implement canonical SMILES generation from MoleculeGraphs

singa-bio / singa

:leaves: SiNGA (Simulation of Natural Systems using Graph Automata) is an open-source library containing tools especially for structural bioinformatics and systems biology.

MIT License

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implement canonical SMILES generation from MoleculeGraphs #86

Open fkaiserbio opened 5 years ago

fkaiserbio commented 5 years ago

as parsing of molecule graphs from SMILES strings is implemented, it would be nice to have it also the other way around
generation of SMILES strings from arbitrary MoleculeGraph objects could follow the algorithm described here : http://organica1.org/seminario/smile_2_1988.pdf
alternatively, one could have a look at the RDKit implementation: rdkit.Chem.rdmolfiles.MolToSmiles

cleberecht commented 5 years ago

This seems like a logical step to round off the SMILES processing. Currently I don't have the capacity to delve into this. Maybe you could start an implementation and get hold of some pseudo code?

cleberecht commented 5 years ago

The book Tutorials in Chemoinformatics has a nice chapter on SMILES generation.

cleberecht commented 5 years ago

maybe try https://github.com/johnmay/beam

fkaiserbio commented 5 years ago

implemented with Beam as of bae6fd0d11380926da7bf7cbd7be90ceb2084654
I suggest moving the SMILES parsing to Beam as well or at least provide an option to do so