Re: [Rdkit-discuss] Problems with Conformer ID assignment

[markus <m.k...@tu...>]

Greg Landrum wrote:
> Hi Markus,
>
> On Thu, Aug 21, 2008 at 1:34 PM, markus <m.k...@tu...> wrote:
>   
>> Hi,
>> somehow I do not get the way RDKit organizes the IDs of conformers:
>>     
>
> Yes, the way conformers is handled is confusing at first.
>
> First I'll show you how to do what I think you were trying to do, then
> I'll try and explain what the problem was:
>
>   
>>  >>> from Chem import AllChem as Chem
>>  >>> import copy
>>  >>> mol=Chem.MolFromSmiles('c1ccccc1N')
>>  >>> Chem.EmbedMultipleConfs(mol,10)
>> <rdBase._vecti object at 0x8301e2c>
>>  >>> mol2=copy.deepcopy(mol)
>>  >>> for i in range(mol.GetNumConformers()):
>> ...     print mol.GetConformer(i)
>> ...
>>     
>
> The best way to loop over a molecule's conformers is using its
> GetConformers() method:
>
> [14]>>> m = Chem.MolFromSmiles('c1ccccc1N')
> [15]>>> AllChem.EmbedMultipleConfs(m,10)
> Out[15] <rdBase._vecti object at 0x218182c>
> [16]>>> [conf.GetId() for conf in m.GetConformers()]
> Out[16] [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
>
> The molecule's GetConformer(x) method doesn't actually return the
> conformer with index X, it returns the conformer with ID x. This is
> what causes the problem here:
>
>   
>>  >>> mol.AddConformer(mol2.GetConformer(4))
>> 4
>>  >>> print 'NumConfs: %d\n' %(mol.GetNumConformers())
>> NumConfs: 11
>>
>>  >>> for i in range(mol.GetNumConformers()):
>> ...     print mol.GetConformer(i)
>> ...
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> <Chem.rdchem.Conformer object at 0x831448c>
>> Traceback (most recent call last):
>>  File "<stdin>", line 2, in <module>
>> ValueError: Bad Conformer Id
>>  >>>
>>     
>
> Continuing my example from above will help show what went wrong :
> [17]>>> m2 = copy.deepcopy(m)
> [18]>>> m.AddConformer(m2.GetConformer(4))
> Out[18] 4
> [21]>>> [conf.GetId() for conf in m.GetConformers()]
> Out[21] [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 4]
>
> You can see that there are two conformers with id 4, but none with id
> 10, which is what you were trying to retrieve above. Note that the
> second conformer with id 4 cannot be retrieved using m.GetConformer :
> that always returns the first conformer with the corresponding Id.
>
>   
>> Why can't I iterate over the conformers the second time?
>> Do I have to assign a ConfID explicitly, when adding a Conformer?
>>     
>
> No, you don't. But if you're adding a conformer to a molecule that
> already has a set of conformers, you might want to use the optional
> assignId argument to Mol.AddConformer to tell the molecule to
> automatically assign a new Id:
>
> [22]>>> m.AddConformer(m2.GetConformer(5),assignId=True)
> Out[22] 10
> [23]>>> [conf.GetId() for conf in m.GetConformers()]
> Out[23] [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 4, 10]
>
> To summarize and expand a bit:
> A molecule's conformers don't have to have sequential ids and the ids
> can be arbitrary positive values. So if a molecule has 10 conformers,
> you can't be sure that mol.GetConformer(3) will work. If you want to
> loop over a molecule's conformers use the GetConformers() method.
>
> I hope this helps,
> -greg
>   
O.K,
Conformer IDs and Indices are not the same, that's what I got wrong.
Just to get certain on a detail:
Calling GetConformers() returns the List of Conformers in a defined 
order, doesn't it?
So I could repeatedly index by calling GetConformers()[X] to get the 
same Conformer (at Position Number X
in the List) as an alternative to calling by previously assigned IDs.

Cheers Markus