rdkit-devel — Developers information and discussion.

Re: [Rdkit-devel] ImportError: No module named 'pidSVG'

[Cyrus H. <cy...@bo...>]

Ok, continuing to try debug my own silly problems… I forgot about RDBASE, PYTHONPATH, etc...

When I run the tests with:

PYTHONPATH=/home/sly/projects/rdkit/ RDBASE=/home/sly/projects/rdkit/ LD_LIBRARY_PATH=/home/sly/projects/rdkit/lib ctest

I get 64% of the tests passing. An improvement, but still not 100%. Is this to be expected?

thanks,

Cyrus

> On Apr 3, 2015, at 3:51 PM, Cyrus Harmon <cy...@bo...> wrote:
> 
> Hi Greg,
> 
> Thanks for looking into this. Some time has gone by and I’m not sure if the changes you were referring to have been checked in yet, but I’m back to trying to get things running on both macos and linux.
> 
> Unfortunately, things seem to be getting worse. While everything seems to build OK, when I run “make test” on macos, I get only 46% of tests passing. About half of the failures are seg faults, the other half are failures. Is this to be expected? On my linux box, it’s actually even worse, 38% of tests passing.
> 
> I’m happy to send the list of failing tests, but I figured I’m probably doing something wrong and that I should get the basics working first before I try to figure out which specific tests are failing (much less solve my SVG problem). It’s quite possible that the twisty maze of multiple versions of python (not to mention python libraries), boost, etc… are rearing the ugly head and I’m not quite sure where to begin trying to fix things. Suggestions?
> 
> thanks,
> 
> Cyrus
> 
>> On Mar 9, 2015, at 10:37 PM, Greg Landrum <gre...@gm... <mailto:gre...@gm...>> wrote:
>> 
>> Hi Cyrus,
>> 
>> That's something we missed when we did the Python3 port of the RDKit.
>> It turns out that there are a few of these problems in the rdkit.sping package that need to be brought up to date.
>> 
>> I will get those fixed and checked in the next day or so.
>> 
>> Thanks for reporting the problem,
>> -greg
>> 
>> 
>> On Tue, Mar 10, 2015 at 2:37 AM, Cyrus Harmon <cy...@bo... <mailto:cy...@bo...>> wrote:
>> I’m trying to get a python program that uses rdkit running on macos and I keep getting the following error:
>> 
>>   File "./rdkit-2d-draw.py", line 31, in <module>
>>     Draw.MolToFile(mol,args.output,size=(500,500))
>>   File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py", line 167, in MolToFile
>>     canvas = Canvas(size=size,name=fileName,imageType=imageType)
>>   File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py", line 33, in __init__
>>     from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
>>   File "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py", line 3, in <module>
>>     from pidSVG import *
>> ImportError: No module named 'pidSVG'
>> 
>> It works for me on my unix box that uses the debian packaged rdkit, but fails for me on MacOS. Surely I’m doing something wrong in configuring my various python libraries, but I’m at a loss as to how to fix this.
>> 
>> Any suggestions on how to make my program find the pidSVG stuff?
>> 
>> thanks,
>> 
>> Cyrus
>> 
>> 
>> ------------------------------------------------------------------------------
>> 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/ <http://goparallel.sourceforge.net/>
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li... <mailto:Rdk...@li...>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel <https://lists.sourceforge.net/lists/listinfo/rdkit-devel>
>> 
> 
> ------------------------------------------------------------------------------
> 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/_______________________________________________
> Rdkit-devel mailing list
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> https://lists.sourceforge.net/lists/listinfo/rdkit-devel

Re: [Rdkit-devel] ImportError: No module named 'pidSVG'

[Cyrus H. <cy...@bo...>]

Hi Greg,

Thanks for looking into this. Some time has gone by and I’m not sure if the changes you were referring to have been checked in yet, but I’m back to trying to get things running on both macos and linux.

