Indeed with the latest release there is no problem any more.
Ling
>________________________________
> From: Greg Landrum <[email protected]>
>To: S.L. Chan <[email protected]>
>Cc: "[email protected]"
><[email protected]>
>Sent: Thursday, August 22, 2013 6:57 PM
>Subject: Re: [Rdkit-discuss] GetSubstructMatches()
>
>
>
>Dear Ling,
>
>
>On Thu, Aug 22, 2013 at 11:49 PM, S.L. Chan <[email protected]> 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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