[Rdkit-discuss] Element in reaction

[Nitzan Tzanani]

Hello all,

I am working on reactions in generalized form, such as

rxn = AllChem.ReactionFromSmarts('[C:1]=[N,O,S:2]>>[C:1]-[*:2]')

Is there an easy way to find out what were the elements in the reactant?
Was the second atom an oxygen, nitrogen or sulfur?
I hope someone can help me with this issue.

Thanks,

Nitzan
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[Rdkit-discuss] Conda-rdkit custom build

[Jennifer Wei]

Hi Greg,

I would be using it for myself, and maybe a few other labmates who are
interested.

After reading more about conda build, I have tried editing the meta.yaml
file to point to my fork of rdkit/rdkit with the necessary changes. This
works mostly, except now the build fails the tests. This is the case even
when I use conda-build to build the 2016-09 branch of the main rdkit/rdkit.

Connor, I'll try using your rdkit fork next.

Thank you!
Jennifer


On Tue, Oct 3, 2017 at 7:56 AM Greg Landrum  wrote:

> Hi Jennifer,
>
> On Mon, Oct 2, 2017 at 12:59 AM, Jennifer Wei  > wrote:
>
>>
>> I have one more question: I am a bit stuck as to how to rebuild my rdkit.
>> Ideally I would like to create a separate conda environment with the
>> modified rdkit. I have mostly followed the instructions from here:
>> https://github.com/rdkit/conda-rdkit
>> 
>>
>> How do I modify the instructions to make a package from my customized
>> rdkit source code? The instructions seem to be for getting the general
>> conda build rather than making your own conda environment from customized
>> source code in rdkit/rdkit.
>>
>
> Are you looking to build a copy just for you to run or do you want to
> distribute it to others?
>
> -greg
>
>
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Re: [Rdkit-discuss] Building RDKit from source

[Tyler Backman]

This might also be of interest, I have a Dockerfile here which builds
RDKit, including the postgresql cartridge:
https://github.com/JBEI/clusterCAD/blob/master/debian-cheminformatics/Dockerfile

Sincerely,
Tyler Backman

On Tue, Oct 3, 2017 at 2:45 AM, Greg Landrum  wrote:
> Thanks for sharing that Kovas.
> I'm sure this will be helpful for people who don't want to/can't use
> anaconda.
>
> Best,
> -greg
>
>
> On Mon, Oct 2, 2017 at 7:34 PM, Kovas Palunas 
> wrote:
>>
>> Hi all,
>>
>>
>> I thought I'd share a script I wrote to build RDKit and Boost together
>> which has worked for me on Linux (CentOS) and Mac machines so far.  I run
>> RDKit in a virtualenv Python environment (not in anaconda), so this may only
>> be helpful for a small group of RDKitters.  Hopefully some of you do find
>> this useful - it has personally saved me a lot of time getting RDKit
>> installed on multiple machines.
>>
>>
>> Note: please skim through the script to make sure you know what variables
>> inside it are set to what before running - there are multiple ways to
>> specify what code to build that may be useful for different purposes (and
>> some are commented out).
>>
>>
>> Make sure you pip install numpy before running (I should probably just add
>> this to the script).
>>
>>
>> Also, I have only tested this on RDKit 2016_09_3 and Boost 1_63_0.
>>
>>
>>  - Kovas
>>
>>
>>
>>
>> --
>> 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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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
>
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-- 
Tyler W. H. Backman
Postdoctoral Fellow
Lawrence Berkeley National Laboratory
Joint BioEnergy Institute
Agile BioFoundry

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Re: [Rdkit-discuss] How to number the outputs of a reaction?

[Greg Landrum]

Hi Jennifer,

On Mon, Oct 2, 2017 at 12:59 AM, Jennifer Wei 
wrote:

>
> I have one more question: I am a bit stuck as to how to rebuild my rdkit.
> Ideally I would like to create a separate conda environment with the
> modified rdkit. I have mostly followed the instructions from here:
> https://github.com/rdkit/conda-rdkit
>
> How do I modify the instructions to make a package from my customized
> rdkit source code? The instructions seem to be for getting the general
> conda build rather than making your own conda environment from customized
> source code in rdkit/rdkit.
>

Are you looking to build a copy just for you to run or do you want to
distribute it to others?

-greg
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Re: [Rdkit-discuss] Building RDKit from source

[Greg Landrum]

Thanks for sharing that Kovas.
I'm sure this will be helpful for people who don't want to/can't use
anaconda.

Best,
-greg


On Mon, Oct 2, 2017 at 7:34 PM, Kovas Palunas 
wrote:

> Hi all,
>
>
> I thought I'd share a script I wrote to build RDKit and Boost together
> which has worked for me on Linux (CentOS) and Mac machines so far.  I run
> RDKit in a virtualenv Python environment (not in anaconda), so this may
> only be helpful for a small group of RDKitters.  Hopefully some of you
> do find this useful - it has personally saved me a lot of time getting
> RDKit installed on multiple machines.
>
>
> Note: please skim through the script to make sure you know what variables
> inside it are set to what before running - there are multiple ways to
> specify what code to build that may be useful for different purposes (and
> some are commented out).
>
>
> Make sure you pip install numpy before running (I should probably just add
> this to the script).
>
>
> Also, I have only tested this on RDKit 2016_09_3 and Boost 1_63_0.
>
>
>  - Kovas
>
>
> 
> --
> 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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