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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