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.