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  • this is insanely cool
    by toast_x
  • Does this handle, e.g., water of hydration CaSO4 . 2H2O? states of matter H2O(g)? does it preserve subunit information, as in (C6H5)CH2COOH? Writing a parser for basic formulae is such a tiny tiny part of the actual problem... deciding the scope of what you want to handle and how is the real problem
    by brilee
  • This code is jibberish to me, but it appears the target is just parsing how many atoms are in a molecule string of some representation. That's cool, but to do just about anything useful in chemistry we need the bond graph (and often more - bond orders stereochemistry, plus much more for biopolymers).
    by mwt
  • Does the SMILE (or Simplified Molecular Input Line Entry System) code have an EBNF definition ? https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Lin... Claims there is a context free grammar.
    by whitten
  • Note: There are two standardized formats for this called SMILES and SELFIES. SMILES is much better supported, but SELFIES is more robust. I'm integrating them into some bio and chem software I'm working on.

    You can do things like look up, using PubChem's API, similar molecules etc to a SMILES string.

    I believe most molecule editors can load and save SMILES.

    by the__alchemist
  • Does this do structural formulae too?

    Was thinking of InChI[0] but on Googling SMILES and SELFIES I found this[1] talk, this[2] paper and my goodness I've been down a few rabbit holes since...

    [0] https://en.wikipedia.org/wiki/International_Chemical_Identif... [1] https://www.inchi-trust.org/wp/wp-content/uploads/2019/12/18... [2] https://pubs.rsc.org/en/content/articlehtml/2022/dd/d1dd0001...

    by logifail

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Parsing Chemistry · Birbla