Thanks for the documentation fix, I had read the same as Francois.


----
Brian Kelley

> On Jun 15, 2017, at 8:02 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 
> 
> 
>> On Thu, Jun 15, 2017 at 6:30 AM, Francois BERENGER 
>> <beren...@bioreg.kyushu-u.ac.jp> wrote:
>> 
>> I am afraid that in AllChem.GetConfomerRMSD: one doesn't get the RMSD
>> between the two conformers but an upper bound of it.
> 
> The documentation to this function is misleading:
> 
> In [21]: AllChem.GetConformerRMS?
> Signature: AllChem.GetConformerRMS(mol, confId1, confId2, atomIds=None, 
> prealigned=False)
> Docstring:
> Returns the RMS between two conformations.
> By default, the conformers will be aligned to the first conformer
> of the molecule (i.e. the reference) before RMS calculation and,
> as a side-effect, will be left in the aligned state.
> 
> Arguments:
>   - mol:        the molecule
>   - confId1:    the id of the first conformer
>   - confId2:    the id of the second conformer
>   - atomIds:    (optional) list of atom ids to use a points for
>                 alingment - defaults to all atoms
>   - prealigned: (optional) by default the conformers are assumed
>                 be unaligned and will therefore be aligned to the
>                 first conformer
> 
> 
> The alignment is done to the first conformer (i.e confId1).[1]
> Here's a demonstration of that:
> In [31]: AllChem.GetConformerRMS(m,0,1,prealigned=True)
> Out[31]: 9.1593890932638349
> 
> In [32]: AllChem.GetConformerRMS(m,0,2,prealigned=True)
> Out[32]: 3.8219771356556071
> 
> In [33]: AllChem.GetConformerRMS(m,1,2,prealigned=True)
> Out[33]: 8.597878324406647
> 
> In [34]: AllChem.GetConformerRMS(m,1,2)
> Out[34]: 1.1067869816465845   # conformer 2 is now aligned to conformer 1
> 
> In [35]: AllChem.GetConformerRMS(m,0,1,prealigned=True)
> Out[35]: 9.1593890932638349   # the RMS between confs 0 and 1 hasn't changed
> 
> In [36]: AllChem.GetConformerRMS(m,0,2,prealigned=True)
> Out[36]: 9.4691776880629508   # the RMS between confs 0 and 2 has changed
> 
> I will clean that documentation up.
> 
> 
> -greg
> [1] since that's a "conformer of the molecule" the documentation isn't 
> actually wrong, but it's misleading enough to be effectively wrong.
>  
>> 
>> I understand from the doc that if they are aligned, they are aligned
>> to the first conformer of the molecule.
>> 
>> To get the real RMSD between two conformers, they must
>> be superimposed together, not to a third conformer.
>> 
>> Please tell me if I'm wrong.
>> 
>> Regards,
>> F.
>> 
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