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What happens if you create 2D coordinates? <p dir="auto

Lomap MCS throws ValueError if rdkit.Mol created from SMILES about lomap HOT 3 OPEN

dwhswenson commented on July 30, 2024

Lomap MCS throws ValueError if rdkit.Mol created from SMILES

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Comments (3)

IAlibay commented on July 30, 2024

What happens if you create 2D coordinates?

edit: ok yeah so it seems fine if you do Chem.rdCoordGen.AddCoords, so it's expecting "any conformer info" I guess?

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dwhswenson commented on July 30, 2024

What happens if you create 2D coordinates?

That fixes:

Chem.rdDepictor.Compute2DCoords(toluene2)
Chem.rdDepictor.Compute2DCoords(methylcyclohexane2)
mapping = mcs.MCS(toluene2, methylcyclohexane2)
# no error

Should this be done internally when needed?

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IAlibay commented on July 30, 2024

(follow up from a quick slack discusion)

My main question is - I have no idea if max3d should even be applied if there are non-3D coordinates, does it make sense to trim the MCS in 2D space?

The two options I could see are:

At init MCS checks for conformers, if there are non then max3d gets set to 0 (I'm not 100% sure what the impact of this is, but it would reflect not having any positional data)
At init if there are no conformers then either gracefully fail and ask for coords, or attempt to get some coords via some user-defined flag?

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