Paolo's answer provides you with the (possibly very useful) path (in atom
indices) between the two atoms.
If you just want the distances, you can use Chem.GetDistanceMatrix(m):
In [7]: Chem.GetDistanceMatrix?
Docstring:
GetDistanceMatrix( (Mol)mol [, (bool)useBO=False [, (bool)useAtomWts=False
[, (bool)force=False [, (str)prefix='']]]]) -> object :
Returns the molecule's topological distance matrix.
ARGUMENTS:
- mol: the molecule to use
- useBO: (optional) toggles use of bond orders in calculating the
distance matrix.
Default value is 0.
- useAtomWts: (optional) toggles using atom weights for the
diagonal elements of the
matrix (to return a "Balaban" distance matrix).
Default value is 0.
- force: (optional) forces the calculation to proceed, even if
there is a cached value.
Default value is 0.
- prefix: (optional, internal use) sets the prefix used in the
property cache
Default value is .
RETURNS: a Numeric array of floats with the distance matrix
On Thu, Oct 20, 2016 at 5:47 AM, Paolo Tosco <paolo.to...@unito.it> wrote:
> Hi Hongbin,
>
> I think rdmolops.GetShortestPath() might help you with this.
>
> Cheers,
> p.
>
>
> On 10/20/16 09:47, 杨弘宾 wrote:
>
> Hi, guys.
> I wanted to calculate the topological distance between two
> substructures. For example, the distance between carboxyl and acetyl in
> aspirin is 3 (or 4 if consider bond numbers) which are carbon, carbon and
> oxygen.
> My idea is to compare all the matched atoms between the two
> substructures.
>
> >>> m = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')
> >>> carboxyl = Chem.MolFromSmarts('C(=O)[OH]')
> >>> m.GetSubstructMatch(carboxyl)
> (10, 11, 12)
> >>> acetyl = Chem.MolFromSmarts('[CH3]C(=O)O')
> >>> m.GetSubstructMatch(acetyl)
> (0, 1, 2, 3)
>
> So, What I want is :
> a = [10,11,12]
> b = [0,1,2,3]
> def distrance(id1,id2):
> m = Chem.MolFromSmiles('CC(=O)Oc1ccccc1C(=O)O')
> ...
> return d
> >>> min ( map(distance, [(x,y) for x in a for y in b] ) )
> 3 ( or 4)
>
> Unnecessary to consider that using m as a parameter is better.
>
> Is it possible to define the distrance function with rdkit python API ? I
> tried to use atom pair but found that it seemed helpless.
>
> ------------------------------
> Hongbin Yang
>
>
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