According to
http://www.rdkit.org/docs/api/rdkit.Chem.rdMolAlign-module.html#AlignMol,
the function returns the RMSD, and the probe molecule is modified in
place. Look at the coordinates for mol2 before and after the
transformation:
mol = Chem.MolFromSmiles('CCCOC(=O)[O-]')
> Chem.rdDistGeom.EmbedMolecule(mol)
>
>> 0
>
> mol2 = Chem.MolFromSmiles('CC')
> Chem.rdDistGeom.EmbedMolecule(mol2)
>
>> 0
>
> mol2.GetConformer(0).GetPositions()
>
>> array([[ 0.75549098, 0. , 0. ],
>> [-0.75549098, 0. , 0. ]])
>
> Chem.rdMolAlign.AlignMol(mol2,mol, atomMap = ((0,0),(1,1)))
>
>> 0.005493118189962501
>
> mol2.GetConformer(0).GetPositions()
>
>> array([[ 3.10580323, -0.07674776, -0.45975102],
>> [ 1.75185317, 0.36881027, 0.04161089]])
>
>
Jason Biggs
On Tue, Jul 31, 2018 at 3:41 PM Phuong Chau <pc...@smith.edu> wrote:
> Hello everyone,
>
> I want to align chem B based on the 3D coordinates of chemical A and
> output the 3D coordinates of chemical B (alignment that center of mass of
> chem B is the same as chem A). I looked at the AlignMol() and Open3D align
> but it returns either a RMS value or a score. Is there a way that I convert
> either of these numbers to 3D coordinates?
>
> Thank you so much for your time and consideration.
>
> --
> Phuong Chau
>
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