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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Phenols should also remain coplanar. #157

Closed primaryodors closed 1 year ago

primaryodors commented 1 year ago

Similar to #89 , if an aromatic ring or a double-bonded carbon has a hydroxyl or amine attached, the bond should not be able to rotate, although it can be allowed to flip. This does not apply if the substituent is e.g. an alkoxy group, since those apparently are free to rotate, so only enforce the rule if the attached pnictogen or chalcogen has bonds only to the sp2 carbon and hydrogen.

electronicsbyjulie commented 1 year ago

The Bond::can_flip property was not tied to some of the relevant code (AABondDef does not even have a can_flip property!) so I am adding these in the amino acid class.

electronicsbyjulie commented 1 year ago

Testing the molecule class with:

clear; make test/molecule_test && test/molecule_test 'Oc1ccccc1O' 'O'