Dear Ling,
On Thu, Aug 22, 2013 at 11:49 PM, S.L. Chan <slch...@yahoo.com> wrote:
> Good afternoon folks,
>
> I would imagine that if you remove the hydrogens, the
> resulting molecule would be a substructure of the
> original molecule. However, when I do the following
> to the attached MDL mol file, there is no matches.
>
I would expect it to be a substructure.
> >>> from rdkit import Chem
> >>> mol = Chem.MolFromMolFile('temp.mol', removeHs=False)
> >>> mhvy = Chem.RemoveHs(mol)
> >>> matches = mol.GetSubstructMatches(mhvy)
>
> matches turns out to be empty.
>
Which version of the RDKit are you using? I cannot reproduce this with the
most recent release:
In [5]: m = Chem.MolFromMolFile('temp.mol',removeHs=False)
In [6]: mhvy = Chem.RemoveHs(m)
In [7]: len(m.GetSubstructMatches(mhvy))
Out[7]: 1
In [8]: from rdkit import rdBase
In [9]: rdBase.rdkitVersion
Out[9]: '2013.06.1'
-greg
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