I tried the code: AllChem.EmbedMolecule(x, params = AllChem.ETKDGv2())
but it shows me the error:
AttributeError: 'module' object has no attribute 'ETKDGv2'
How do I fix this problem? I imported rdkit.Chem and AllChem.
On Fri, Jul 6, 2018 at 10:03 AM, Sereina <[email protected]> wrote:
> The default conformer generator in RDKit is plain distance geometry, which
> is known to not be able to provide perfectly flat aromatic rings.
> You can use the ETKDG conformer generator instead:
>
> AllChem.EmbedMolecule(mol, params=AllChem.ETKDGv2())
>
> Best,
> Sereina
>
>
> On 6 Jul 2018, at 17:54, Phuong Chau <[email protected]> wrote:
>
> Follow up question regarding to PDB file:
>
> Thank you for your help. I was able to create the non-zero coordinates of
> the chemical. However, when I tried to view it on VMD, the chemical that I
> used is c1ccccc1 (benzene). The ring itself (and the atoms coming off it,
> which are mostly hydrogens) should all be in-plane but the pdb file shows
> that it is slightly puckered. Would anyone explain this for me? How can I
> make it be in-plane ?
>
> Here is a screenshot of the molecule.
> <Screenshot from 2018-07-06 09-53-12.png>
>
>
> On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
> [email protected]> wrote:
>
>> On 7/5/2018 1:39 PM, Paolo Tosco wrote:
>>
>> As the PDB format includes no stereochemistry, no coordinates are needed,
>>> and by default they are zero, as the molecule does not have a conformation
>>> yet.
>>>
>>
>> Hmm. One could argue that PDB format *is* 3D coordinates, so a block with
>> all zeroes is quite pointless. And of course counter-intuitive.
>>
>> Dima
>>
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>> [email protected]
>> 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
> [email protected]
> 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
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
