Re: [Rdkit-discuss] Structure-Based Drug Design

[Malitha Kabir]

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, Mar 18, 2019 at 1:39 PM Bakary N'tji Diallo 
wrote:

> 2) For visualization nglview  has lot
> of capabilities. I run simulation on a cluster and with nglview in a
> Notebook, the final trajectories can be directly be loaded in the notebook
> for visualization.  Here is a gallery of different usages for visualization
> with nglview .  Loading
> trajectories can be done through pytraj
>  which
> also has tone of analytical capabilities.  It will be interesting to see to
> see notebook with free energy calculation for protein-ligand systems,
> especially including QM techniques.
>
> Le sam. 16 mars 2019 à 18:54, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> a écrit :
>
>> RDkit Discussion Group,
>>
>> RDkit has quite a number of useful tools and algorithms for
>> ligand-based
>> drug design (LBDD).  However, what about structure-based drug design
>> (SBDD)?
>> Perhaps a few questions to motivate the discussion.
>>
>> 1) Since RDkit supposedly includes the force field MMFF, does this
>> mean
>> that one can read in reasonably prepared proteins (from a PDB file) and
>> ligands
>> (from a MOL file) and compute energies of the complex, proteins, and
>> ligands and
>> presumably interaction energies, etc?
>>
>> 2) Visualization is clearly important in SBDD.  Has anyone developed
>> a tool
>> that nicely integrates macromolecular editing and visualization with
>> RDkit?
>>
>> 3) Given the visualization capabilities of Jupyter, has anyone
>> developed
>> Jupyter/RDkit scripts for #1 and #2?
>>
>> I welcome thoughts and comments especially from those who have been
>> thinking
>> about or are wrestling with SBDD and RDkit integration.  Thank you.
>>
>> Regards,
>> Jim Metz
>>
>>
>>
>>
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>>
>
>
> --
>
> Bakary N’tji DIALLO
>
> PhD Student (Bioinformatics) , Research
> Unit in Bioinformatics (RUBi) 
>
> Mail: diallobaka...@gmail.com |  Skype: diallobakary4
>
> Tel:  +27798233845 | +223 74 56 57 22 | +223 97 39 77 14
>
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Re: [Rdkit-discuss] Error if run Draw in Python

[Malitha Kabir]

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 such as MolToSmiles,
> FingerPrintMol(),... but somehow the Draw.MolToSmile() function does not
> work. It kept throw errors of:
>  File "PairsFinder.py", line 53, in 
>
> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png')
>   File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/__init__.py",
> line 182, in MolToFile
> canvas.save()
>   File "/usr/lib/python2.7/dist-packages/rdkit/Chem/Draw/spingCanvas.py",
> line 111, in save
> self.canvas.save()
>   File "/usr/lib/python2.7/dist-packages/rdkit/sping/PIL/pidPIL.py", line
> 166, in save
> self._image.save(filename, format=format)
>   File "/usr/lib/python2.7/dist-packages/PIL/Image.py", line 1672, in save
> fp = builtins.open(filename, "wb")
> IOError: [Errno 2] No such file or directory:
> '~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png'
> My script is :
> chem = Chem.MolFromSmiles('Nc1c1F')
> Draw.MolToFile(chem,'~/Desktop/work/2018/July/10/500_v2/Chem1_avg7.png')
>
> Would anyone help me please? How do I run Draw in python script?
>
> Thank you so much for your help
> --
> Phuong Chau
> Smith College '20
> Engineering Major
>
> --
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Re: [Rdkit-discuss] PDBBlock file

[Malitha Kabir]

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  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 
> 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  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 
>>> 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  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 c1c1 (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.
 
 ​

 On Fri, Jul 6, 2018 at 6:21 AM, Dmitri Maziuk via Rdkit-discuss <
 rdkit-discuss@lists.sourceforge.net> 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
 
 --
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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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>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
>
>
> --
> Phuong Chau
> Smith College '20
> Engineering Major
>
> 
> --
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>
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Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

[Malitha Kabir]

Dear Jason,
The geometry that you/me visualized in a 2D plot necessarily doesn't exist
in real world except a few planner molecules. To view 3D geometry of a
molecule, 2D representation doesn't work. Please feel free to do whatever
you want to do with your molecule while producing 2D graph. Everyone
understands that the plots are only for representation purpose. And please
consider geometry optimization/minimization of your molecule although ETKDG
produces very good quality geometry. Hope it helps! - malitha

On Sat, Dec 2, 2017 at 12:11 AM, Jason Biggs <jasondbi...@gmail.com> wrote:

> Thank you Malitha,
>
> If I'm understanding the Draw code (not a given, my python ist nicht gut),
> then MolToMPL (or MolToImage) is just using the 3D conformation generated
> by EmbedMolecule.  Is it just chopping off the z-coordinate?  For
> acetylene, this works out because it gets embedded mostly in the XY plane
> by default, but it would fail if the 3D conformer were aligned along the
> z-axis.
>
> I would think GenerateDepictionMatching3DStructure is the safe way to do
> this, but it also seems to have trouble with acetylene
>
> m = Chem.MolFromSmiles('C#C')
> m2=Chem.rdmolops.AddHs(m)
> AllChem.EmbedMolecule(m2, AllChem.ETKDG())
> m3=Chem.rdmolops.AddHs(m)
> Chem.rdDepictor.GenerateDepictionMatching3DStructure(m3,m2)
> m3.GetConformer(0).GetPositions()
>
>
> array([[  1.60734892e-16,   7.5000e-01,   0.e+00],
>[ -1.14810637e-16,  -7.5000e-01,   0.e+00],
>[ -4.82204677e-16,  -7.5000e-01,   0.e+00],
>[  4.36280422e-16,   7.5000e-01,   0.e+00]])
>
>
> The above seems to happen with any terminal alkyne hydrogen.  I will 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 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)
>>
>> *** source code link (non specific to your question though)
>> https://github.com/rdkit/rdkit
>>
>> Thanks. - malitha
>>
>>
>> On Fri, Dec 1, 2017 at 6:42 AM, Jason Biggs <jasondbi...@gmail.com>
>> wrote:
>>
>>>
>>> m = Chem.MolFromSmiles('C#C')
>>>
>>>
>>> renders fine
>>>
>>> [image: Inline image 1]
>>>
>>> but adding in the hydrogens, they don't snap to a linear arrangement
>>>
>>> m2=Chem.rdmolops.AddHs(m)
>>>
>>>
>>> [image: Inline image 3]
>>>
>>>
>>> This doesn't just affect acetylene, but any terminal alkyne, like
>>> 'c1ccc(CCC#C)cc1'.
>>>
>>> I can write a hack on my end to look for this special case, but where in
>>> the drawing code does it decide where to place hydrogens?
>>>
>>> Jason Biggs
>>>
>>>
>>> 
>>> --
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>>>
>>>
>>
>
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Re: [Rdkit-discuss] bad coordinates for acetylenic hydrogens

