Replies: 4 comments
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curiously if I 'port' the SMARTS directly to SMILES (asserting a double bond in place of
False |
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OK this was to do with aromaticity AND explicit hydrogens. Firstly, removing the explicit hydrogens by hand + kekulizing with removal of aromaticity flags works:
but this requires editing by hand.
note Hs are still there. So I settled on this. Take a round-trip through a RWMol, deleting hydrogens. For each hydrogen deleted, record it's parent atom. Then expand the query on that parent atom to enforce the correct degree. After kekulizing and removing aromaticity flags on the test molecule, it passes. Hopefully this works on a large scale automatically:
output:
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hi David - thank you so much lot for looking at this! Do you know if the reverse is possible - 'aromatizing' the SMARTS pattern? The context is that I'm looking to apply a query/rxn RDFile containing queries and replacement structures (for standardizing tautomers). I could indeed add hydrogens, remove aromatic flags, and iterate over all kekule forms in a library to check if each form is a match. This is not much more human effort, but a bit more computational time on large libraries. From what I can tell, RDFiles like this (originating from Biovia or chemaxon I think) are not well-suited to interfacing with RDKit mols, unless I'm doing something wrong. thanks again |
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Hi all,
I'd like to apply syngenta's business rules for tautomer standardization, but am failing to match a query to a molecule that was designed to match it.
In short, this pattern:
isn't a substructure of this molecule, although all the bonds and atoms are correct (as far as I can see! see below for pic):
I tried adding explicit hydrogens to the molecule, since two hydrogens are explicitly defined in the SMARTS pattern, but no dice:
Does anyone understand what I've done wrong? Thank you!
See gist or pictures here:
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