Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

[Markus Sitzmann]

Hi JP,

From the Docker log you posted it is obvious that the build starts from the 
latest miniconda version which than will use python 3.6 as default, however one 
of the python packages still relies python 3.5. 

One thing you can try is to tell the conda install command in the docker script 
to go back to python 3.5 or create a python 3.5 based environment. 
Unfortunately I just don’t remember out of my head which option you have to use 
for this but you fill find it in the conda documentation. 

And as much I like the idea of conda, it is unfortunately one of the biggest 
troublemakers in my personal projects.

Another point is, if you look for one of the recent post from Greg here on the 
list, there is another problem with the latest conda version you might run into.


Markus


-
|  Markus Sitzmann
|  markus.sitzm...@gmail.com

> On 21. Nov 2017, at 16:53, Tim Dudgeon  wrote:
> 
> I've got some dockerfiles that might be worth a look.
> https://github.com/InformaticsMatters/docker_jupyter
> 
> Not sure if they will help.
> 
> Tim
> 
> 
>> On 21/11/2017 15:25, JP wrote:
>> Yo RDKitters,
>> 
>> I am running a CADD workshop for a group of MSc students and would like to 
>> show them some some RDKit awesomeness.
>> 
>> I thought the best way to do this is to use an rdkit enabled docker image + 
>> jupyter notebooks (they are comfortable with python).
>> 
>> In preparation, I tried building the docker image from the docker file at 
>> https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3 but 
>> this fails on Ubuntu 16.04.3 LTS with the following error:
>> 
>> $ docker build -t run_rdkit_conda 
>> https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
>> Downloading build context from remote url: 
>> https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
>>  357B
>> Sending build context to Docker daemon  2.048kB
>> Step 1/7 : FROM continuumio/miniconda3
>> latest: Pulling from continuumio/miniconda3
>> 85b1f47fba49: Pull complete 
>> 6b3cb0c49789: Pull complete 
>> fecb432dacf0: Pull complete 
>> f461f7e3890d: Pull complete 
>> Digest: 
>> sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc
>> Status: Downloaded newer image for continuumio/miniconda3:latest
>>  ---> f700f7f570c7
>> Step 2/7 : MAINTAINER Greg Landrum 
>>  ---> Running in ad6a648c18ba
>>  ---> 18e6d6093d5b
>> Removing intermediate container ad6a648c18ba
>> Step 3/7 : ENV PATH /opt/conda/bin:$PATH
>>  ---> Running in e21cf8e5332f
>>  ---> ddef65292068
>> Removing intermediate container e21cf8e5332f
>> Step 4/7 : ENV LANG C
>>  ---> Running in efa12ef17f37
>>  ---> 137d7e20350d
>> Removing intermediate container efa12ef17f37
>> Step 5/7 : RUN conda config --add channels  https://conda.anaconda.org/rdkit
>>  ---> Running in 79566bf4b6e9
>>  ---> 032965875391
>> Removing intermediate container 79566bf4b6e9
>> Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
>>  ---> Running in c5aa6417a63a
>> Fetching package metadata .
>> Solving package specifications: .
>> 
>> UnsatisfiableError: The following specifications were found to be in 
>> conflict:
>>   - cairocffi -> python 3.5* -> xz 5.0.5
>>   - python 3.6*
>> Use "conda info " to see the dependencies for each package.
>> 
>> The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo cairocffi 
>> jupyter' returned a non-zero code: 1
>> 
>> Any ideas?
>> JP
>> 
>> 
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Re: [Rdkit-discuss] How to create a list of molecules and iterate

[abhik]

Dear Maciek,

Thanks for the help. This has solved my problem.

Regards,
Abhik

On 2017-11-21 14:49, Maciek Wójcikowski wrote:

Hi,

Wrap the reader into a list() function:


mols = list(SDMolSupplier('in.sdf'))



Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-11-21 15:39 GMT+01:00 abhik :


Hi,

I am running a similarity search process using rdkit where my query
consists of ~20 templates and my target consists of ~1000 molecules.
How can I create a list (or any container) of molecules that I can
iterate later.

My present algorithm is

read template create molecule > read target create molecule >
calculate similarity
go back to template and follow the same process

But by doing this I am creating same molecule multiple times, which
is increasing the run time.

Thank in advance for any helps.
Regards,
Abhik



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Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

[Tim Dudgeon]

I've got some dockerfiles that might be worth a look.
https://github.com/InformaticsMatters/docker_jupyter

Not sure if they will help.

Tim



On 21/11/2017 15:25, JP wrote:

Yo RDKitters,

I am running a CADD workshop for a group of MSc students and would 
like to show them some some RDKit awesomeness.


I thought the best way to do this is to use an rdkit enabled docker 
image + jupyter notebooks (they are comfortable with python).


