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 ;) ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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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 <[hidden email]> 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 > [hidden email] > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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): 2017-06-19 15:53 GMT+02:00 Noel O'Boyle <[hidden email]>: This would be a useful API function. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
The last BeginModify should be EndModify. 2017-06-19 16:39 GMT+02:00 Maciek Wójcikowski <[hidden email]>:
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In reply to this post by mwojcikowski
On Jun 19, 2017, at 16:39, Maciek Wójcikowski <[hidden email]> 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, atomsToUse=idxs)? http://www.rdkit.org/docs-beta/api/rdkit.Chem.rdmolfiles-module.html#MolFragmentToSmiles Andrew [hidden email] ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Noel O'Boyle
> 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 combination of atoms as a mask onto the OBMol. -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Andrew Dalke
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! :] Andrew [hidden email] ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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In reply to this post by Geoff Hutchison
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 <[hidden email]> wrote: >> 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 combination of atoms as a mask onto the OBMol. > > -Geoff > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > [hidden email] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
In reply to this post by Andrew Dalke
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. 2017-06-19 17:12 GMT+02:00 Andrew Dalke <[hidden email]>: Me: ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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] 2017-06-19 17:19 GMT+02:00 Maciek Wójcikowski <[hidden email]>:
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Yes, this method was from Craig James for fragment-based fingerprints, IIRC. It would be nice to get it up into OBMol as well. -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss |
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