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

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

Hi Josh,

https://gist.github.com/ptosco/3797986d7c01d052a774a2f6c43a3bc7

(disclaimer: there may be better/faster ways)

Cheers,
p.


On 07/02/18 17:42, Joshua Meyers wrote:
> Hey Again,
>
> Back to this problem because I didn't isolate the problem well enough 
> in the first place - my bad!
>
> I would like to get the original atom indices of the r groups created 
> by the ReplaceCore function.
> The issue is that the atom indices are reset by the ReplaceCore() 
> function (and seemingly any other function that deletes atoms).
>
> Any idea how I would get these?
>
> In [1]: from rdkit import Chem
>
> In [2]: from rdkit.Chem.Scaffolds import MurckoScaffold
>
> In [3]: m = Chem.MolFromSmiles('c1cc(C)c(CC(=O)[13C])cc1')
>
> In [4]: murcko = MurckoScaffold.GetScaffoldForMol(m)
>
> In [5]: rGroups = Chem.ReplaceCore(m, murcko, useChirality=True, 
> labelByIndex=True)
>
> In [6]: rGroup_idxs = []
>    ...: rGroups = Chem.GetMolFrags(rGroups, asMols=True, 
> fragsMolAtomMapping=rGroup_idxs)
>    ...: rGroup_idxs
>    ...:
> Out[6]: [(0, 5), (1, 2, 3, 4, 6)]
>
> I know that the two sets of indices I want from the original molecule 
> m are
> ((3,2),(5,6,7,8))
>
> (found by depicting the indices - see attached)
>
>
>
>
> Any idea how I can achieve this?
>
> Cheers in advance,
> Josh
>
>
> On 26 June 2018 at 12:25, Paolo Tosco <pao...@gm... 
> <mailto:pao...@gm...>> wrote:
>
>     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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