In preparation, I tried building the docker image from the docker file 
at 
https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3 
but this fails on Ubuntu 16.04.3 LTS with the following error:


$ docker build -t run_rdkit_conda 
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
Downloading build context from remote url: 
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile 
   357B

Sending build context to Docker daemon  2.048kB
Step 1/7 : FROM continuumio/miniconda3
latest: Pulling from continuumio/miniconda3
85b1f47fba49: Pull complete
6b3cb0c49789: Pull complete
fecb432dacf0: Pull complete
f461f7e3890d: Pull complete
Digest: 
sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc

Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> f700f7f570c7
Step 2/7 : MAINTAINER Greg Landrum >

 ---> Running in ad6a648c18ba
 ---> 18e6d6093d5b
Removing intermediate container ad6a648c18ba
Step 3/7 : ENV PATH /opt/conda/bin:$PATH
 ---> Running in e21cf8e5332f
 ---> ddef65292068
Removing intermediate container e21cf8e5332f
Step 4/7 : ENV LANG C
 ---> Running in efa12ef17f37
 ---> 137d7e20350d
Removing intermediate container efa12ef17f37
Step 5/7 : RUN conda config --add channels 
https://conda.anaconda.org/rdkit

 ---> Running in 79566bf4b6e9
 ---> 032965875391
Removing intermediate container 79566bf4b6e9
Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
 ---> Running in c5aa6417a63a
Fetching package metadata .
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in 
conflict:

  - cairocffi -> python 3.5* -> xz 5.0.5
  - python 3.6*
Use "conda info " to see the dependencies for each package.

The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo 
cairocffi jupyter' returned a non-zero code: 1


Any ideas?
JP


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Re: [Rdkit-discuss] How to create a list of molecules and iterate

[Maciek Wójcikowski]

Hi,

Wrap the reader into a list() function:

> mols = list(SDMolSupplier('in.sdf'))




Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2017-11-21 15:39 GMT+01:00 abhik :

> Hi,
>
> I am running a similarity search process using rdkit where my query
> consists of ~20 templates and my target consists of ~1000 molecules. How
> can I create a list (or any container) of molecules that I can iterate
> later.
>
> My present algorithm is
>
> read template create molecule > read target create molecule > calculate
> similarity
> go back to template and follow the same process
>
> But by doing this I am creating same molecule multiple times, which is
> increasing the run time.
>
>
> Thank in advance for any helps.
> Regards,
> Abhik
>
> 
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[Rdkit-discuss] Docker with (latest) rdkit+jupyter

[JP]

Yo RDKitters,

I am running a CADD workshop for a group of MSc students and would like to
show them some some RDKit awesomeness.

I thought the best way to do this is to use an rdkit enabled docker image +
jupyter notebooks (they are comfortable with python).

In preparation, I tried building the docker image from the docker file at
https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3 but
this fails on Ubuntu 16.04.3 LTS with the following error:

$ docker build -t run_rdkit_conda
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
Downloading build context from remote url:
https://raw.githubusercontent.com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
   357B
Sending build context to Docker daemon  2.048kB
Step 1/7 : FROM continuumio/miniconda3
latest: Pulling from continuumio/miniconda3
85b1f47fba49: Pull complete
6b3cb0c49789: Pull complete
fecb432dacf0: Pull complete
f461f7e3890d: Pull complete
Digest:
sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc
Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> f700f7f570c7
Step 2/7 : MAINTAINER Greg Landrum 
 ---> Running in ad6a648c18ba
 ---> 18e6d6093d5b
Removing intermediate container ad6a648c18ba
Step 3/7 : ENV PATH /opt/conda/bin:$PATH
 ---> Running in e21cf8e5332f
 ---> ddef65292068
Removing intermediate container e21cf8e5332f
Step 4/7 : ENV LANG C
 ---> Running in efa12ef17f37
 ---> 137d7e20350d
Removing intermediate container efa12ef17f37
Step 5/7 : RUN conda config --add channels  https://conda.anaconda.org/rdkit
 ---> Running in 79566bf4b6e9
 ---> 032965875391
Removing intermediate container 79566bf4b6e9
Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
 ---> Running in c5aa6417a63a
Fetching package metadata .
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in
conflict:
  - cairocffi -> python 3.5* -> xz 5.0.5
  - python 3.6*
Use "conda info " to see the dependencies for each package.

The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo cairocffi
jupyter' returned a non-zero code: 1

Any ideas?
JP
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[Rdkit-discuss] How to create a list of molecules and iterate

[abhik]

Hi,

I am running a similarity search process using rdkit where my query 
consists of ~20 templates and my target consists of ~1000 molecules. How 
can I create a list (or any container) of molecules that I can iterate 
later.


My present algorithm is

read template create molecule > read target create molecule > calculate 
similarity

go back to template and follow the same process

But by doing this I am creating same molecule multiple times, which is 
increasing the run time.



Thank in advance for any helps.
Regards,
Abhik

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Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

[Chris Earnshaw]

Hi

Oops - typo! The chlorate and perchlorate oxygens should all be [O-].
I was copying by hand from a different computer...

