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Chemical Identifier Resolver – KNIME

The CIR KNIME Plugin contains a KNIME node that 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 the conversion of a given structure identifier into another representation or structure identifier.


Some useful applications of the node are:

  • prepare your dataset starting from different identifiers
  • cure your dataset identifying erroneous representation of chemical structures
  • get molecular formula and chemical properties starting from different molecule representations

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

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

Example

You can download a simple example workflow of the CIR KNIME Plugin from here.

CIR KNIME

Install

You can install the CIR KNIME Plugin directly with KNIME:

  • Make sure you have an updated version of KNIME (at least 3.7.1)
  • Make sure the “KNIME Community Extensions (Experimental)” (the old name was “Stable Community Contributions”) is present and checked in the list of the Available Software Sites (File -> Preferences -> Install/Update -> Available Software Sites)
  • To install the node click File -> Install KNIME Extensions… and search for CIR
  • The node will be then available in the section Community Nodes -> Alvascience