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.
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.
Contributors
This node has been developed by Alvascience. Alvascience provides services and products in the field of chemoinformatics, for industries (chemical and pharmaceutical) and research (institutions, universities, regulatory authorities).
Installation
You can download the CIR KNIME Plugin directly from KNIME:
- Make sure you’ve 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
License
The CIR extension is released under GPLv3.