[Malitha Kabir]

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)

*** source code link (non specific to your question though)
https://github.com/rdkit/rdkit

Thanks. - malitha


On Fri, Dec 1, 2017 at 6:42 AM, Jason Biggs  wrote:

>
> m = Chem.MolFromSmiles('C#C')
>
>
> renders fine
>
> [image: Inline image 1]
>
> but adding in the hydrogens, they don't snap to a linear arrangement
>
> m2=Chem.rdmolops.AddHs(m)
>
>
> [image: Inline image 3]
>
>
> This doesn't just affect acetylene, but any terminal alkyne, like
> 'c1ccc(CCC#C)cc1'.
>
> I can write a hack on my end to look for this special case, but where in
> the drawing code does it decide where to place hydrogens?
>
> Jason Biggs
>
>
> 
> --
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Re: [Rdkit-discuss] Non-redundant database of molecules

[Malitha Kabir]

That's great to hear you got things running. That was basically due to the
path update. Have a great day! - malitha.

On Sep 15, 2017 3:44 AM, "Wandré" <wandrevel...@gmail.com> wrote:

> I don't know what I do, but now everything *is working fine.*
> My last commands:
>
> Reinstall Anaconda2
>
> Trying to compile the RDKit
>
>- sudo tar xzvf RDKit_2016_03_1.tgz -C ~/anaconda2/
>- vim ~/.bashrc (update the variables with the new path of rdkit)
>- . ~/.bashrc
>- cd ~/anaconda2/rdkit
>- mkdir build
>- cd build
>- cmake -DRDK_BUILD_INCHI_SUPPORT=ON ..
>- make -j 4 (ERROR on 50%)
>- make install (ERROR on 24%)
>
>
> sudo apt-get install python-rdkit librdkit1 rdkit-data
> sudo apt-get update
> conda install -c rdkit rdkit
>
>
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> 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 Sistemas - LBS, DCC, UFMG
>
> 2017-09-14 18:28 GMT-03:00 Wandré <wandrevel...@gmail.com>:
>
>> I really can't do this right...
>> I am thinking in reinstall Ubuntu and try again. Now the RDKit doesn't
>> works.
>>
>>
>> --
>> Wandré Nunes de Pinho Veloso
>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
>> 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 Sistemas - LBS, DCC, UFMG
>>
>> 2017-09-14 15:07 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>>
>>> Hi Wandré,
>>>
>>> Sorry to see you in trouble again.
>>>
>>> If you see the massages then
>>> # All requested packages already installed.
>>> # packages in environment at /home/wandre/anaconda2:
>>> #
>>> rdkit 2017.03.3   np111py27_1rdkit
>>>
>>> so your rdkit should be at
>>> /home/wandre/anaconda2/
>>>
>>> But it is trying to import from
>>> /opt/rdkit-Release_2016_03_1/rdkit/
>>>
>>> So the path variable is still NOT correct. It is good to see that you
>>> installed conda correctly and rdkit i think installed correctly.
>>>
>>> Therefore I suspect that you need to remove the previously path for
>>> rdkit (you probably set those during installing from source).
>>>
>>> I forgot what linux command will do that for you. Have a great day!
>>>
>>> *** I will update the answer whenever I get the appropriate linux
>>> command.
>>>
>>> - malitha
>>>
>>>
>>>
>>> On Thu, Sep 14, 2017 at 11:38 PM, Wandré <wandrevel...@gmail.com> wrote:
>>>
>>>> Thanks Malitha,
>>>>
>>>> When I install Anaconda I said yes to all questions.
>>>> When I trying to reinstall the RDKit, this message appears:
>>>>
>>>> wandre@wandreLinux:~/anaconda2$ conda install -c rdkit rdkit
>>>> Fetching package metadata ...
>>>> Solving package specifications: .
>>>>
>>>> # All requested packages already installed.
>>>> # packages in environment at /home/wandre/anaconda2:
>>>> #
>>>> rdkit 2017.03.3   np111py27_1rdkit
>>>>
>>>> When I run "python", appears:
>>>>
>>>> Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016,
>>>> 23:09:15)
>>>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>> Anaconda is brought to you by Continuum Analytics.
>>>> Please check out: http://continuum.io/thanks and https://anaconda.org
>>>> >>> import rdkit
>>>> >>> from rdkit import Chem
>>>> Traceback (most recent call last):
>>>>   File "", line 1, in 
>>>>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18,
&g

Re: [Rdkit-discuss] Non-redundant database of molecules

[Malitha Kabir]

Hi Wandré,

Sorry to see you in trouble again.

If you see the massages then
# All requested packages already installed.
# packages in environment at /home/wandre/anaconda2:
#
rdkit 2017.03.3   np111py27_1rdkit

so your rdkit should be at
/home/wandre/anaconda2/

But it is trying to import from
/opt/rdkit-Release_2016_03_1/rdkit/

So the path variable is still NOT correct. It is good to see that you
installed conda correctly and rdkit i think installed correctly.

