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

[Stephen R. <s.d...@go...>]

You could try looping over all your atoms and calling setIntProp on each
one to set a property with the original index, then get that property value
back rather than the new atom indices.

 Steve


On Mon, 2 Jul 2018, 17:43 Joshua Meyers, <jos...@be...>
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...> 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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