Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Soren Wacker 
OK, there was a problem with the environment variables. 
I can now import rdBase, however it seems to be outdated?

I would like to find out my old version. I went to the location of my old 
version.
imported rdkit 
and -to find out the version- I have to import rdBase first... which did not 
work.
It is my old version that complains about not finding libboost_python.so.1.54.0

Why is there still no function rdkit.version()? I have seen such discussion 
from 4 years ago. Such a function would be really useful sometimes. Especially, 
if you have no internet connection to find out that you have to look at
rdBase.rdkitVersion or if you know that, but cannot load rdBase, like in my 
case.

It is not even possible to grep the version apparently, since rdBase is a 
binary file.
How can I find out the version then??


For example the function dkit.Chem.Descriptors.fr_Al_COO is not present.

Now, my old version is messed up, and I cannot use the new version :-(

kind regards
Sören


From: Soren Wacker [swac...@ucalgary.ca]
Sent: Friday, January 30, 2015 12:26 PM
To: Riccardo Vianello
Cc: RDKit Developers List; Greg Landrum
Subject: Re: [Rdkit-devel] Install RDKit

No, there is no boost 1.54 on my system. I have a 1.57. Apparently, that was 
build by conda.
I have found a
./anaconda/conda-bld/linux-64/boost-1.56.0-py27_0.tar.bz2

but no anaconda/pkgs/boost-1.56... only 1.57.

I tried to generate a symbolic link from the 1.57 version to the 1.54 file, but 
that did not work.
rdBase was still complaining that it could not find it.


What is about the env. variables LD_LIBRARY_PATH and RDBASE ?
I pointed them to

RDBASE=.../anaconda/pkgs/rdkit-2014.09.2-np19py27_0/lib/python2.7/site-packages/rdkit
and
LD_LIBRARY_PATH=$RDBASE/lib

is that right?

Do I have to activate an anaconda enviroment before I can use it??


kind regards
Sören

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swac...@ucalgary.ca


From: Riccardo Vianello [riccardo.viane...@gmail.com]
Sent: Friday, January 30, 2015 4:44 AM
To: Soren Wacker
Cc: Greg Landrum; RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

until recently, boost packages were not provided by the anaconda distribution, 
and this is basically the reason we provide recipes to build boost too. When a 
few weeks ago boost packages targeting version 1.57.0 have been added to the 
conda default channels (for linux and windows at least, I couldn't find any 
boost package in the osx repository last time I checked), they caused some 
confusion because the rdkit recipe doesn't specify a version for the boost 
package, and version 1.57.0 is by default installed because it's more recent 
than the version we build locally.

When executed, the boost recipe from the rdkit github repository should have 
built boost 1.56.0 (you could probably find the package in the local channel at 
./Programme/anaconda/conda-bld/linux-64), but the rdkit build probably used 
boost version 1.57.0 (based on the info from your last message it most likely 
did so when testing the rdkit package and in istalling it into envs/rdkit-env). 
I tried building the rdkit with the boost package provided by anaconda in a 
couple of linux environments and it worked ok for me, so in principle I think 
it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any boost 
package matching that version and installed as part of the system linux 
distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker 
mailto:swac...@ucalgary.ca>> wrote:
I tried that. I was able to compile rdkit, apparently just by typing

conda build boost
conda build rdkit

but, when I use that build I get

from rdkit import rdBase

> ImportError: libboost_python.so.1.54.0: cannot open shared object file: No 
> such file or directory

strange thing is, that anaconda build 1.57 version... 1.54 does not exist on my 
system.

./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
./Programme/anaconda/envs/_test/lib/libboost_python.so
./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0

kind regards
Soren
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Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Soren Wacker 
No, there is no boost 1.54 on my system. I have a 1.57. Apparently, that was 
build by conda.
I have found a 
./anaconda/conda-bld/linux-64/boost-1.56.0-py27_0.tar.bz2

but no anaconda/pkgs/boost-1.56... only 1.57.

I tried to generate a symbolic link from the 1.57 version to the 1.54 file, but 
that did not work. 
rdBase was still complaining that it could not find it. 


What is about the env. variables LD_LIBRARY_PATH and RDBASE ? 
I pointed them to 

RDBASE=.../anaconda/pkgs/rdkit-2014.09.2-np19py27_0/lib/python2.7/site-packages/rdkit
and 
LD_LIBRARY_PATH=$RDBASE/lib

is that right?