Unfortunately, things seem to be getting worse. While everything seems to build OK, when I run “make test” on macos, I get only 46% of tests passing. About half of the failures are seg faults, the other half are failures. Is this to be expected? On my linux box, it’s actually even worse, 38% of tests passing.

I’m happy to send the list of failing tests, but I figured I’m probably doing something wrong and that I should get the basics working first before I try to figure out which specific tests are failing (much less solve my SVG problem). It’s quite possible that the twisty maze of multiple versions of python (not to mention python libraries), boost, etc… are rearing the ugly head and I’m not quite sure where to begin trying to fix things. Suggestions?

thanks,

Cyrus

> On Mar 9, 2015, at 10:37 PM, Greg Landrum <gre...@gm...> wrote:
> 
> Hi Cyrus,
> 
> That's something we missed when we did the Python3 port of the RDKit.
> It turns out that there are a few of these problems in the rdkit.sping package that need to be brought up to date.
> 
> I will get those fixed and checked in the next day or so.
> 
> Thanks for reporting the problem,
> -greg
> 
> 
> On Tue, Mar 10, 2015 at 2:37 AM, Cyrus Harmon <cy...@bo... <mailto:cy...@bo...>> wrote:
> I’m trying to get a python program that uses rdkit running on macos and I keep getting the following error:
> 
>   File "./rdkit-2d-draw.py", line 31, in <module>
>     Draw.MolToFile(mol,args.output,size=(500,500))
>   File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py", line 167, in MolToFile
>     canvas = Canvas(size=size,name=fileName,imageType=imageType)
>   File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py", line 33, in __init__
>     from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
>   File "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py", line 3, in <module>
>     from pidSVG import *
> ImportError: No module named 'pidSVG'
> 
> It works for me on my unix box that uses the debian packaged rdkit, but fails for me on MacOS. Surely I’m doing something wrong in configuring my various python libraries, but I’m at a loss as to how to fix this.
> 
> Any suggestions on how to make my program find the pidSVG stuff?
> 
> thanks,
> 
> Cyrus
> 
> 
> ------------------------------------------------------------------------------
> 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/ <http://goparallel.sourceforge.net/>
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li... <mailto:Rdk...@li...>
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel <https://lists.sourceforge.net/lists/listinfo/rdkit-devel>
> 

Re: [Rdkit-devel] ImportError: No module named 'pidSVG'

[Greg L. <gre...@gm...>]

Hi Cyrus,

That's something we missed when we did the Python3 port of the RDKit.
It turns out that there are a few of these problems in the rdkit.sping
package that need to be brought up to date.

I will get those fixed and checked in the next day or so.

Thanks for reporting the problem,
-greg


On Tue, Mar 10, 2015 at 2:37 AM, Cyrus Harmon <cy...@bo...> wrote:

> I’m trying to get a python program that uses rdkit running on macos and I
> keep getting the following error:
>
>   File "./rdkit-2d-draw.py", line 31, in <module>
>     Draw.MolToFile(mol,args.output,size=(500,500))
>   File
> "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py", line
> 167, in MolToFile
>     canvas = Canvas(size=size,name=fileName,imageType=imageType)
>   File
> "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py",
> line 33, in __init__
>     from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
>   File
> "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py", line
> 3, in <module>
>     from pidSVG import *
> ImportError: No module named 'pidSVG'
>
> It works for me on my unix box that uses the debian packaged rdkit, but
> fails for me on MacOS. Surely I’m doing something wrong in configuring my
> various python libraries, but I’m at a loss as to how to fix this.
>
> Any suggestions on how to make my program find the pidSVG stuff?
>
> thanks,
>
> Cyrus
>
>
>
> ------------------------------------------------------------------------------
> 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/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] ImportError: No module named 'pidSVG'

[Cyrus H. <cy...@bo...>]

I’m trying to get a python program that uses rdkit running on macos and I keep getting the following error:

