Hi,
I am using the 2015.03.1 version. How do I update to the newest version? I
used the same command line as it mentioned in this website:
https://github.com/rdkit/rdkit/releases
sudo apt-get install python-rdkit librdkit1 rdkit-data
On Fri, Jul 6, 2018 at 10:47 AM, Greg Landrum <[email protected]>
wrote:
> How old is the version of the RDKit that you are using?
> If you are using the most recent version, AllChem.EmbedMolecule() will use
> the correct parameters by default.
>
> -greg
>
>
> On Fri, Jul 6, 2018 at 6:28 PM Phuong Chau <[email protected]> wrote:
>
>> 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
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> 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
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>>>
>>>
>>>
>>
>>
>> --
>> 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
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