Chemical Identifier Resolver for KNIME (trusted extension)

About the nodes

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 one to convert a given structure identifier into another representation or structure identifier.

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;
  • chemspider_id - ChemSpider ID (input must be 'chemspider_id=1234567').

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;
  • chemspider_id - ChemSpider ID;
  • 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.

Contributors

This node has been developed in collaboration with Kode Chemoinformatics. Kode Chemoinformatics provides services and products in the field of chemoinformatics, for industries (chemical and pharmaceutical) and research (institutions, universities, regulatory authorities). Kode chemoinformatics is the official reseller of Dragon software. Dragon is one of the most known and cited software for the calculation of molecular descriptors.

Installation and source code

Since KNIME 2.9 Chemical Identifier Resolver for KNIME belongs to the Trusted Community Contributions, it can easily be installed by selecting File --> Install KNIME Extensions in KNIME. CIR node can be found in KNIME Community Contributions - Cheminformatics  --> CIR KNIME integration.

The source code can be accessed using KNIME by selecting File --> Install KNIME Extensions.   CIR node source code can be found in KNIME Community Contributions Sources -->  Source for CIR KNIME integration or at https://anonymous:knime@community.knime.org/svn/nodes4knime/trunk/org.talete.

License

The CIR extension is released under LGPLv3.