  File "./rdkit-2d-draw.py", line 31, in <module>
    Draw.MolToFile(mol,args.output,size=(500,500))
  File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/__init__.py", line 167, in MolToFile
    canvas = Canvas(size=size,name=fileName,imageType=imageType)
  File "/usr/local/lib/python3.4/site-packages/rdkit/Chem/Draw/spingCanvas.py", line 33, in __init__
    from rdkit.sping.SVG.pidSVG import SVGCanvas as _Canvas
  File "/usr/local/lib/python3.4/site-packages/rdkit/sping/SVG/__init__.py", line 3, in <module>
    from pidSVG import *
ImportError: No module named 'pidSVG'

It works for me on my unix box that uses the debian packaged rdkit, but fails for me on MacOS. Surely I’m doing something wrong in configuring my various python libraries, but I’m at a loss as to how to fix this.

Any suggestions on how to make my program find the pidSVG stuff?

thanks,

Cyrus

Re: [Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

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 [sw...@uc...]
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:  sw...@uc...

________________________________________
From: Riccardo Vianello [ric...@gm...]
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 <sw...@uc...<mailto:sw...@uc...>> 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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Rdk...@li...<mailto:Rdk...@li...>
https://lists.sourceforge.net/lists/listinfo/rdkit-devel

------------------------------------------------------------------------------
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/
_______________________________________________
Rdkit-devel mailing list
Rdk...@li...
https://lists.sourceforge.net/lists/listinfo/rdkit-devel

Re: [Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

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:  sw...@uc...

________________________________________
From: Riccardo Vianello [ric...@gm...]
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 <sw...@uc...<mailto:sw...@uc...>> 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/
_______________________________________________
Rdkit-devel mailing list
Rdk...@li...<mailto:Rdk...@li...>
https://lists.sourceforge.net/lists/listinfo/rdkit-devel

Re: [Rdkit-devel] Install RDKit

[Riccardo V. <ric...@gm...>]

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 <sw...@uc...> 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/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

Re: [Rdkit-devel] Canonical atom order

[Maciek W. <ma...@wo...>]

Thanks Greg!

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
ma...@wo...

2015-01-30 4:30 GMT+01:00 Greg Landrum <gre...@gm...>:

> 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 <ma...@wo...
> > 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
>> ma...@wo...
>>
>>
>> ------------------------------------------------------------------------------
>> 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/
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>>
>

Re: [Rdkit-devel] Canonical atom order

[Greg L. <gre...@gm...>]

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 <ma...@wo...>
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
> ma...@wo...
>
>
> ------------------------------------------------------------------------------
> 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/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

Re: [Rdkit-devel] Install RDKit

[Greg L. <gre...@gm...>]

I believe you need to install the version of the rdkit you just built in
your conda environment with conda install and make sure that environment is
active.

It looks like it's finding a different build. You can confirm this by doing:
 python -c 'import rdkit;print(rdkit.__file__)'
and looking at the output.

-greg



On Fri, Jan 30, 2015 at 12:09 AM, Soren Wacker <sw...@uc...> 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

Re: [Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

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

Re: [Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

Uh! Wow!
Awesome news!!
Good work ;-)

--
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:  sw...@uc...
________________________________
From: Greg Landrum [gre...@gm...]
Sent: Wednesday, January 28, 2015 10:32 PM
To: Soren Wacker
Cc: RDKit Developers List
Subject: Re: [Rdkit-devel] Install RDKit

Hi Soren,

On Thu, Jan 29, 2015 at 2:03 AM, Soren Wacker <sw...@uc...<mailto:sw...@uc...>> wrote:

I would highly appreciate a
conda install rdkit

way of doing it, but that is probably not so easy to realize.

