Hi James,
As Paul mentioned about RDKit-3Dmol.js integration, I would like to share
additional information. I wrote those scripts about 2 years ago and those
do not have structure editing capabilities. I have plan to update those
after June this year. Thank you.
Best regards,
- malitha
On Mon,
Hi,
Probably the designated folder is missing. So, rdkit cannot create the file
in specified path. Thanks.
- malitha
On Wed, Jul 11, 2018, 5:46 AM Phuong Chau wrote:
> Hello,
>
> I was trying to draw the 2D structure of a molecule inside a python script
> (.py). It works with other functions
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
file
> an issue for this
>
> Jason
>
> Jason Biggs
>
>
> On Fri, Dec 1, 2017 at 4:59 AM, Malitha Kabir <malitha12...@gmail.com>
> wrote:
>
>> Hi Jason,
>>
>> I hope the following codes will help you a little.
>>
>> from rdkit impor
Hi Jason,
I hope the following codes will help you a little.
from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem import AllChem
size = (120, 120)
m = Chem.MolFromSmiles('C#C')
m2=Chem.rdmolops.AddHs(m)
AllChem.EmbedMolecule(m2, AllChem.ETKDG())
Draw.MolToMPL(m2, size=size)
***
Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>> Inteligência Computacional - UNIFEI
>> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
>> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
>> Laboratório de Bioinformática e Siste
nteligência Computacional - UNIFEI
> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>
> 2017-09-14 9:17 GMT-03:00 Malitha Kabir <malitha12...@gma
gt; Inteligência Computacional - UNIFEI
> Membro do Grupo de Pesquisa Assinaturas Biológicas da FIOCRUZ
> Membro do Grupo de Pesquisa Bioinformática Estrutural da UFMG
> Laboratório de Bioinformática e Sistemas - LBS, DCC, UFMG
>
> 2017-09-13 17:32 GMT-03:00 Malitha Kabir
>>>>>> My worry now is if the RDKit will generate different SMILES or InChI
>>>>>> in same SDF molecule or equals in different molecules (molecules from
>>>>>> RCSB
>>>>>> PDB, PubChem, ChemBL, for example).
>>>>&
Hi Wandré,
It seems you already did intense research on it. Kindly accept my comments
as an addition to your idea (not the answer you trying to find out). In my
idea, categorizing molecules using it's descriptor should reduce
computation time. RDKit currently offer calculation of about 200
litha, this is a great piece of work and I highly recommend all
>> RDKitters to have a look at it..
>>
>>
>>
>> Paul
>>
>>
>>
>> *Von:* Malitha Kabir [mailto:malitha12...@gmail.com]
>> *Gesendet:* Donnerstag, 31. August 2017 01:54
>> *An:*
Dear all,
I am about to share news on 3D molecule visualization in RDKit.
This summer I have worked as Google Summer Of Codes (GSoC) participant
under supervision of Paul Czodrowski and Greg Landrum. The codes were
reviewed several times by Peter Gedeck and finally merged by Brian Kelley
at
k, a sketch of a solution for what you
> want to do.
>
> https://gist.github.com/greglandrum/da88ead12b396ada4e1b3258fab771a7
>
> Best,
> -greg
>
>
> On Tue, Jul 4, 2017 at 5:18 PM, Malitha Kabir <malitha12...@gmail.com>
> wrote:
>
>> Hi,
>&
Hi,
I want to create RDKit Mol object manually. I can create RWMol object with
appropriate (I guess) atoms and bonds. The required atoms and bond
information are taken from another Mol object. It is indeed a tedious
coding gymnastic you can say. Unfortunately, the end molecule lacks the 3D
Dear Paolo Tosco,
Thank you very much for offering a concrete coding lesson in your previous
email. This will help me a lot. I have got all the answers.
-Malitha
On Tue, Jun 27, 2017 at 3:58 PM, Malitha Kabir <malitha12...@gmail.com>
wrote:
> Dear Maciek Wójcikowski,
>
> list(
olecule.
> http://www.rdkit.org/Python_Docs/rdkit.Chem.rdchem.Mol-class.html#
> GetPropsAsDict which should do what you want.
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-06-27 11:26 GMT+02:00 Malitha Kabir <malitha12...@g
Hi,
Thank you very much in advance for kindly looking into this.
My question is in short:
Is there any method that can create a list of available properties from SD
file?
I am describing the scenario here:
You can view a sample SD file from the following github link:
Darmstadt |
> Germany
>
> Phone: +49 6151 72 3218 <+49%206151%20723218>
>
> E-mail: paul.czodrow...@merckgroup.com | www.merckgroup.com
>
> Mandatory information can be found at: http://www.merckgroup.com/
> mandatories
>
> Pflichtangaben finden Sie unter: http://www
Dear Paul,
Kindly consider a few pieces of information provided below.
For your 2nd question:
Widgets are rendered in web browsers. So, in my sense, Python 2.7.13
instead of Python 3.5.3 should not cause problem with widget rendering.
Python 2.7.13 should work. My conda install uses Python
> -P.
>
> On Tue, May 9, 2017 at 6:52 PM, Malitha Kabir <malitha12...@gmail.com>
> wrote:
>
>> Notes to Peter,
>> Dear sir,
>> Thank you very much for your time on writing an excellent welcome note
>> together with advice. I will definity work on anyt
row...@merckgroup.com> wrote:
>
>> Dear RDkitters,
>>
>>
>>
>> This is to inform you exciting community Malitha Kabir who will working
>> as a GoogeSummerOfCode (GSoC) student over the next couple couple of weeks
>> on the RDKit-Py3DMol integration.
&g
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