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).
Parsing Chemistry
11–20 of 30 posts
Re: Parsing Chemistry
#12This 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).
That was my initial reaction too, but I suspect this is has utility in applications other than what you and I are looking for. From context, I gather this may be for thermodynamic arithmetic, or reaction product arithmetic.
Re: Parsing Chemistry
#13Note: 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.
SMILES and SELFIES are molecular graph representations and aren't meant to solve the "parse this sum formula" problem. SELFIES are for genAI. If you ask a VAE to generate SMILES, it will spit out some strings that are invalid - can't happen with SELFIES, that is the one application where they are robust.
It's still being argued if you really need SELFIES, or if SMILES autoencoders can be trained to only generate valid molecules, or if generating invalid molecules is useful (I'm in camp SELFIES, but I also want better ways to represent and learn on graphical chemical structures, ratehr than serialized strings).
Re: Parsing Chemistry
#14This 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).
That was my initial reaction too, but I suspect this is has utility in applications other than what you and I are looking for. From context, I gather this may be for thermodynamic arithmetic, or reaction product arithmetic.
I'd be really interested to know of anybody making money with those topics (and doesn't already have their own domain-specific practice for the problem)
Re: Parsing Chemistry
#15[dead]
Re: Parsing Chemistry
#16Does 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.
[dead]
Re: Parsing Chemistry
#17Note: 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.
What about inchi? Isn’t that a common way of describing molecules as well?
InChI isn't really meant to be used as a format to store 2D molecules say for rendering but rather serves as a unique descriptive chemical identifier. InChI has many flavors but the Standard InChI yields one unique identifier for multiple forms (tautomers) of the same molecule.
Re: Parsing Chemistry
#18Earlier quoted context omitted.
That was my initial reaction too, but I suspect this is has utility in applications other than what you and I are looking for. From context, I gather this may be for thermodynamic arithmetic, or reaction product arithmetic.
I'd be really interested to know of anybody making money with those topics (and doesn't already have their own domain-specific practice for the problem)
Cheminformatics is such an example. Heavily used in computational drug discovery.
Re: Parsing Chemistry
#19this is insanely cool
… It is just a parser? Sure the parser is written very succinctly and that’s neat. But parser generators for other languages can do it similarly.
Re: Parsing Chemistry
#20Does 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.
That's "SMILES".
Yes. Here is the yacc grammar for the SMILES parser in the RDKit. https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Smi...
There's also one from OpenSMILES at http://opensmiles.org/opensmiles.html#_grammar . It has a shift/reduce error (as I recall) that I was not competent enough to fix.
I prefer to parser almost completely in the lexer, with a small amount of lexer state to handle balanced parens, bracket atoms, and matching ring closures. See https://hg.sr.ht/~dalke/opensmiles-ragel and more specifically https://hg.sr.ht/~dalke/opensmiles-ragel/browse/opensmiles.r... .