It wasn't easy to realize but fortunately Riccardo has already done the work:
https://github.com/rdkit/conda-rdkit
We have a binstar channel available with some pre-built binaries too:
https://conda.binstar.org/rdkit

Best,
-greg

[Rdkit-devel] Canonical atom order

[Maciek W. <ma...@wo...>]

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
ma...@wo...

Re: [Rdkit-devel] Install RDKit

[Greg L. <gre...@gm...>]

Hi Soren,

On Thu, Jan 29, 2015 at 2:03 AM, Soren Wacker <sw...@uc...> wrote:

>
> I would highly appreciate a
> conda install rdkit
>
> way of doing it, but that is probably not so easy to realize.
>

It wasn't easy to realize but fortunately Riccardo has already done the
work:
https://github.com/rdkit/conda-rdkit
We have a binstar channel available with some pre-built binaries too:
https://conda.binstar.org/rdkit

Best,
-greg

Re: [Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

Yes, it exists. But it always installs it into the source directory...

Plus, I managed to compile it, but when I use the iphython notebook and import it.
The kernel crashes. Installing RDKit causes lots of troubles, unfortunately.

I would highly appreciate a
conda install rdkit

way of doing it, but that is probably not so easy to realize.

Kind regards
Soren

--
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:  sw...@uc...
________________________________
From: Paul Emsley [pe...@mr...]
Sent: Wednesday, January 28, 2015 3:13 PM
To: rdk...@li...
Subject: Re: [Rdkit-devel] Install RDKit

On 28/01/15 20:14, Soren Wacker wrote:
Hi,

I want to install RDKit to a certain directory.
However, when I am in the source directory and do

md build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/home/.../Programme/RDKit

make
make install

RDKit is build and installed, but not to the directory.
Where is RDKit then located? And why is it ignoring the installation prefix.
That could to be a cmake/make error.



  -DCMAKE_INSTALL_PREFIX=$install_prefix
is the correct form

$ make install
will tell you where it (want to) install things.
Perhaps that will help?

Does /home/.../Programme/RDKit exist?

Paul.

Re: [Rdkit-devel] Install RDKit

[Paul E. <pe...@mr...>]

On 28/01/15 20:14, Soren Wacker wrote:
> Hi,
>
> I want to install RDKit to a certain directory.
> However, when I am in the source directory and do
>
> md build
> cd build
> cmake .. -DCMAKE_INSTALL_PREFIX=/home/.../Programme/RDKit
>
> make
> make install
>
> RDKit is build and installed, but not to the directory.
> Where is RDKit then located? And why is it ignoring the installation 
> prefix.
> That could to be a cmake/make error.
>
>

   -DCMAKE_INSTALL_PREFIX=$install_prefix
is the correct form

$ make install
will tell you where it (want to) install things.
Perhaps that will help?

Does /home/.../Programme/RDKit exist?

Paul.

Re: [Rdkit-devel] Install RDKit

[David H. <li...@co...>]

my guess:
-DRDK_INSTALL_INTREE=OFF

-David

On Wed, Jan 28, 2015 at 3:14 PM, Soren Wacker <sw...@uc...> wrote:

>  Hi,
>
> I want to install RDKit to a certain directory.
> However, when I am in the source directory and do
>
>  md build
> cd build
>  cmake .. -DCMAKE_INSTALL_PREFIX=/home/.../Programme/RDKit
>
>  make
>  make install
>
> RDKit is build and installed, but not to the directory.
> Where is RDKit then located? And why is it ignoring the installation
> prefix.
> That could to be a cmake/make error.
>
> I have no idea what's going wrong.
> 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/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

[Rdkit-devel] Install RDKit

[Soren W. <sw...@uc...>]

Hi,

I want to install RDKit to a certain directory.
However, when I am in the source directory and do

md build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=/home/.../Programme/RDKit

make
make install

RDKit is build and installed, but not to the directory.
Where is RDKit then located? And why is it ignoring the installation prefix.
That could to be a cmake/make error.

