Re: [Rdkit-discuss] Python 3, windows 64, rdkit builds

[Riccardo Vianello]

Hi Paolo,

That would be really great, I would be definitely interested in trying to
wrap your scripts into the conda recipe for the boost package.

Thanks,
Riccardo

​
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Re: [Rdkit-discuss] Python 3, windows 64, rdkit builds

[Clyde Fare]

Thanks all,

The error reported on attempting to build is attached below. The colleague
in question noted that it seemed to be looking for python2.7? It may well
be that some trivial error has been made. When I get access to a windows
machine I will have a go at building rdkit from source as report my
results. Thanks for all the information.

Cheers

Clyde



U:\packages\source\Anaconda\conda-rdkit-master>conda build rdkit >
c:\temp\conda .log

WARNING: conda-build appears to be out of date. You have version
1.14.1 but the latest version is 1.17.0. Run

conda update -n root conda-build

to get the latest version.

Cloning into bare repository
'C:*/Anaconda3/conda-bld/git_cache/*__github.com_rdki
t_rdkit.git'...
remote: Counting objects: 42834, done.
remote: Compressing objects:  98% (153/156)eceiving objects:   0% (1/42834)
remote: Compressing objects: 100% (156/156), done.
Receiving objects: 100% (42834/42834), 71.59 MiB | 6.61 MiB/s, done.
emote: Total 42834 (delta 80), reused 0 (delta 0), pack-reused 42677
Resolving deltas: 100% (31951/31951), done.
Checking connectivity... done.
Cloning into 'C:\Anaconda3\conda-bld\work'...
done.
Note: checking out 'Release_2015_03_1'.

You are in 'detached HEAD' state. You can look around, make
experimental changes and commit them, and you can discard any commits
you make in this state without impacting any branches by performing
another checkout.

If you want to create a new branch to retain commits you create, you
may do so (now or later) by using -b with the checkout command again.
Example:

   git checkout -b 

HEAD is now at 4efed71... update release notes Python Install
directory C:\Anaconda3\envs\_build\Lib\site-packages

Microsoft (R) Program Maintenance Utility Version 10.00.30319.01
Copyright (C) Microsoft Corporation.  All rights reserved.

NMAKE : fatal error U1073: don't know how to make
'C:\Anaconda3\envs\_build\libs \python27.lib'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
Studio 10.0 \VC\BIN\amd64\nmake.exe"' : return code '0x2'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
Studio 10.0 \VC\BIN\amd64\nmake.exe"' : return code '0x2'
Stop.

Microsoft (R) Program Maintenance Utility Version 10.00.30319.01
Copyright (C) Microsoft Corporation.  All rights reserved.

NMAKE : fatal error U1077: 'echo' : return code '0x8'
Stop.

Microsoft (R) Program Maintenance Utility Version 10.00.30319.01
Copyright (C) Microsoft Corporation.  All rights reserved.

NMAKE : fatal error U1073: don't know how to make
'C:\Anaconda3\envs\_build\libs \python27.lib'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
Studio 10.0 \VC\BIN\amd64\nmake.exe"' : return code '0x2'
Stop.
NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
Studio 10.0 \VC\BIN\amd64\nmake.exe"' : return code '0x2'
Stop.
Command failed: C:\Windows\system32\cmd.exe /c call bld.bat

U:\packages\source\Anaconda\conda-rdkit-master>nmake

Microsoft (R) Program Maintenance Utility Version 10.00.30319.01
Copyright (C) Microsoft Corporation.  All rights reserved.

NMAKE : fatal error U1064: MAKEFILE not found and no target specified Stop.

U:\packages\source\Anaconda\conda-rdkit-master>


On 24 September 2015 at 08:55, Greg Landrum  wrote:

>
>
> On Wed, Sep 23, 2015 at 8:55 AM, Clyde Fare  wrote:
>
>>
>> Some colleagues have been trying to get rdkit to work with a python 3
>> anaconda environment running on a windows machine and have been running
>> into difficulties.
>>
>
> I'd love to hear about these in some more detail.
>
>
>>
>> I notice there is no python 3 windows rdkit binary, nor is there a
>> windows conda package for python 3.
>>
>> Is there some windows python 3 related problem?
>>
>
> I agree with Riccardo here: I can't think of any reason that the python3
> version of the code should not work on Windows.
>
> Past releases have not include a Python 3 build simply because the demand
> hasn't been there and the current release process is extremely manual. I
> will plan to do a Python3 version with the next release.[1]
>
> -greg
> [1] A caveat here: if I cannot find a pre-compiled version of boost for
> python3 on windows, this may not happen.
>
>
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Re: [Rdkit-discuss] Python 3, windows 64, rdkit builds

[Greg Landrum]

On Wed, Sep 23, 2015 at 8:55 AM, Clyde Fare  wrote:

>
> Some colleagues have been trying to get rdkit to work with a python 3
> anaconda environment running on a windows machine and have been running
> into difficulties.
>

I'd love to hear about these in some more detail.