Therefore I suspect that you need to remove the previously path for rdkit
(you probably set those during installing from source).

I forgot what linux command will do that for you. Have a great day!

*** I will update the answer whenever I get the appropriate linux command.

- malitha



On Thu, Sep 14, 2017 at 11:38 PM, Wandré <wandrevel...@gmail.com> wrote:

> Thanks Malitha,
>
> When I install Anaconda I said yes to all questions.
> When I trying to reinstall the RDKit, this message appears:
>
> wandre@wandreLinux:~/anaconda2$ conda install -c rdkit rdkit
> Fetching package metadata ...
> Solving package specifications: .
>
> # All requested packages already installed.
> # packages in environment at /home/wandre/anaconda2:
> #
> rdkit 2017.03.3   np111py27_1rdkit
>
> When I run "python", appears:
>
> Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> Anaconda is brought to you by Continuum Analytics.
> Please check out: http://continuum.io/thanks and https://anaconda.org
> >>> import rdkit
> >>> from rdkit import Chem
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18, in
> 
> from rdkit import rdBase
> ImportError: cannot import name rdBase
>
>
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> 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 Sistemas - LBS, DCC, UFMG
>
> 2017-09-14 9:17 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>
>> Hi Wandré,
>>
>> Good day! It's malitha.
>>
>> Considering your first question I would say, the path variable NOT set
>> correctly. To avoid having gymnastic with linux system you may consider the
>> following steps:
>>
>>1. Install miniconda or andcona from https://conda.io/miniconda.html
>>and command yes (y) when it says to add path variable to python shipped
>>with conda. I mean python within conda would be your default python. After
>>installing it, when you run the command <<<<>>>>> from shell you
>>will see something like <<>> at the screen
>>2. Install rdkit from https://anaconda.org/rdkit/rdkit on top of conda
>>
>>
>> For question regarding energy minimization, you may find the following
>> link helpful.
>> https://sourceforge.net/p/rdkit/mailman/message/28298074/
>>
>> I hope, it helps!
>>
>> - malitha
>>
>> On Thu, Sep 14, 2017 at 4:22 PM, Wandré <wandrevel...@gmail.com> wrote:
>>
>>> So,
>>> 1) I run all the commands in tutorial of installation of RDKit in Conda (
>>> https://github.com/rdkit/conda-rdkit), but, when I run python and try
>>> to import Chem ("from rdkit import Chem") appears an error message:
>>> Traceback (most recent call last):
>>>   File "", line 1, in 
>>>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18,
>>> in 
>>> from rdkit import rdBase
>>> ImportError: cannot import name rdBase
>>>
>>> 2) Thanks for all the references
>>>
>>> 3) Which function generate this "energy minimized molecule"?
>>>
>>> --
>>> Wandré Nunes de Pinho Veloso
>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>> UFMG
>>> Pesquisador do INSILICO - Grupo Interdisciplinar em Simulação e
>>> Inteligência Computacional - UNIFEI
>>> Membro do Grupo de Pesquisa Ass

Re: [Rdkit-discuss] Non-redundant database of molecules

[Malitha Kabir]

Hi Wandré,

Good day! It's malitha.

Considering your first question I would say, the path variable NOT set
correctly. To avoid having gymnastic with linux system you may consider the
following steps:

   1. Install miniconda or andcona from https://conda.io/miniconda.html and
   command yes (y) when it says to add path variable to python shipped with
   conda. I mean python within conda would be your default python. After
   installing it, when you run the command <<<<>>>>> from shell you
   will see something like <<>> at the screen
   2. Install rdkit from https://anaconda.org/rdkit/rdkit on top of conda


For question regarding energy minimization, you may find the following link
helpful.
https://sourceforge.net/p/rdkit/mailman/message/28298074/

I hope, it helps!

- malitha

On Thu, Sep 14, 2017 at 4:22 PM, Wandré <wandrevel...@gmail.com> wrote:

> So,
> 1) I run all the commands in tutorial of installation of RDKit in Conda (
> https://github.com/rdkit/conda-rdkit), but, when I run python and try to
> import Chem ("from rdkit import Chem") appears an error message:
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/opt/rdkit-Release_2016_03_1/rdkit/Chem/__init__.py", line 18, in
> 
> from rdkit import rdBase
> ImportError: cannot import name rdBase
>
> 2) Thanks for all the references
>
> 3) Which function generate this "energy minimized molecule"?
>
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> 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 Sistemas - LBS, DCC, UFMG
>
> 2017-09-13 17:32 GMT-03:00 Malitha Kabir <malitha12...@gmail.com>:
>
>> Hi Wandré,
>>
>> 1) apt-get installs rdkit 2013 (link below). So, please install it
>> through conda (as Markus suggested)
>> https://packages.ubuntu.com/trusty/python/python-rdkit
>>
>> 2) I am not familiar with the case of wrong SMILE generation. But the
>> link below says something more that I think you need to know.
>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495655/
>>
>> 3) As you are trying to store data, it would be great to consider whether
>> you are storing energy minimized molecule or not. (my opinion). Surface
>> area related descriptors will yield different result and bond connectivity
>> related descriptor will yield same result in both cases.
>>
>> 4) Sharing my personal experience, during my undergraduate school part of
>> my final year project was stressed up with conceptual questions. I failed
>> to utilize the  blessing of advanced development due to the lack of time.
>> The later experience was not so good.
>>
>> Please keep in mind that we can generate a non redundant database with
>> few molecules but for millions of molecules it should be quite though task.
>> Have a great day!
>>
>> - malitha
>>
>>
>>
>>
>> On Thu, Sep 14, 2017 at 2:05 AM, Markus Sitzmann <
>> markus.sitzm...@gmail.com> wrote:
>>
>>> PS. The conda version has InChI support
>>>
>>> On Wed, Sep 13, 2017 at 10:04 PM, Markus Sitzmann <
>>> markus.sitzm...@gmail.com> wrote:
>>>
>>>> Strong recommendation: use the conda version:
>>>>
>>>> http://www.rdkit.org/docs/Install.html
>>>>
>>>> On Wed, Sep 13, 2017 at 9:58 PM, Wandré <wandrevel...@gmail.com> wrote:
>>>>
>>>>> I just run sudo apt-get install python-rdkit librdkit1 rdkit-data 
>>>>> I'm trying to solve this with this link: http://www.blopig.com/bl
>>>>> og/2013/02/how-to-install-rdkit-on-ubuntu-12-04/
>>>>>
>>>>> --
>>>>> Wandré Nunes de Pinho Veloso
>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>>>> UFMG
>>>>> 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 Sistemas - LBS, DCC, UFMG
>>>>>
>>>>&g

