Re: [Rdkit-discuss] GetMolFrags asMols with persistent atom indexes

[Paolo T. <pao...@gm...>]

Hi Josh,

if you pass empty lists as the frags and as the fragsMolAtomMapping 
parameters of GetMolFrags() they will be filled with indices referring 
to the indices of the original molecule (see lines highlighted in red 
below).

Hope that helps, cheers
p.


      GetMolFrags(...)


	

GetMolFrags( (Mol)mol [, (bool)asMols=False [, (bool)sanitizeFrags=True
     [, (AtomPairsParameters)frags=None [, (AtomPairsParameters)fragsMolAtomMapping=None]]]]) -> tuple :
     Finds the disconnected fragments from a molecule.
     
       For example, for the molecule 'CC(=O)[O-].[NH3+]C' GetMolFrags() returns
       ((0, 1, 2, 3), (4, 5))
     
       ARGUMENTS:
     
         - mol: the molecule to use
         - asMols: (optional) if this is provided and true, the fragments
           will be returned as molecules instead of atom ids.
         - sanitizeFrags: (optional) if this is provided and true, the fragments
           molecules will be sanitized before returning them.
- frags: (optional, defaults to None) if this is provided as an empty 
list, the result will be mol.GetNumAtoms() long on return and will 
contain the fragment assignment for each Atom - fragsMolAtomMapping: 
(optional, defaults to None) if this is provided as an empty list, the 
result will be a a numFrags long list on return, and each entry will 
contain the indices of the Atoms in that fragment: [(0, 1, 2, 3), (4, 5)]      
       RETURNS: a tuple of tuples with IDs for the atoms in each fragment
                or a tuple of molecules.


On 26/06/2018 10:29, Joshua Meyers wrote:
> Hey All,
>
> I am chopping parts out of molecules and picking up the pieces using 
> the Chem.GetMolFrags() function.
> I would like to separate fragments into distinct mol objects but keep 
> the original atom indexes however setting the asMols=True flag seems 
> to reset the indexes, is this expected behaviour? Is there a way 
> around this?
>
> Here's some code:
>
> In [1]: from rdkit import Chem
>
> In [2]: m = Chem.MolFromSmiles('c1ccccc1.CCO')
>
> In [3]: Chem.GetMolFrags(m)
> Out[3]: ((0, 1, 2, 3, 4, 5), (6, 7, 8)) <----- desired indexes
>
> In [4]: frags = Chem.GetMolFrags(m, asMols=True)
>
> In [5]: for frag in frags:
>    ...:     print([a.GetIdx() for a in frag.GetAtoms()])
>    ...:
> [0, 1, 2, 3, 4, 5]
> [0, 1, 2] < ------ indexes have been reset
>
>
> Many thanks in advance,
> Josh
>
>
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