Regards,
Chris

On 21 November 2017 at 09:19, Paolo Tosco  wrote:
> Hi Chris,
>
> if the behaviour with chlorate and perchlorate is the one you report
>
> chlorate [O-][Cl2+]([O+])[O-]
> perchlorate [O-][Cl3+]([O-])([O+])[O-]
>
> it looks wrong to me as there is an overall formal charge of +1. All O's
> should bear a -1 charge.
>
> Cheers,
> p.
>
>
>
> On 11/21/17 09:12, Chris Earnshaw wrote:
>>
>> Hi
>>
>> Sometime between 2014 and now there appears to have been a change in
>> the way hypervalent halogen structures are handled. The old behaviour
>> (involving some tweaking of atomic_data.cpp to allow the higher
>> oxidation states) was to have a neutral halogen with double bonds to
>> most of the oxygens, e.g.
>> chlorate O=Cl(=O)[O-]
>> perchlorate O=Cl(=O)(=O)[O-]
>>
>> The current behaviour is to 'charge separate' the dative bonds, giving
>> chlorate [O-][Cl2+]([O+])[O-]
>> perchlorate [O-][Cl3+]([O-])([O+])[O-]
>>
>> Although this may be regarded as 'correct' (arguable!), it  can cause
>> problems of compatibility with other software and looks remarkably
>> ugly. It's also inconsistent with the handling of hypervalent P and S
>> compounds. Using the same convention, we should have -
>>
>> trimethylphosphine oxide C[P+]([O-])(C)C
>> dimethylsulfoxide C[S+]([O-])C
>> dimethylsulfone C[S2+]([O-])([O-])C
>>
>> - and I really don't want this to happen!
>>
>> Does anyone know a way to restore the old behaviour for chlorites,
>> bromates, periodates etc.?
>>
>> Best regards,
>> Chris Earnshaw
>>
>>
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[Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

[Chris Earnshaw]

Hi

Sometime between 2014 and now there appears to have been a change in
the way hypervalent halogen structures are handled. The old behaviour
(involving some tweaking of atomic_data.cpp to allow the higher
oxidation states) was to have a neutral halogen with double bonds to
most of the oxygens, e.g.
chlorate O=Cl(=O)[O-]
perchlorate O=Cl(=O)(=O)[O-]

The current behaviour is to 'charge separate' the dative bonds, giving
chlorate [O-][Cl2+]([O+])[O-]
perchlorate [O-][Cl3+]([O-])([O+])[O-]

Although this may be regarded as 'correct' (arguable!), it  can cause
problems of compatibility with other software and looks remarkably
ugly. It's also inconsistent with the handling of hypervalent P and S
compounds. Using the same convention, we should have -

trimethylphosphine oxide C[P+]([O-])(C)C
dimethylsulfoxide C[S+]([O-])C
dimethylsulfone C[S2+]([O-])([O-])C

- and I really don't want this to happen!

Does anyone know a way to restore the old behaviour for chlorites,
bromates, periodates etc.?

Best regards,
Chris Earnshaw

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Re: [Rdkit-discuss] Having trouble getting RDKIT to recognize LiAsF6

[Chris Earnshaw]

Hi

A quick follow-up to my last message, w.r.t. halogens. The issue is
not that higher oxidation state halogen ions can't be constructed at
all, but they end up with bizarre charges on the halogen which are
frequently not recognised by other software.

Chris

On 21 November 2017 at 08:22, Chris Earnshaw  wrote:
> Hi
>
> The entries for P and As in RDKit's atomic_data.cpp are -
> 15  P   0.750.892.0830.974  5   31
> 30.97376163 3   5   7
> 33  As  1.211.2 1.8574.922  5   75
> 74.9215965   3   5
>
> So the required 'connectivities' for PF6- are present in the file
> (final 3 values, '7' being the relevant one here), but not for As. I'm
> not quite sure why this should be so as the phosphorus is P(V) in PF6,
> but this appears to be the cause. You'll have to add the '7' in the As
> entry and rebuild RDKit to allow AsF6- to be processed. A similar fix
> would be needed for antimony too. Someone please let me know if
> there's a more convenient solution!
>
> There are similar issues for the halogens as well. Only iodine has
> values > 1, so by default it's not possible to construct e.g.
> chlorates, or bromates, and no perhalates are allowed.
>
> Regards,
> Chris Earnshaw
>
> On 20 November 2017 at 23:03, Yoolhee Kim  wrote:
>> Hello,
>>
>> I'm trying to get RDKIT to recognize LiAsF6 from the SMILES Formula
>> "[Li+].F[As-](F)(F)(F)(F)F" but it seems that RDKIT will not read it
>> correctly and is unable to create a molecule object.
>>
>> RDKIT is able to understand LiPF6 from the SMILES formula
>> "[Li+].F[P-](F)(F)(F)(F)F" so I tried using that and replacing P with As
>> using both replaceatom and replacesubstruct functions, but that had some
>> issues as well.
>>
>> Has anyone faced a similar issue or have any suggestions?
>>
>> Thanks!
>>
>> -Yoolhee
>>
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