Thank you so much for your help! My problem is solved :)
On Tue, Jul 31, 2018 at 3:31 PM, Jason Biggs <jasondbi...@gmail.com> wrote:
> 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
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
--
Phuong Chau
Smith College '20
Engineering Major
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