Do I have to activate an anaconda enviroment before I can use it??


kind regards
Sören

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swac...@ucalgary.ca


From: Riccardo Vianello [riccardo.viane...@gmail.com]
Sent: Friday, January 30, 2015 4:44 AM
To: Soren Wacker
Cc: Greg Landrum; RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

until recently, boost packages were not provided by the anaconda distribution, 
and this is basically the reason we provide recipes to build boost too. When a 
few weeks ago boost packages targeting version 1.57.0 have been added to the 
conda default channels (for linux and windows at least, I couldn't find any 
boost package in the osx repository last time I checked), they caused some 
confusion because the rdkit recipe doesn't specify a version for the boost 
package, and version 1.57.0 is by default installed because it's more recent 
than the version we build locally.

When executed, the boost recipe from the rdkit github repository should have 
built boost 1.56.0 (you could probably find the package in the local channel at 
./Programme/anaconda/conda-bld/linux-64), but the rdkit build probably used 
boost version 1.57.0 (based on the info from your last message it most likely 
did so when testing the rdkit package and in istalling it into envs/rdkit-env). 
I tried building the rdkit with the boost package provided by anaconda in a 
couple of linux environments and it worked ok for me, so in principle I think 
it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any boost 
package matching that version and installed as part of the system linux 
distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker 
mailto:swac...@ucalgary.ca>> wrote:
I tried that. I was able to compile rdkit, apparently just by typing

conda build boost
conda build rdkit

but, when I use that build I get

from rdkit import rdBase

> ImportError: libboost_python.so.1.54.0: cannot open shared object file: No 
> such file or directory

strange thing is, that anaconda build 1.57 version... 1.54 does not exist on my 
system.

./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
./Programme/anaconda/envs/_test/lib/libboost_python.so
./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0

kind regards
Soren
--
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Re: [Rdkit-devel] Install RDKit

2015-01-30 Thread Riccardo Vianello 
Hi Soren,

until recently, boost packages were not provided by the anaconda
distribution, and this is basically the reason we provide recipes to build
boost too. When a few weeks ago boost packages targeting version 1.57.0
have been added to the conda default channels (for linux and windows at
least, I couldn't find any boost package in the osx repository last time I
checked), they caused some confusion because the rdkit recipe doesn't
specify a version for the boost package, and version 1.57.0 is by default
installed because it's more recent than the version we build locally.

When executed, the boost recipe from the rdkit github repository should
have built boost 1.56.0 (you could probably find the package in the local
channel at ./Programme/anaconda/conda-bld/linux-64), but the rdkit build
probably used boost version 1.57.0 (based on the info from your last
message it most likely did so when testing the rdkit package and in
istalling it into envs/rdkit-env). I tried building the rdkit with the
boost package provided by anaconda in a couple of linux environments and it
worked ok for me, so in principle I think it could work for you too.

But I have no explanation for the reference to boost 1.54.0. Is there any
boost package matching that version and installed as part of the system
linux distribution?

Best,
Riccardo



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker  wrote:

> I tried that. I was able to compile rdkit, apparently just by typing
>
> conda build boost
> conda build rdkit
>
> but, when I use that build I get
>
> from rdkit import rdBase
>
> > ImportError: libboost_python.so.1.54.0: cannot open shared object file:
> No such file or directory
>
> strange thing is, that anaconda build 1.57 version... 1.54 does not exist
> on my system.
>
> ./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so
> ./Programme/anaconda/envs/rdkit-env/lib/libboost_python.so.1.57.0
> ./Programme/anaconda/envs/_test/lib/libboost_python.so
> ./Programme/anaconda/envs/_test/lib/libboost_python.so.1.57.0
> ./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so
> ./Programme/anaconda/pkgs/boost-1.57.0-0/lib/libboost_python.so.1.57.0
>
> kind regards
> Soren
>
> --
> Dive into the World of Parallel Programming. The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is
> your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now. http://goparallel.sourceforge.net/
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Re: [Rdkit-devel] Canonical atom order

2015-01-30 Thread Maciek Wójcikowski 
Thanks Greg!


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

2015-01-30 4:30 GMT+01:00 Greg Landrum :

> There's not currently a way to do this. It's pretty easy to add to the
> python wrapper though, so I will go ahead and do that.
> Here's the github issue:
> https://github.com/rdkit/rdkit/issues/421
>
> -greg
>
>
> On Thu, Jan 29, 2015 at 4:57 PM, Maciek Wójcikowski  > wrote:
>
>> Hello RDKiters,
>>
>> I'd like somehow to get canonical atoms order for RDKit Mol in python. Is
>> there a method/hack to get it? I've went though some code on github, but
>> cant see any method to get those data in python...
>>
>> 
>> Pozdrawiam,  |  Best regards,
>> Maciek Wójcikowski
>> mac...@wojcikowski.pl
>>
>>
>> --
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>>
>
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