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:
*
mol: the molecule to use
*
idx1: index of the first atom
*
idx2: index of the second atom
C++ signature :
boost::python::tuple GetShortestPath(RDKit::ROMol,int,int)
On 4/1/2021 8:24 AM, Guillaume GODIN via Rdkit-discuss wrote:
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
<https://www.rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.GetDistanceMatrix>*
**
Guillaume
*De : *cmaye...@umbc.edu <cmaye...@umbc.edu>
*Date : *jeudi, 1 avril 2021 à 15:27
*À : *rdkit-discuss@lists.sourceforge.net
<rdkit-discuss@lists.sourceforge.net>
*Objet : *[*External*] [Rdkit-discuss] finding atoms at multiple bond
distances from target
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
stereochemistry (D or L) to alpha-amino acids, which (to my first
estimation) depends on the atomic numbers of the sidechain atoms
within the first 2 bond distances of the alpha-carbon. I’m currently
iterating through the sidechain atoms after identifying the backbone
heavy atoms (alpha-nitrogen, alpha-carbon, and carboxylate carbon),
and am curious if there is some way to simplify this process by
getting a list of atoms at progressively larger bond distances from a
specific atom.
Thanks for your time, any advice is welcome.
-Chris
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