Thank you, Paolo!
That was not obvious for me how RDKit manage hydrogens in this case.
Pavel.
On 22/03/2019 12:15, Paolo Tosco wrote:
Hi Pavel,
After you have first called AddHs(), all hydrogens in your molecule
are now in the molecule graph as real atoms, and there are no more
implicit/explicit Hs .
Therefore, when you call RemoveAtom(), you are removing a real atom
from the molecule graph, and the implicit/explicit H count stays 0 for
the parent heavy atom. Hence calling again AddHs() does not add any
hydrogens.
If you wish the hydrogen to come back when you call AddHs(), you need
to increase the explicit H count on the parent heavy atom:
print('---- load mol ----')
m = Chem.MolFromSmiles('c1ccccc1O')
print(Chem.MolToSmiles(m, allHsExplicit=True))
print('---- add Hs ----')
m = Chem.AddHs(m)
print(Chem.MolToSmiles(m, allHsExplicit=True))
print('---- remove H ----')
nbrs = m.GetAtomWithIdx(7).GetNeighbors()
if (len(nbrs) == 1 and nbrs[0].GetAtomicNum() > 1):
nbrs[0].SetNumExplicitHs(nbrs[0].GetNumExplicitHs() + 1)
em = Chem.EditableMol(m)
em.RemoveAtom(7)
print(Chem.MolToSmiles(em.GetMol(), allHsExplicit=True))
print('---- add Hs ----')
mm = Chem.AddHs(em.GetMol())
print(Chem.MolToSmiles(mm, allHsExplicit=True))
---- load mol ----
[OH][c]1[cH][cH][cH][cH][cH]1
---- add Hs ----
[H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H]
---- remove H ----
[H][O][c]1[cH][c]([H])[c]([H])[c]([H])[c]1[H]
---- add Hs ----
[H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H]
HTH, cheers,
p.
On 03/22/19 10:20, Pavel wrote:
Hello,
I encountered with an issue which I cannot understand and solve.
This might be a bug or a feature. After removal of some specific
hydrogens I could not add them back. Is it expected behavior or
should I create an issue on github?
print('---- load mol ----')
m = Chem.MolFromSmiles('c1ccccc1O')
print(Chem.MolToSmiles(m, allHsExplicit=True))
print('---- add Hs ----')
m = Chem.AddHs(m)
print(Chem.MolToSmiles(m, allHsExplicit=True))
print('---- remove H ----')
em = Chem.EditableMol(m)
em.RemoveAtom(7)
print(Chem.MolToSmiles(em.GetMol(), allHsExplicit=True))
print('---- add Hs ----')
mm = Chem.AddHs(em.GetMol())
print(Chem.MolToSmiles(mm, allHsExplicit=True))
print('---- update property cache ----')
mm.UpdatePropertyCache()
print(Chem.MolToSmiles(mm, allHsExplicit=True))
output:
---- load mol ----
[OH][c]1[cH][cH][cH][cH][cH]1
---- add Hs ----
[H][O][c]1[c]([H])[c]([H])[c]([H])[c]([H])[c]1[H]
---- remove H ----
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
---- add Hs ----
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
---- update property cache ----
[H][O][c]1[c][c]([H])[c]([H])[c]([H])[c]1[H]
Pavel.
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