bonds;
- ring_count - Number of Rings;
- ringsys_count - Number of Ring Systems.

Sometimes an input structure identifier can return multiple results (e.g. output as structure names or CAS). The query function will return every result.

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Workflows

• Bioactive compound libraryKNIME Hub
• Convert_InChiKeyTOsmileKNIME Hub
• SmilesTO_InChIKey_toIUPACnameKNIME Hub

Links

• Chemical Namesby elsamuel on 2020-09-29

  forum.knime.com/p/104311
• InCHi to a SMILESby andrea.mauri on 2019-03-04

  forum.knime.com/p/55550
• Errors with RDkit and Vernalis after latest updatesby Alkaline on 2019-07-08

  forum.knime.com/p/64748

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