> I was wrong, the "F" option retains bonds' order and it even works for
> aromatic atoms.
> For future reference, to generate smiles of fragment by atom indices in
> Python you can do:
> idxs = [1,2,3,4]
> mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip()
Yes, this method was from
I was wrong, the "F" option retains bonds' order and it even works for
aromatic atoms.
For future reference, to generate smiles of fragment by atom indices in
Python you can do:
> idxs = [1,2,3,4]
> mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip()
Pozdrawiam, | Best regards,
No worries :) I planned to do Chem.FindAtomEnvironmentOfRadiusN() and
Chem.PathToSubMol() in RDKit, but the function you've suggested is also
feasible.
@Geoff - the smiles fragment does not perserve any bond information from
what I've tested so far.
Pozdrawiam, | Best regards,
Maciek Wójci
Actually, for the task described, it's perfect. It can take any
subset, but I was hesitant to suggest it as it doesn't give the same
results as subsetting the molecule (e.g. you can have a portion of an
aromatic ring).
- Noel
On 19 June 2017 at 16:07, Geoffrey Hutchison wrote:
>> If it's a disco
Me:
> Perhaps you want Chem.MolFragmentToSmiles(mol, atomsToUse=idxs)?
>
> http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-module.html#MolFragmentToSmiles
Err, umm, *blush*. Forgot which list I was reading.
[Andrew! It says it right in the subject line! :]
> 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.
It doesn't have to be a disconnected portion. That feature to the SMILES writer
will take a bit mask for the fragment -- it can be any combi
On Jun 19, 2017, at 16:39, Maciek Wójcikowski wrote:
>
> 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):
Perhaps you want Chem.MolFragmentToSmiles(mol, ato
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
The last BeginModify should be EndModify.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski :
> I'm trying to get back the ECFP environments, most preferably as smiles.
> So it's literally a list of connected atoms.
>
> The
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 wrote:
> Hi all,
>
> Quick question: I have OBMol and w
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...@wojc
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