That's a bug (and one that should be relatively straightforward to fix).
Please do put something in github (so that you "get credit" for it) and I
will fix it.
Thanks for the concise, but complete report of how to reproduce the problem!
-greg
On Tue, May 30, 2017 at 3:52 PM, Pavel Polishchuk <pavel_polishc...@ukr.net>
wrote:
> Hello,
>
> probably this is a message mainly to developers.
> I discovered some strange behavior of removeHs function applied for
> '[H][*:1]' molecule.
>
> If I create that mol from smiles, RemoveHs does not remove a single H
> from the mol:
>
> mmm = Chem.MolFromSmiles('[H][*:1]')
> Chem.MolToSmiles(Chem.RemoveHs(mmm))
>
> output:
> '[H][*:1]'
>
> If I apply RemoveHs to fragments obtained after MMPA cuts it removes H
> and keeps only '[*:1]'
>
> mmm = Chem.MolFromSmiles('c1ccccc1C')
> mmm = Chem.AddHs(mmm)
> fr = rdMMPA.FragmentMol(mmm, pattern="[*]!@!=!#[!#1]", maxCuts=1,
> resultsAsMols=True, maxCutBonds=30)
> for f in fr:
> ff = Chem.GetMolFrags(f[1], asMols=True)
> print(Chem.MolToSmiles(ff[0]), Chem.MolToSmiles(Chem.RemoveHs(ff[0])))
> print(Chem.MolToSmiles(ff[1]), Chem.MolToSmiles(Chem.RemoveHs(ff[1])))
>
> output:
> [H]c1c([H])c([H])c([*:1])c([H])c1[H] c1ccc([*:1])cc1
> [H]C([H])([H])[*:1] C[*:1]
> [H]c1c([H])c([H])c([*:1])c(C([H])([H])[H])c1[H] Cc1ccccc1[*:1]
> [H][*:1] [*:1]
> [H]c1c([H])c(C([H])([H])[H])c([H])c([*:1])c1[H] Cc1cccc([*:1])c1
> [H][*:1] [*:1]
> [H]c1c([H])c([*:1])c([H])c([H])c1C([H])([H])[H] Cc1ccc([*:1])cc1
> [H][*:1] [*:1]
> [H]c1c([H])c([H])c(C([H])([H])[*:1])c([H])c1[H] c1ccc(C[*:1])cc1
> [H][*:1] [*:1]
>
> If this is a bug I can create an issue on github
>
> Pavel.
>
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