Hi,
The easiest way to install rdkit is as follows:
1. install conda (miniconda/anaconda) (i use miniconda):
https://conda.io/docs/user-guide/install/index.html
2. install rdkit on top of miniconda: https://anaconda.org/rdkit/rdkit
*** to avoid trouble, make sure you have added python path to environment
variable during conda installation. the conda installer should prompt you
to do so.
Official link for rdkit installation guideline:
http://www.rdkit.org/docs/Install.html
Thanks.
- malitha
On Sat, Jul 7, 2018 at 1:30 AM, Phuong Chau <[email protected]> wrote:
> 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
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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
> _______________________________________________
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>
>
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