I have no idea what's going wrong.
kind regards
Soren

Re: [Rdkit-devel] Enhancements to the 2D drawing API

[Greg L. <gre...@gm...>]

Hi Igor,

The new functions are:
virtual void drawPolygon( const std::vector<std::pair<float,float> > &cds )
= 0;
virtual void drawEllipse( const std::pair<float,float> &cds1 ,const
std::pair<float,float> &cds2 );

I've done drawPolygon() already but haven't tested it. The second does not
*need* to be implemented (there is code that simulates it if it's not
present), but it certainly makes things faster if it's there.

The other change that would need to be made is to support the toggling of
filled polygons in drawPolygon, drawTriangle, and drawEllipse. Here's how
the cairo drawer handles it:
https://github.com/rdkit/rdkit/blob/Issue417/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp#L77

-greg

On Wed, Jan 28, 2015 at 2:41 PM, Igor Filippov <igo...@gm...>
wrote:

> Greg,
>
> Sure, no problem - I have a code for PNG drawer already, I can get it to
> you.
> Are there prototypes (declarations) for the new functions already
> available? If so, I can take a look how easy it is to translate to
> wxWidgets api.
>
> Igor
>
> On Wed, Jan 28, 2015 at 12:17 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> Dear all,
>>
>> I created an issue to track some enhancements I want to make to the C++
>> 2D drawing API:
>> https://github.com/rdkit/rdkit/issues/417
>>
>> I'm doing the changes themselves on this branch;
>> https://github.com/rdkit/rdkit/tree/Issue417
>>
>> Here's the current state:
>> - [x] add drawPolygon()  Mandatory in canvas
>> - [ ] add drawCurve()  Optional in canvas
>> - [x] add drawEllipse()  Optional in canvas
>> - [ ] add drawRect()  Optional in canvas
>> - [x] add setLineWidth()
>> - [x] move draw commands to public interface
>> - [ ] support specification of a particular conformer for drawing
>> - [x] make fills optional for closed shapes
>>
>> I haven't added support for the optional fills in the wx drawer. Igor: if
>> you have time to do this and, ideally, add a test to the test1.cpp file
>> that uses wx to create PNGs (so it's easier to verify future changes) I'd
>> really appreciate it.
>>
>> I'd love feedback or suggestions for further enhancements.
>> -greg
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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/
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>>
>

Re: [Rdkit-devel] Enhancements to the 2D drawing API

[Igor F. <igo...@gm...>]

Greg,

Sure, no problem - I have a code for PNG drawer already, I can get it to
you.
Are there prototypes (declarations) for the new functions already
available? If so, I can take a look how easy it is to translate to
wxWidgets api.

Igor

On Wed, Jan 28, 2015 at 12:17 AM, Greg Landrum <gre...@gm...>
wrote:

> Dear all,
>
> I created an issue to track some enhancements I want to make to the C++ 2D
> drawing API:
> https://github.com/rdkit/rdkit/issues/417
>
> I'm doing the changes themselves on this branch;
> https://github.com/rdkit/rdkit/tree/Issue417
>
> Here's the current state:
> - [x] add drawPolygon()  Mandatory in canvas
> - [ ] add drawCurve()  Optional in canvas
> - [x] add drawEllipse()  Optional in canvas
> - [ ] add drawRect()  Optional in canvas
> - [x] add setLineWidth()
> - [x] move draw commands to public interface
> - [ ] support specification of a particular conformer for drawing
> - [x] make fills optional for closed shapes
>
> I haven't added support for the optional fills in the wx drawer. Igor: if
> you have time to do this and, ideally, add a test to the test1.cpp file
> that uses wx to create PNGs (so it's easier to verify future changes) I'd
> really appreciate it.
>
> I'd love feedback or suggestions for further enhancements.
> -greg
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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/
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

[Rdkit-devel] Enhancements to the 2D drawing API

[Greg L. <gre...@gm...>]