>
> I notice there is no python 3 windows rdkit binary, nor is there a windows
> conda package for python 3.
>
> Is there some windows python 3 related problem?
>

I agree with Riccardo here: I can't think of any reason that the python3
version of the code should not work on Windows.

Past releases have not include a Python 3 build simply because the demand
hasn't been there and the current release process is extremely manual. I
will plan to do a Python3 version with the next release.[1]

-greg
[1] A caveat here: if I cannot find a pre-compiled version of boost for
python3 on windows, this may not happen.
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[Rdkit-discuss] molecule standardization in cartridge search

[Tim Dudgeon]

I'm trying to get to grips with using the RDKit cartridge, and so far 
its going well.
One thing I'm concerned about is molecule standardization, along the 
lines of the ChemAxon Standardizer that allows substructure searches to 
be done is a way that is largely independent of the quirks of structure 
representation. The classic example would be how nitro groups are 
represented, so that it didn't matter which nitro representation was in 
the query or target structures, because both were converted to a 
canonical form.

My initial thoughts are that this would be done by:
1. loading the "raw" structures into a source column that would never be 
changed
2. defining a function that performed the necessary transform to 
generate the canonical form of a molecule.
3. generating a "canonical" structure column that was the result of 
passing the raw structures through that function
4. building the SSS index on that canonical column
5. executing queries using that function to canonicalize the query structure

The problem I'm finding is that there do not seem to be postgres 
functions defined for doing molecular transforms (essentially a reaction 
transform) and doing things like removing explicit hydrogens. At least 
not in the functions listed on this page: 
http://rdkit.org/docs/Cartridge.html#functions

Am I missing something here, or might I be barking up completely the 
wrong tree?

Tim




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Re: [Rdkit-discuss] Generation of stereo-isomers

[Greg Landrum]

Hi Soren,

That functionality isn't currently there, but it's been requested a few
times and shouldn't be that tough to get into the next release.

-greg

On Thursday, September 24, 2015, Soren Wacker  wrote:

> Hi,
>
> is it possible with RDKit to generate all stereoisomers of a given
> compound?
>
> If not, is anyone working on it?
>
> If not, how difficult would it be / what would be the best way to
> implement such a function.
>
> best regards
>
> Soren
>
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Re: [Rdkit-discuss] Generation of stereo-isomers

[Paolo Tosco]

Dear Soren,

I have recently used the RDKit to enumerate stereocentres.
The approach I followed was to generate a 3D structure for the molecule 
of interest (including hydrogens) using EmbedMolecule(), followed by 
MMFF optimization; do not pay attention to stereochemistry at this 
stage. Then I used FindMolChiralCenters() to find the n chiral centres 
in the 3D structure thus obtained; there are 2^n theoretical possible 
diastereomers. You may enumerate all of them with a "for i in range (0, 
2^n)" loop; converting i to binary, and considering 0 for S and 1 for R, 
you may easily find all possible combinations. Use SetChiralTag() to set 
the chirality on each stereocentre, then rebuild 3D coordinates with 
EmbedMolecule() followed by MMFF optimization. Carry out a final check 
to verify that the chirality of the molecule is the one you initially 
required; if not, try to rebuild 3D coordinates. If you fail, say, 20 
times in a row, it means you are attempting to build a diastereomer that 
cannot give rise to a sensible 3D geometry (such as the case mentioned 
by Peter); then give up.
You will also need to check if any of the structures that you obtain 
during the enumeration has more chiral centres than the initial one (for 
which you didn't specify steeochemistry); in fact, it could be that you 
started from a meso structure. If this happens, just restart enumeration 
from scratch with the increased number of stereocentres.
I also carried out some geometry checks on the generated stereocentres 
coupled with MMFF energy evaluation relative to the most stable 
diastereomer to make sure that the diastereomers obtained where 
reasonable and not unreasonably strained.
This brute-force enumeration is easy to implement, reasonably fast, and 
it worked very well for me.


Kind regards,
Paolo

On 24/09/2015 22:17, Soren Wacker wrote:

Hi,

is it possible with RDKit to generate all stereoisomers of a given 
compound?


If not, is anyone working on it?

If not, how difficult would it be / what would be the best way to 
implement such a function.


best regards

Soren


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[Rdkit-discuss] Generation of stereo-isomers

[Soren Wacker]

Hi,

is it possible with RDKit to generate all stereoisomers of a given compound?

If not, is anyone working on it?

If not, how difficult would it be / what would be the best way to implement
such a function.

best regards

Soren
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Re: [Rdkit-discuss] Generation of stereo-isomers

[Peter Shenkin]

Umm... would that be all stereoisomers or all realizable stereoisomers? For
example consider two bridgeheads in a norbonane-type compound. In this
case, only a particular enantiomeric pair would be realizable, and not all
four diastereomers.
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