Re: [Rdkit-discuss] Non-redundant database of molecules

[Malitha Kabir]

Hi Wandré,

1) apt-get installs rdkit 2013 (link below). So, please install it through
conda (as Markus suggested)
https://packages.ubuntu.com/trusty/python/python-rdkit

2) I am not familiar with the case of wrong SMILE generation. But the link
below says something more that I think you need to know.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3495655/

3) As you are trying to store data, it would be great to consider whether
you are storing energy minimized molecule or not. (my opinion). Surface
area related descriptors will yield different result and bond connectivity
related descriptor will yield same result in both cases.

4) Sharing my personal experience, during my undergraduate school part of
my final year project was stressed up with conceptual questions. I failed
to utilize the  blessing of advanced development due to the lack of time.
The later experience was not so good.

Please keep in mind that we can generate a non redundant database with few
molecules but for millions of molecules it should be quite though task.
Have a great day!

- malitha




On Thu, Sep 14, 2017 at 2:05 AM, Markus Sitzmann <markus.sitzm...@gmail.com>
wrote:

> PS. The conda version has InChI support
>
> On Wed, Sep 13, 2017 at 10:04 PM, Markus Sitzmann <
> markus.sitzm...@gmail.com> wrote:
>
>> Strong recommendation: use the conda version:
>>
>> http://www.rdkit.org/docs/Install.html
>>
>> On Wed, Sep 13, 2017 at 9:58 PM, Wandré <wandrevel...@gmail.com> wrote:
>>
>>> I just run sudo apt-get install python-rdkit librdkit1 rdkit-data 
>>> I'm trying to solve this with this link: http://www.blopig.com/bl
>>> og/2013/02/how-to-install-rdkit-on-ubuntu-12-04/
>>>
>>> --
>>> Wandré Nunes de Pinho Veloso
>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>> UFMG
>>> 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 Sistemas - LBS, DCC, UFMG
>>>
>>> 2017-09-13 16:55 GMT-03:00 Markus Sitzmann <markus.sitzm...@gmail.com>:
>>>
>>>> How did you install rdkit so far? And where? Is it the conda/anaconda
>>>> version?
>>>>
>>>> On Wed, Sep 13, 2017 at 9:39 PM, Wandré <wandrevel...@gmail.com> wrote:
>>>>
>>>>> How to install RDKit with InChI?
>>>>> When I run Chem.inchi.INCHI_AVAILABLE, the result is False
>>>>>
>>>>> --
>>>>> Wandré Nunes de Pinho Veloso
>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>>>> UFMG
>>>>> 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 Sistemas - LBS, DCC, UFMG
>>>>>
>>>>> 2017-09-13 16:30 GMT-03:00 Wandré <wandrevel...@gmail.com>:
>>>>>
>>>>>> Thanks Malitha.
>>>>>> I choose this descriptors because I will store this on my database,
>>>>>> so, will be fast compare one molecule before insert them in database.
>>>>>> 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).
>>>>>>
>>>>>> --
>>>>>> Wandré Nunes de Pinho Veloso
>>>>>> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
>>>>>> Doutorando em Bioinformática - Universidade Federal de Minas Gerais -
>>>>>> UFMG
>>>>>> 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 Sistemas - LBS, DCC, UFMG
>>>>>>
>>>>>> 2017-09-13 16:22 GMT-03:00 Malitha Kabir <mali

Re: [Rdkit-discuss] Non-redundant database of molecules

[Malitha Kabir]

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
descriptors! So, a careful look up at those makes a lot of sense to me.
Conceptually, descriptor matching should follow a sequence (I don't know
what sequence would be ideal) - for example MolWt should match first (H
contribution and ions should be taken into consideration here) and then
subsequent matching of other descriptors (might be different while writing
programs). There are a few reading materials on molecular fingerprint and
database schema. You may have a look at those.

The links are from Daylight. I am neither involved with the company nor
their product.
http://www.daylight.com/dayhtml/doc/theory/theory.finger.html
http://www.daylight.com/dayhtml/doc/theory/theory.thor.html

Best regards,
- malitha


On Thu, Sep 14, 2017 at 12:43 AM, Wandré  wrote:

> Thanks for all the answers.
>
> Reading all answers, I think in something different... If the SMILES
> (Chem.MolToSmiles(mol,isomericSmiles=True)) and Inchi
> (Chem.MolToInchi(mol)) can generate the same value in different molecules,
> I will generate others descriptors (NumHDonors, NumHAcceptors,
> RingCount, GetNumAtoms, TPSA, pyLabuteASA, MolWt, CalcNumRotatableBonds
> and MolLogP) to compare all the molecules that SMILES and Inchi are the
> same.
> If all this data are the same, I will generate the fingerprint (Atompair
> for exemple) and use Tanimoto coefficient and, if this value, when I
> compare two molecules, is 1, this molecules are the same.
>
> Where is my mistake (I think that is, one or more, mistakes)?
>
> Thanks!
>
> --
> Wandré Nunes de Pinho Veloso
> Professor Assistente - Unifei - Campus Avançado de Itabira-MG
> Doutorando em Bioinformática - Universidade Federal de Minas Gerais - UFMG
> 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 Sistemas - LBS, DCC, UFMG
>
> 2017-09-13 14:19 GMT-03:00 Dimitri Maziuk :
>
>> On 09/13/2017 11:46 AM, Markus Sitzmann wrote:
>> > The case that you have 3D information available for a molecule dataset
>> is rare, if you want it trustworthy it gets even worse than that. And what
>> is the point then to generate the configuration of a molecule first if you
>> can not trust that either?
>>
>> Veering further off topic, do you even care in the first place? E.g. if
>> your molecule always exists as a mixture of isomers, except in some
>> megabuck-per-microgram painstakingly created reference samples, a
>> 3D-based system will represent it as two distinct molecules. Whereas you
>> want it represented as one.
>>
>> Last I looked PDB Ligand Expo had two different benzenes. Their software
>> doesn't (didn't?) do the circle version so they don't have the third one.
>>
>> --
>> Dimitri Maziuk
>> Programmer/sysadmin
>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
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>>
>>
>
> 
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Re: [Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

[Malitha Kabir]

Hi,

I have submitted a pull request at rdkit GSoC2017 branch for merging the
most recent development on 3D visualization of molecules. Your comment on
that for further improvement is highly appreciate.

And please feel free to let me know about the new features. I will
definitely try to include those too.

Pull request link:
https://github.com/rdkit/rdkit/pull/1562

Files at pull request are

   1. IPythonConsoleIntegration.py (at folder rdkit/Chem/Draw)
   2. LigandExtract.py (at folder rdkit/Chem/ChemUtils)
   3. Notebooks (7 notebooks without images - size : 5/6 KB each)

I have added the *notebooks, associated images, and pull request link* at
following link. You may have a look at the images too.
https://github.com/malithakabir/RDKitGSoC2017/tree/master/updateAfterGSoC

Thank you very much for your time. Have a great day!

sincerely,
- malitha

On Wed, Sep 6, 2017 at 2:44 PM, Greg Landrum <greg.land...@gmail.com> wrote:

> The plan here is that this code will eventually be merged onto master so
> that it becomes part of the main RDKit distribution.
>
> I will try to do some more testing so that this can be done before the
> 2017_09 release, but I'm not sure that I will be able to do that. Feedback
> from the rest of the community is very welcome and would help with this
> process.
>
> Best,
> -greg
>
>
> On Fri, Sep 1, 2017 at 5:43 AM, Paul Czodrowski <
> paul.czodrow...@merckgroup.com> wrote:
>
>> Malitha, 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:* rdkit <rdkit-discuss@lists.sourceforge.net>
>> *Betreff:* [Rdkit-discuss] News on 3D molecule visualization in RDKit
>> (project: RDKit - 3Dmol.js integration)
>>
>>
>>
>> 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 rdkit:GSoC2017 branch.
>>
>>
>>
>> I would like to request you to check whether those can come in use and
>> drop your feedback for the improvement. I will keep working on it's
>> improvement throughout the coming month also. Kindly feel free to visit the
>> following link for work details: https://github.com/malithakabi
>> r/RDKitGSoC2017
>>
>>
>>
>> In future, I will request information in mailing list whenever I face in
>> trouble in codes rdkit code related issues. I wish, you will gladly helping
>> me providing information and directions. Many thanks in advance for that.
>>
>>
>>
>> I am extremely sorry of being unresponsive in mailing list due to the
>> lack of my knowledge/ability to answer those. I am trying my best to be
>> responsive in mailing list to provide community support.
>>
>>
>>
>> On a personal note I would like to express my sincere gratitude to my
>> mentors (paul and greg) and reviewer (peter) for their time and guidance
>> throughout the summer 2017. And warm thanks to Brian for merging the codes.
>>
>>
>>
>> Thank you very much for your time. Have a great day!
>>
>>
>>
>> Sincerely,
>>
>> - malitha
>>
>>
>>
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>> ---

[Rdkit-discuss] News on 3D molecule visualization in RDKit (project: RDKit - 3Dmol.js integration)

[Malitha Kabir]

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 rdkit:GSoC2017 branch.

I would like to request you to check whether those can come in use and drop
your feedback for the improvement. I will keep working on it's improvement
throughout the coming month also. Kindly feel free to visit the following
link for work details: https://github.com/malithakabir/RDKitGSoC2017

In future, I will request information in mailing list whenever I face in
trouble in codes rdkit code related issues. I wish, you will gladly helping
me providing information and directions. Many thanks in advance for that.

I am extremely sorry of being unresponsive in mailing list due to the lack
of my knowledge/ability to answer those. I am trying my best to be
responsive in mailing list to provide community support.

On a personal note I would like to express my sincere gratitude to my
mentors (paul and greg) and reviewer (peter) for their time and guidance
throughout the summer 2017. And warm thanks to Brian for merging the codes.

Thank you very much for your time. Have a great day!

Sincerely,
- malitha
--
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Re: [Rdkit-discuss] Molecule Editting in RDKit

[Malitha Kabir]

To Gerg Landrum,
Dear sir,
Your script worked as expected and I have got idea on what to do. Many
thanks for the tutorial.
Sincerely,
Malitha


On Jul 5, 2017 12:07 AM, "Greg Landrum" <greg.land...@gmail.com> wrote:

> Hi Malitha,
>
> Here's a gist that provides, I think, 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,
>>
>> 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
>> geometry information (xyz).
>>
>> However, my question is:
>>
>> Is it possible to set custom coordinates (xyz) to any kinds of RDKit
>> object that represents a molecule class?
>>
>> *** it would be great if you kindly manage time to provide me a complete
>> molecule building tutorial. I'm very very confused about the events that
>> happen behind the seen when we typically create molecules from SD file
>> through Python API.
>>
>> *** I am travelling right now. So, I will be able to respond against your
>> queries/suggestions after 10/15 hours.
>>
>> Many thanks for kindly looking into it.
>>
>> Best regards,
>> -Malitha
>>
>> 
>> --
>> 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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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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[Rdkit-discuss] Molecule Editting in RDKit

[Malitha Kabir]

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
geometry information (xyz).