Dear all,

I created an issue to track some enhancements I want to make to the C++ 2D
drawing API:
https://github.com/rdkit/rdkit/issues/417

I'm doing the changes themselves on this branch;
https://github.com/rdkit/rdkit/tree/Issue417

Here's the current state:
- [x] add drawPolygon()  Mandatory in canvas
- [ ] add drawCurve()  Optional in canvas
- [x] add drawEllipse()  Optional in canvas
- [ ] add drawRect()  Optional in canvas
- [x] add setLineWidth()
- [x] move draw commands to public interface
- [ ] support specification of a particular conformer for drawing
- [x] make fills optional for closed shapes

I haven't added support for the optional fills in the wx drawer. Igor: if
you have time to do this and, ideally, add a test to the test1.cpp file
that uses wx to create PNGs (so it's easier to verify future changes) I'd
really appreciate it.

I'd love feedback or suggestions for further enhancements.
-greg

Re: [Rdkit-devel] new C++ drawing code

[Igor F. <igo...@gm...>]

Greg, David,

> One small point, which I'm sure is down to my poorly annotated/documented
code, is that drawTriangle should draw a solid, filled shape.

Good catch about filled triangles  - I should have seen it myself.
The fix is easy  - just need to change DrawLines to DrawPolygon (attached).

Is there anything special about dashes? I saw something strange going on in
drawLine in cairo version, not sure what it does.

Greg, please go ahead - the fixed version is attached.

Igor


On Thu, Jan 22, 2015 at 5:01 AM, Greg Landrum <gre...@gm...>
wrote:

> Thanks Igor!
> Ok with you if I check this in?
>
> On Wed, Jan 21, 2015 at 10:16 PM, Igor Filippov <igo...@gm...
> > wrote:
>
>> This is very nice!
>> Here is a shim to draw to wxWidgets, header-file only.
>> If anyone needs an example how to use it please let me know.
>>
>> Igor
>>
>> On Tue, Jan 20, 2015 at 2:41 AM, Greg Landrum <gre...@gm...>
>> wrote:
>>
>>> I merged the pull request this morning. The new C++ drawing code is now
>>> available on master.
>>>
>>> Best,
>>> -greg
>>>
>>>
>>> On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum <gre...@gm...>
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> I just created a pull request for integration of some new C++ drawing
>>>> code into the RDKit:
>>>> https://github.com/rdkit/rdkit/pull/412
>>>>
>>>> This is a big one, so I will leave the PR active until the weekend for
>>>> people to look at and comment on before I merge onto the master.
>>>>
>>>> The new code supports rendering to SVG, Cairo (optional), and Qt
>>>> (optional). Adding support for a new backend is pretty straightforward.
>>>>
>>>> There's still work to be done to allow this to be a replacement for the
>>>> Python-based rendering code in rdkit.Chem.Draw, but it's a big step forward.
>>>>
>>>> The original design and code is from Dave Cosgrove. Many thanks to Dave
>>>> for the contribution, which is really going to help improve the quality of
>>>> the molecule drawings the RDKit produces.
>>>>
>>>> Best,
>>>> -greg
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
>>> GigeNET is offering a free month of service with a new server in Ashburn.
>>> Choose from 2 high performing configs, both with 100TB of bandwidth.
>>> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
>>> http://p.sf.net/sfu/gigenet
>>> _______________________________________________
>>> Rdkit-devel mailing list
>>> Rdk...@li...
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>>
>>>
>>
>

Re: [Rdkit-devel] new C++ drawing code

[Greg L. <gre...@gm...>]

Thanks Igor!
Ok with you if I check this in?

