Hi Ling,
this can be a workaround if RDKit does not have a built-in function
to extract a submolecule by atom ids. You may assign atom property
labels to these atoms and then looping over atoms in EditableMol remove
those ones which do not have this property assigned.
Kind regards,
Pavel.
Hi Ling,
I think I've run into something similar before, have you tried using
FragmentOnBonds followed by Chem.GetMolFrags? GetMolFrags lets you toggle a few
things (e.g. (bool)asMols=False [, (bool)sanitizeFrags=True) to provide some
workarounds with sanitization.
Best,
Kangway
__
Yes, Kangway, that was what I first tried, as mentioned in the first post.
I did not have any problem with obtaining the primary fragments (applying
all cuts) . Just that I have not yet figured out how to obtain the
secondary fragments, either from recombining the primary fragments, or from
fragmen
>> *I did manage to achieve what I want by going
through Chem.MolFragmentToSmiles and then convert the Smiles back to a Mol.
But is there a neater way?*
Oops, I wrote too soon. Actually I did not achieve what I want. The
conversion from the smiles from Chem.MolFragmentToSmiles sometimes crashes,
b
Thank you Mark for your suggestion. It sounds good and I gave it a try.
However, this leads to another question that may sound dumb.
I have the atom indices of a fragment. For example, the fragment comes from
atoms [3,4,5,9,10,11,14] of the original molecule. How can I extract this
fragment from t
Or you could loop over atom pairs calculating the shortest path.
Cheers,
Gareth
|rdkit.Chem.rdmolops.||GetShortestPath|(/(Mol)arg1/, /(int)arg2/,
/(int)arg3/) → tuple :
Find the shortest path between two atoms using the Bellman-Ford
algorithm.
ARGUMENTS:
*
Hello,
You can use the “topological” distance Matrix to have the atoms at a given
distance of one atom. It’s not direct but it’s a good start:
https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.GetDistanceMatrix
Guillaume
De : cmaye...@umbc.edu
Date : jeudi, 1 avri
Good morning,
I'm familiar with the atom.GetNeighbors() function to find all atoms within
one bond distance of a given atom. Is there any method (either built-in or
user-created) to find all atoms within n bond distances (n >= 2) of a given
atom? I'm working on a method to assign relative ste
Hi Ling,
Having done something similar (but not in RDKit), I would suggest a different
algorithm. I think that fragmenting the molecule first and then stitching the
bits together is always going to be very complicated. Instead, just fragment
the molecule in the ways that you want:
- Find the s
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