However, my question is:

Is it possible to set custom coordinates (xyz) to any kinds of RDKit object
that represents a molecule class?

*** it would be great if you kindly manage time to provide me a complete
molecule building tutorial. I'm very very confused about the events that
happen behind the seen when we typically create molecules from SD file
through Python API.

*** I am travelling right now. So, I will be able to respond against your
queries/suggestions after 10/15 hours.

Many thanks for kindly looking into it.

Best regards,
-Malitha
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Re: [Rdkit-discuss] How to get a list of available properties from SD file

[Malitha Kabir]

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(m0.GetPropNames()) returned the object I need.
> Thank you very much.
>
> -Malitha
>
>
>
>
> On Tue, Jun 27, 2017 at 3:45 PM, Maciek Wójcikowski <mac...@wojcikowski.pl
> > wrote:
>
>> Hi,
>>
>> There is a method GetPropsAsDict() or GetPropNames() for RDKit molecule.
>> 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...@gmail.com>:
>>
>>> 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:
>>> https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf
>>>
>>> That file contains previously calculated properties (eg: Cluster,
>>> MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:
>>>
>>> from rdkit.Chem.rdmolfiles import SDMolSupplier
>>> file1='cdk2.sdf'
>>> data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
>>> strictParsing=True)
>>>
>>> I can access the first molecule by using the following code:
>>> m0=data[0]
>>>
>>> Now the object m0 (rdkit Mol object) contains all the necessary
>>> information about the molecule including properties.
>>>
>>> I need to create a list of previously calculated properties from that
>>> file without seeing the file visually.
>>>
>>> Any direction is warmly appreciated. Thank you very much. Have a great
>>> day!
>>>
>>> -Malitha
>>>
>>>
>>>
>>> 
>>> --
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>>>
>>>
>>
>
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Re: [Rdkit-discuss] How to get a list of available properties from SD file

[Malitha Kabir]

Dear Maciek Wójcikowski,

list(m0.GetPropNames()) returned the object I need.
Thank you very much.

-Malitha




On Tue, Jun 27, 2017 at 3:45 PM, Maciek Wójcikowski <mac...@wojcikowski.pl>
wrote:

> Hi,
>
> There is a method GetPropsAsDict() or GetPropNames() for RDKit molecule.
> 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...@gmail.com>:
>
>> 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:
>> https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf
>>
>> That file contains previously calculated properties (eg: Cluster,
>> MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:
>>
>> from rdkit.Chem.rdmolfiles import SDMolSupplier
>> file1='cdk2.sdf'
>> data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
>> strictParsing=True)
>>
>> I can access the first molecule by using the following code:
>> m0=data[0]
>>
>> Now the object m0 (rdkit Mol object) contains all the necessary
>> information about the molecule including properties.
>>
>> I need to create a list of previously calculated properties from that
>> file without seeing the file visually.
>>
>> Any direction is warmly appreciated. Thank you very much. Have a great
>> day!
>>
>> -Malitha
>>
>>
>>
>> 
>> --
>> 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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[Rdkit-discuss] How to get a list of available properties from SD file

[Malitha Kabir]

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:
https://github.com/rdkit/rdkit/blob/master/Docs/Book/data/cdk2.sdf

That file contains previously calculated properties (eg: Cluster,
MODEL.SOURCE etc.). I can read the file in RDKit using the following codes:

from rdkit.Chem.rdmolfiles import SDMolSupplier
file1='cdk2.sdf'
data=SDMolSupplier(fileName=file1, sanitize=True, removeHs=False,
strictParsing=True)

I can access the first molecule by using the following code:
m0=data[0]

Now the object m0 (rdkit Mol object) contains all the necessary information
about the molecule including properties.

I need to create a list of previously calculated properties from that file
without seeing the file visually.

Any direction is warmly appreciated. Thank you very much. Have a great day!

-Malitha
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Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Malitha Kabir]

Dear Paul,

>From your response, I think your ipywidgets is working fine. Now, you are
facing trouble with py3Dmol.

py3Dmol basically generates JavaScript codes (3Dmol.js) and IPython injects
those in web browser. So, will you kindly share what error printed in your
browser console?

Off topic: The following link shows how to see browser console from Google
Chrome https://developers.google.com/web/tools/chrome-devtools/console/

Best regards,
Malitha



On Tue, Jun 20, 2017 at 3:33 PM, Paul Czodrowski <
paul.czodrow...@merckgroup.com> wrote:

