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cdk / depict

SMILES Depiction Generator
GNU Lesser General Public License v2.1
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send MOLfile in body of post request #28

Closed vinc3PO closed 3 years ago

vinc3PO commented 3 years ago

There is might a more elegant way to check if the smiles parameter is empty. Also I added the possibility to keep the original orientation of the molecules coming from a MOLfile with the option reorient. By default set as true.

johnmay commented 3 years ago

The default for reorient should probably be false, also "clean2d" is probably a more conventual naming. Why are you using MOLfile at all - if you need to you should be able to pass coordinates via CXSMILES

vinc3PO commented 3 years ago

The defaut reorient is indeed defaulted to True. I do also agree to the clean2d naming make it clearer to what it does.

Long story short for the reason to use MOLfile. The source where we are getting the chemical structure have a limited output format. Unfortunately CXSMILES is not one of them. Also in order to confuse chemist we'd like to keep the molecule as they drew it.