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Does the SMILE (or Simplified Molecular Input Line Entry System) code have an EBNF definition ? https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Line_En

by whitten 11mo ago

Does the SMILE (or Simplified Molecular Input Line Entry System) code have an EBNF definition ? https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Line_Entry_System https://en.wikipedia.org/wiki/Simplified_Molecular_Input_Lin... Claims there is a context free grammar.

fred_tandemai 11mo ago
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dalke 11mo 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/SmilesParse/smiles.yy https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Smi... There's also one from OpenSMILES at http://opensmiles.org/opensmiles.html#_grammar 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 https://hg.sr.ht/~dalke/opensmiles-ragel and more specifically https://hg.sr.ht/~dalke/opensmiles-ragel/browse/opensmiles.rl?rev=tip https://hg.sr.ht/~dalke/opensmiles-ragel/browse/opensmiles.r... .
- dalke 11mo ago
  Oh, I should have pointed out my Python lexer-driven parser at https://hg.sr.ht/~dalke/smiview/browse/smiview.py https://hg.sr.ht/~dalke/smiview/browse/smiview.py The lexer: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L337 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#L364 https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...
dekhn 11mo ago
I wrote a very simple SMILES parser using pyparsing https://github.com/dakoner/smilesparser/tree/master 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.
- dalke 11mo 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

by whitten 11mo ago

fred_tandemai 11mo ago

[dead]

dalke 11mo 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/SmilesParse/smiles.yy https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Smi... There's also one from OpenSMILES at http://opensmiles.org/opensmiles.html#_grammar 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 https://hg.sr.ht/~dalke/opensmiles-ragel and more specifically https://hg.sr.ht/~dalke/opensmiles-ragel/browse/opensmiles.rl?rev=tip https://hg.sr.ht/~dalke/opensmiles-ragel/browse/opensmiles.r... .

dalke 11mo ago
Oh, I should have pointed out my Python lexer-driven parser at https://hg.sr.ht/~dalke/smiview/browse/smiview.py https://hg.sr.ht/~dalke/smiview/browse/smiview.py The lexer: https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L337 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#L364 https://hg.sr.ht/~dalke/smiview/browse/smiview.py?rev=tip#L3...

dekhn 11mo ago

I wrote a very simple SMILES parser using pyparsing https://github.com/dakoner/smilesparser/tree/master 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.

dalke 11mo 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