> Dear Malitha,
>
> Dear RDKitters,
>
>
>
> thanks a lot for your investigations!
>
>
>
> Indeed, this issue seems somehow browser-related; please check the
> attachment which shows the output in a different browser (Firefox@openSUSE
> vs. IE11@Win7 from my previous mail).
>
>
>
> I’m now able to find a button-like widget but no structure…
>
>
>
>
>
> This presumably looks like off-topic for this mailing list. However, if
> anyone can point into the right direction: that would be highly appreciated.
>
>
>
>
>
> Cheers,
> Paul
>
>
>
>
>
>
>
>
>
> 
> Paul Czodrowski, PhD
>
>
>
> Global Research & Development | Discovery Technologies
>
>
>
> *Merck*
>
>
>
> Merck KGaA | Frankfurter Str. 250 | Postcode: A019/001 | 64293 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.merckgroup.com/mandatories
>
>
>
> *Von:* Malitha Kabir [mailto:malitha12...@gmail.com]
> *Gesendet:* Dienstag, 20. Juni 2017 10:58
> *An:* Paul Czodrowski <paul.czodrow...@merckgroup.com>
> *Cc:* rdkit-discuss@lists.sourceforge.net
>
> *Betreff:* Re: [Rdkit-discuss] ipywidgets & py3Dmol
>
>
>
> 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 2.7.12 and it is
> working well with the notebook you attached.
>
>
>
> For your 1st question:
>
>
>
> The following stackoverflow discussion might help.
>
> https://stackoverflow.com/questions/36351109/ipython-
> notebook-ipywidgets-does-not-show
>
>
>
> Kindly consider the readme of ipywidgets. https://github.com/jupyter-
> widgets/ipywidgets/blob/master/README.md As per their suggestions, if you
> install ipywidgets using pip then you need to enable widgetsnbextension
> (widgets notebook extension) manually.
>
>
>
> Running the following line from shell will do that for you.
>
> jupyter nbextension enable --py --sys-prefix widgetsnbextension
>
> Kindly try out the following code. It should show a slider in your
> notebook if everything is fine.
>
>
>
> from __future__ import print_function
>
> import ipywidgets as widgets
>
>
>
> slider = widgets.SelectionSlider(
>
> options=[1,2,3],
>
> value=1
>
> )
>
> slider
>
>
>
> Probably trying with different web browser may help (I am not sure though)
>
>
>
> Best Regards,
>
> Malitha
>
>
>
>
>
>
>
> On Tue, Jun 20, 2017 at 1:56 PM, Paul Czodrowski <
> paul.czodrow...@merckgroup.com> wrote:
>
> Dear Axel,
>
>
>
> thanks a lot for this very helpful information!
>
>
>
>
>
> The only difference I could figure out:
>
> Python 2.7.13 instead of Python 3.5.3
>
>
>
> @RDKitters:
>
> Can this really cause such a different behavior?
>
>
>
> Cheers,
>
> Paul
>
>
>
> P.S.: I’m aware of http://www.python3statement.org/ ;)
>
>
>
>
>
> *Von:* Axel Pahl [mailto:axelp...@gmx.de]
> *Gesendet:* Dienstag, 20. Juni 2017 09:35
> *An:* rdkit-discuss@lists.sourceforge.net
> *Betreff:* Re: [Rdkit-discuss] ipywidgets & py3Dmol
>
>
>
> Hi Paul,
>
> I just tried the example Notebook that you provided and it runs just as in
> Greg's blog post, i.e. with the interactive slider (see attached
> screenshot).
> This is the configuration I used (in Anaconda):
>
> python3.5.3
> rdkit 2017.03.2
> notebook  5.0.0
> ipywidgets6.0.0
> py3Dmol   0.6.3
>
> Kind regards,
> Axel

Re: [Rdkit-discuss] ipywidgets & py3Dmol

[Malitha Kabir]

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 2.7.12 and it is
working well with the notebook you attached.

For your 1st question:

The following stackoverflow discussion might help.
https://stackoverflow.com/questions/36351109/ipython-notebook-ipywidgets-does-not-show

Kindly consider the readme of ipywidgets.
https://github.com/jupyter-widgets/ipywidgets/blob/master/README.md As per
their suggestions, if you install ipywidgets using pip then you need to
enable widgetsnbextension (widgets notebook extension) manually.

Running the following line from shell will do that for you.

jupyter nbextension enable --py --sys-prefix widgetsnbextension

Kindly try out the following code. It should show a slider in your notebook
if everything is fine.

from __future__ import print_function
import ipywidgets as widgets

slider = widgets.SelectionSlider(
options=[1,2,3],
value=1
)
slider

Probably trying with different web browser may help (I am not sure though)

Best Regards,
Malitha



On Tue, Jun 20, 2017 at 1:56 PM, Paul Czodrowski <
paul.czodrow...@merckgroup.com> wrote:

> Dear Axel,
>
>
>
> thanks a lot for this very helpful information!
>
>
>
>
>
> The only difference I could figure out:
>
> Python 2.7.13 instead of Python 3.5.3
>
>
>
> @RDKitters:
>
> Can this really cause such a different behavior?
>
>
>
> Cheers,
>
> Paul
>
>
>
> P.S.: I’m aware of http://www.python3statement.org/ ;)
>
>
>
>
>
> *Von:* Axel Pahl [mailto:axelp...@gmx.de]
> *Gesendet:* Dienstag, 20. Juni 2017 09:35
> *An:* rdkit-discuss@lists.sourceforge.net
> *Betreff:* Re: [Rdkit-discuss] ipywidgets & py3Dmol
>
>
>
> Hi Paul,
>
> I just tried the example Notebook that you provided and it runs just as in
> Greg's blog post, i.e. with the interactive slider (see attached
> screenshot).
> This is the configuration I used (in Anaconda):
>
> python3.5.3
> rdkit 2017.03.2
> notebook  5.0.0
> ipywidgets6.0.0
> py3Dmol   0.6.3
>
> Kind regards,
> Axel
>
> On 20.06.2017 07:48, Paul Czodrowski wrote:
>
> Dear RDKitters,
>
>
>
> When trying to re-run Greg’s wonderful blog entry about the py3Dmol
> integration (https://rdkit.blogspot.de/2016/07/using-ipywidgets-and-
> py3dmol-to-browse.html ), I’m getting a different behavior (check the
> attachment with a screenshot and the jupyter notebook).
>
>
>
> Any help would be appreciated.
>
>
>
> Cheers,
> Paul
>
>
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
> any other person. If you have received this transmission in error, please
> notify the sender immediately and delete the message and any attachment
> from your system. Merck KGaA, Darmstadt, Germany and any of its
> subsidiaries do not accept liability for any omissions or errors in this
> message which may arise as a result of E-Mail-transmission or for damages
> resulting from any unauthorized changes of the content of this message and
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> subsidiaries do not guarantee that this message is free of viruses and does
> not accept liability for any damages caused by any virus transmitted
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>
>
>
>
> --
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> Check out the vibrant tech community on one of the world's most
>
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>
>
>
>
> ___
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>
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>
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>
>
>
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> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
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> notify the sender immediately and delete the message and any attachment
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> not 

Re: [Rdkit-discuss] RDKit-Py3DMol integration

[Malitha Kabir]

Dear Peter,

Thank you very much again. Have a great day!

