The last BeginModify should be EndModify.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski <mac...@wojcikowski.pl>:
> I'm trying to get back the ECFP environments, most preferably as smiles.
> So it's literally a list of connected atoms.
>
> The dumb solution goes as follows:
>
> def submol(mol, idxs):
>> mol_clone = mol.clone
>> mol_clone.OBMol.BeginModify()
>> delete_atoms = []
>> for i in reversed(range(len(mol.atoms))):
>> if i in idxs:
>> continue
>> delete_atoms.append(mol_clone.OBMol.GetAtomById(i))
>> for atom in delete_atoms:
>> mol_clone.OBMol.DeleteAtom(atom)
>> mol_clone.OBMol.BeginModify()
>> return mol_clone
>
>
> ----
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-19 15:53 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:
>
>> This would be a useful API function.
>>
>> If it's a disconnected portion of the molecule, and you wanted to
>> write a smiles, there is a fragment option for the smiles writer that
>> you could use.
>>
>> - Noel
>>
>> On 17 June 2017 at 21:44, Maciek Wójcikowski <mac...@wojcikowski.pl>
>> wrote:
>> > Hi all,
>> >
>> > Quick question: I have OBMol and want to create a sub-molecule from a
>> subset
>> > of atoms given by atom/bond indices. Is there a clever way to do it in
>> > OpenBabel? I'm aware that I can make a copy and prune the unwanted
>> atoms ;)
>> >
>> > ----
>> > Pozdrawiam, | Best regards,
>> > Maciek Wójcikowski
>> > mac...@wojcikowski.pl
>> >
>> > ------------------------------------------------------------
>> ------------------
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>> >
>>
>
>
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