acetylene-parser

A string parser for different chemical nomenclature.

functions

• tokenize(string, type="formula") -> Substance

  Tokenizes a string describing a chemical, yielding a Substance with (optional) functional groups corresponding to (more) fundamental components.

  • "formula" type expects a simple "secondary school" element-symbol naming string.

  • "smiles" expects a chemical name utilizing the SMILES system.

  • TODO: "iupac" expects a chemical name utilizing the IUPAC system.

roadmap

• implement SMILES parsing
• improve struct based on SMILES findings
• decide whether InChI implementation is worth it

references

SMILES

• https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
• http://opensmiles.org/opensmiles.html
• http://www.dalkescientific.com/writings/diary/archive/2004/01/05/tokens.html

IUPAC

• http://www.chem.uiuc.edu/GenChemReferences/nomenclature_rules.html
• https://web.archive.org/web/20100626004648/http://www.acdlabs.co.uk/iupac/nomenclature/93/r93_125.htm
• https://en.wikipedia.org/wiki/IUPAC_nomenclature_of_organic_chemistry
• https://bitbucket.org/dan2097/opsin/src

InChI

• http://iupac.org/who-we-are/divisions/division-details/inchi/
• http://www.inchi-trust.org/downloads/

data

• http://www.chemicalize.org/blog/
• http://www.chemspider.com/