Sincerely
-Malitha



On May 10, 2017 4:55 AM, "Peter S. Shenkin" <shen...@gmail.com> wrote:

> Hi, Malitha,
>
> I was trying to make a bit of joke, but of course the Welcome was sincere.
> ;-)
>
> Best,
> -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 anything that our community
>> wants me to accomplish. Being very realistic, all my targets are now set by
>> Paul and Gerg. My commitment here is to keep participating in RDKit and
>> 3Dmol.js after reaching the initial targets. Thanks much again.
>>
>> Notes to Paul:
>> Dear sir,
>> I am more than grateful to you for introducing me in RDKit community. You
>> are the motivation why I'm here right now. I will put my best effort
>> definitely. Thank you very much for all your worries.
>>
>> Notes to Gerg:
>> Dear sir,
>> Thank you very much for your time in mentoring me and also for putting
>> such useful tool for community use that comes totally free of cost. I will
>> keep working in RDKit development if my skills remain as per requirements.
>> Thank you very much again for reviewing proposal and future help as well.
>>
>> Notes to David Koes:
>> Dear sir,
>> I will come up with specific questions very soon (within one or two
>> weeks). I wish you don't mind getting my touch. Thanks much in advance for
>> your kind help.
>>
>> Sincerely,
>> -Malitha
>>
>>
>>
>> On May 10, 2017 1:59 AM, "Peter S. Shenkin" <shen...@gmail.com> wrote:
>>
>>> Welcome Malitha! The community expects you to fix everything that's
>>> broken ;-)
>>>
>>> (After all, you have the whole summer to do it)
>>>
>>> Cheers,
>>> -P.
>>>
>>> On Tue, May 9, 2017 at 1:06 PM, Paul Czodrowski <
>>> paul.czodrow...@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.
>>>>
>>>>
>>>>
>>>> Let’s give Malitha a warm welcome (and comprehensive replies during his
>>>> GSoC project)!
>>>>
>>>>
>>>>
>>>> On behalf of the mentors: Greg & Paul
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This message and any attachment are confidential and may be privileged
>>>> or otherwise protected from disclosure. If you are not the intended
>>>> recipient, you must not copy this message or attachment or disclose the
>>>> contents to any other person. If you have received this transmission in
>>>> error, please notify the sender immediately and delete the message and any
>>>> attachment from your system. Merck KGaA, Darmstadt, Germany and any of its
>>>> subsidiaries do not accept liability for any omissions or errors in this
>>>> message which may arise as a result of E-Mail-transmission or for damages
>>>> resulting from any unauthorized changes of the content of this message and
>>>> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
>>>> subsidiaries do not guarantee that this message is free of viruses and does
>>>> not accept liability for any damages caused by any virus transmitted
>>>> therewith.
>>>>
>>>>
>>>>
>>>> Click http://www.merckgroup.com/disclaimer to access the German,
>>>> French, Spanish and Portuguese versions of this disclaimer.
>>>>
>>>> 
>>>> --
>>>> 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
>>>>
>>>>
>>>
>>> 
>>> --
>>> 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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>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>
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Re: [Rdkit-discuss] RDKit-Py3DMol integration

[Malitha Kabir]

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 anything that our community
wants me to accomplish. Being very realistic, all my targets are now set by
Paul and Gerg. My commitment here is to keep participating in RDKit and
3Dmol.js after reaching the initial targets. Thanks much again.

Notes to Paul:
Dear sir,
I am more than grateful to you for introducing me in RDKit community. You
are the motivation why I'm here right now. I will put my best effort
definitely. Thank you very much for all your worries.

Notes to Gerg:
Dear sir,
Thank you very much for your time in mentoring me and also for putting such
useful tool for community use that comes totally free of cost. I will keep
working in RDKit development if my skills remain as per requirements. Thank
you very much again for reviewing proposal and future help as well.

Notes to David Koes:
Dear sir,
I will come up with specific questions very soon (within one or two weeks).
I wish you don't mind getting my touch. Thanks much in advance for your
kind help.

Sincerely,
-Malitha



On May 10, 2017 1:59 AM, "Peter S. Shenkin" <shen...@gmail.com> wrote:

> Welcome Malitha! The community expects you to fix everything that's
> broken ;-)
>
> (After all, you have the whole summer to do it)
>
> Cheers,
> -P.
>
> On Tue, May 9, 2017 at 1:06 PM, Paul Czodrowski <
> paul.czodrow...@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.
>>
>>
>>
>> Let’s give Malitha a warm welcome (and comprehensive replies during his
>> GSoC project)!
>>
>>
>>
>> On behalf of the mentors: Greg & Paul
>>
>>
>>
>>
>>
>> This message and any attachment are confidential and may be privileged or
>> otherwise protected from disclosure. If you are not the intended recipient,
>> you must not copy this message or attachment or disclose the contents to
>> any other person. If you have received this transmission in error, please
>> notify the sender immediately and delete the message and any attachment
>> from your system. Merck KGaA, Darmstadt, Germany and any of its
>> subsidiaries do not accept liability for any omissions or errors in this
>> message which may arise as a result of E-Mail-transmission or for damages
>> resulting from any unauthorized changes of the content of this message and
>> any attachment thereto. Merck KGaA, Darmstadt, Germany and any of its
>> subsidiaries do not guarantee that this message is free of viruses and does
>> not accept liability for any damages caused by any virus transmitted
>> therewith.
>>
>>
>>
>> Click http://www.merckgroup.com/disclaimer to access the German, French,
>> Spanish and Portuguese versions of this disclaimer.
>>
>> 
>> --
>> 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
>>
>>
>
> 
> --
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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