Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Pavel Polishchuk
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.

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Chuang, Kangway
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 __

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Ling Chan
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

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Ling Chan
>> *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

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Ling Chan
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

Re: [Rdkit-discuss] [*External*] finding atoms at multiple bond distances from target

2021-04-01 Thread Gareth Jones
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: *

Re: [Rdkit-discuss] [*External*] finding atoms at multiple bond distances from target

2021-04-01 Thread Guillaume GODIN via Rdkit-discuss
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

[Rdkit-discuss] finding atoms at multiple bond distances from target

2021-04-01 Thread cmayerb1
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

Re: [Rdkit-discuss] rejoining pairs of fragments after fragmenting a molecule

2021-04-01 Thread Mark Mackey via Rdkit-discuss
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