Parsing Chemistry (opens in new tab)

(re.factorcode.org)

54 pointskencausey5mo ago27 comments

27 comments

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...

jugoetz4mo ago

No, in Python you can use rdkit (https://github.com/rdkit/rdkit) for that

the__alchemist4mo ago

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.

dachrillz4mo ago

What about inchi? Isn’t that a common way of describing molecules as well?

fred_tandemai4mo ago

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.

the__alchemist4mo ago

Good point!

jugoetz4mo ago

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.

dekhn4mo ago

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).

1 more reply

whitten4mo ago

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.

dalke4mo ago

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... .

dalke4mo ago

Oh, I should have pointed out my Python lexer-driven parser at https://hg.sr.ht/~dalke/smiview/browse/smiview.py

The lexer: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...

The lexer state transitions: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...

dekhn4mo ago

I wrote a very simple SMILES parser using pyparsing https://github.com/dakoner/smilesparser/tree/master I wouldn't say it's intended for production work, but it has been useful in situations where I didn't want to pull in rdkit.

dalke4mo ago

I see you include the dot disconnect "." as part of the Bond definition.

You also define Chain as:

  Chain <<= pp.Group(pp.Optional(Bond) + pp.Or([Atom, RingClosure]))

I believe this means your grammar allows the invalid SMILES C=.N

mwt4mo ago

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).

the__alchemist4mo ago

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.

mwt4mo ago

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)

1 more reply

brilee4mo ago

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

toast_x4mo ago

this is insanely cool

Jaxan4mo ago

… 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.

j / k navigate · click thread line to collapse

27 comments

logifail4mo ago

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...

jugoetz4mo ago

No, in Python you can use rdkit (https://github.com/rdkit/rdkit) for that

the__alchemist4mo ago

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.

dachrillz4mo ago

What about inchi? Isn’t that a common way of describing molecules as well?

fred_tandemai4mo ago

the__alchemist4mo ago

Good point!

jugoetz4mo ago

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.

dekhn4mo ago

1 more reply

whitten4mo ago

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.

dalke4mo ago

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.

dalke4mo ago

Oh, I should have pointed out my Python lexer-driven parser at https://hg.sr.ht/~dalke/smiview/browse/smiview.py

The lexer: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...

The lexer state transitions: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...

dekhn4mo ago

dalke4mo ago

I see you include the dot disconnect "." as part of the Bond definition.

You also define Chain as:

  Chain <<= pp.Group(pp.Optional(Bond) + pp.Or([Atom, RingClosure]))

I believe this means your grammar allows the invalid SMILES C=.N

mwt4mo ago

the__alchemist4mo ago

mwt4mo ago

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)

1 more reply

brilee4mo ago

toast_x4mo ago

this is insanely cool

Jaxan4mo ago

… 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.

j / k navigate · click thread line to collapse