fak / names2ids

This script uses Cameron Neylon's (cameronneylon) chemspipy.py and Matt Swain's (mcs07) CIRpy to convert compound names to chemical identifiers.

This script uses Cameron Neylon's chemspipy.py and Matt Swain's CIRpy to convert a compound name into a chemical identifier. The output format can be specified (eg 'smiles', 'stdinchikey'...)

The script operates in three steps:

• CIRpy to query the NCI structure resolver
• chemspipy.py to queryChemspider
• CIRpy to query the NCI resolver with pattern matching enabled

The first successful match is returned as the first part of tuple, the second part indicating the matching step ['NCI', 'ChemSpi', 'NCI-pattern-match']. Needless to mention that the confidence for matches labelled 'NCI-pattern-match' is a bit lower compared to 'NCI' and 'ChemSpi'.

For the script to work, you need a token from Chemspider, stored as a plain-text string in the file 'chemsp_token' in your working directory. If you don't have a token you can omit the chemspider tab by commenting out the lines 22-29 in names2ids.py.