[Rdkit-discuss] RemoveHs and [H][*:1] mol

[Pavel P. <pav...@uk...>]

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.