On Wed, Jan 21, 2015 at 10:16 PM, Igor Filippov <igo...@gm...>
wrote:

> This is very nice!
> Here is a shim to draw to wxWidgets, header-file only.
> If anyone needs an example how to use it please let me know.
>
> Igor
>
> On Tue, Jan 20, 2015 at 2:41 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> I merged the pull request this morning. The new C++ drawing code is now
>> available on master.
>>
>> Best,
>> -greg
>>
>>
>> On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum <gre...@gm...>
>> wrote:
>>
>>> Dear all,
>>>
>>> I just created a pull request for integration of some new C++ drawing
>>> code into the RDKit:
>>> https://github.com/rdkit/rdkit/pull/412
>>>
>>> This is a big one, so I will leave the PR active until the weekend for
>>> people to look at and comment on before I merge onto the master.
>>>
>>> The new code supports rendering to SVG, Cairo (optional), and Qt
>>> (optional). Adding support for a new backend is pretty straightforward.
>>>
>>> There's still work to be done to allow this to be a replacement for the
>>> Python-based rendering code in rdkit.Chem.Draw, but it's a big step forward.
>>>
>>> The original design and code is from Dave Cosgrove. Many thanks to Dave
>>> for the contribution, which is really going to help improve the quality of
>>> the molecule drawings the RDKit produces.
>>>
>>> Best,
>>> -greg
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
>> GigeNET is offering a free month of service with a new server in Ashburn.
>> Choose from 2 high performing configs, both with 100TB of bandwidth.
>> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
>> http://p.sf.net/sfu/gigenet
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>>
>

Re: [Rdkit-devel] new C++ drawing code

[Igor F. <igo...@gm...>]

This is very nice!
Here is a shim to draw to wxWidgets, header-file only.
If anyone needs an example how to use it please let me know.

Igor

On Tue, Jan 20, 2015 at 2:41 AM, Greg Landrum <gre...@gm...>
wrote:

> I merged the pull request this morning. The new C++ drawing code is now
> available on master.
>
> Best,
> -greg
>
>
> On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum <gre...@gm...>
> wrote:
>
>> Dear all,
>>
>> I just created a pull request for integration of some new C++ drawing
>> code into the RDKit:
>> https://github.com/rdkit/rdkit/pull/412
>>
>> This is a big one, so I will leave the PR active until the weekend for
>> people to look at and comment on before I merge onto the master.
>>
>> The new code supports rendering to SVG, Cairo (optional), and Qt
>> (optional). Adding support for a new backend is pretty straightforward.
>>
>> There's still work to be done to allow this to be a replacement for the
>> Python-based rendering code in rdkit.Chem.Draw, but it's a big step forward.
>>
>> The original design and code is from Dave Cosgrove. Many thanks to Dave
>> for the contribution, which is really going to help improve the quality of
>> the molecule drawings the RDKit produces.
>>
>> Best,
>> -greg
>>
>>
>
>
> ------------------------------------------------------------------------------
> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> GigeNET is offering a free month of service with a new server in Ashburn.
> Choose from 2 high performing configs, both with 100TB of bandwidth.
> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> http://p.sf.net/sfu/gigenet
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
>

Re: [Rdkit-devel] new C++ drawing code

[Greg L. <gre...@gm...>]

I merged the pull request this morning. The new C++ drawing code is now
available on master.

Best,
-greg


On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum <gre...@gm...>
wrote:

> Dear all,
>
> I just created a pull request for integration of some new C++ drawing code
> into the RDKit:
> https://github.com/rdkit/rdkit/pull/412
>
> This is a big one, so I will leave the PR active until the weekend for
> people to look at and comment on before I merge onto the master.
>
> The new code supports rendering to SVG, Cairo (optional), and Qt
> (optional). Adding support for a new backend is pretty straightforward.
>
> There's still work to be done to allow this to be a replacement for the
> Python-based rendering code in rdkit.Chem.Draw, but it's a big step forward.
>
> The original design and code is from Dave Cosgrove. Many thanks to Dave
> for the contribution, which is really going to help improve the quality of
> the molecule drawings the RDKit produces.
>
> Best,
> -greg
>
>