[Rdkit-discuss] Does RDKit Java have the functionality for calculating the 3D descriptors?

[Xuan Cao]

Hi,

I am using the RDKit in java. I found that 2D descriptors can be calculated 
through the RDKFuncs.class, but I couldn't find the 3D descriptors.

Thanks for help!

Xuan
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[Rdkit-discuss] search inside a RXN file

[Jerry Zhang]

Hi, all,

I know Rdkit can search a molecular in a SDF file.
Could Rdkit search a molecular in a RXN file?


Thanks,

Zhang
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Re: [Rdkit-discuss] anaconda and virtualenv

[Jerry Zhang]

Thanks. I also think it is better to switch to Anaconda. I am still new to
Anaconda. Does it have pip3?
I tried to install pip in my Anaconda virtual environment. However, when I
typed "which pip3", it still points to a local version.
It should point to the version in the Anaconda virtual environment.
Does any one know why?

Thanks


On Mon, Mar 18, 2019 at 6:03 AM Matthew Swain  wrote:

> Hi Tom,
>
> If you are using Anaconda, I would recommend just using conda environments
> for this:
>
>
> https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
>
> It is very tricky to get RDKit to work with virtualenv, but really easy
> with conda environments.
>
> Matt
>
> On Mar 18, 2019, at 06:13 AM, Tom Zhang  wrote:
>
> Hi, all,
>
> I am in a conflicting situation now between anaconda and virtualenv.
> I used anaconda to install Rdkit and it works great.
> However, I also have a lot of other python3 code and I use virtualenv for
> that.
> Now, my python3 code in virtualenv has to talk with Rdkit.
> What is the best solution here? Install Rdkit again in virtualenv?
> Could I use anaconda and virtualenv at the same time to run my python code
> and Rdkit?
> Will this cause any conflicting issues?
>
> Thanks,
>
> Tom
>
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Re: [Rdkit-discuss] anaconda and virtualenv

[Matthew Swain via Rdkit-discuss]

Hi Tom,

If you are using Anaconda, I would recommend just using conda environments for 
this:

https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html

It is very tricky to get RDKit to work with virtualenv, but really easy with 
conda environments.

Matt

On Mar 18, 2019, at 06:13 AM, Tom Zhang  wrote:


Hi, all,


I am in a conflicting situation now between anaconda and virtualenv.
I used anaconda to install Rdkit and it works great.
However, I also have a lot of other python3 code and I use virtualenv for that.
Now, my python3 code in virtualenv has to talk with Rdkit. 
What is the best solution here? Install Rdkit again in virtualenv?
Could I use anaconda and virtualenv at the same time to run my python code and 
Rdkit?
Will this cause any conflicting issues?


Thanks,


Tom 


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Re: [Rdkit-discuss] anaconda and virtualenv

[Malgorzata Werner]

Hi Tom,

Why don't you create a virtual environment in Anaconda and install RDkit there?

https://uoa-eresearch.github.io/eresearch-cookbook/recipe/2014/11/20/conda/

Create virtual environments for python with 
conda
uoa-eresearch.github.io
Upadate any packages if necessary by typing y to proceed.; 3. Create a virtual 
environment for your project. In the terminal client enter the following where 
yourenvname is the name you want to call your environment, and replace x.x with 
the Python version you wish to use. (To see a list of available python versions 
first, type conda search "^python$" and press enter.)

Best,

Gosia



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From: Tom Zhang 
Sent: 18 March 2019 07:13:25
To: RDKit Discuss
Subject: [Rdkit-discuss] anaconda and virtualenv

Hi, all,

I am in a conflicting situation now between anaconda and virtualenv.
I used anaconda to install Rdkit and it works great.
However, I also have a lot of other python3 code and I use virtualenv for that.
Now, my python3 code in virtualenv has to talk with Rdkit.
What is the best solution here? Install Rdkit again in virtualenv?
Could I use anaconda and virtualenv at the same time to run my python code and 
Rdkit?
Will this cause any conflicting issues?

Thanks,

Tom

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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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[Rdkit-discuss] anaconda and virtualenv

[Tom Zhang]

Hi, all,

I am in a conflicting situation now between anaconda and virtualenv.
I used anaconda to install Rdkit and it works great.
However, I also have a lot of other python3 code and I use virtualenv for
that.
Now, my python3 code in virtualenv has to talk with Rdkit.
What is the best solution here? Install Rdkit again in virtualenv?
Could I use anaconda and virtualenv at the same time to run my python code
and Rdkit?
Will this cause any conflicting issues?

Thanks,

Tom
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