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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