Re: [Rdkit-discuss] https://sourceforge.net

[Greg Landrum]

The mailing lists and one form of the downloads are hosted there. It's a
very good point that having the trackers still active on sourceforge is
confusing. I just deleted them.

We should also do something about the svn repo that's there, just to make
clear that it's no longer active.

Does anyone see a problem with me doing a commit there that removes all the
code and just leaves a "look in github" readme?


On Fri, Mar 20, 2015 at 7:44 PM, Soren Wacker  wrote:

> Hi,
>
> rdkit has moved to github, but there is still the repository on
> sourceforge.net.
> However, if you google 'rdkit bugs' the sourceforge page comes up first.
> I find that confusing. Is there a reason to keep the sourceforge.net
> stuff?
> If not, why don't you remove the sourceforge repository?
>
> kind regards
> Soren
>
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Re: [Rdkit-discuss] Wired dependencies.

[Soren Wacker]

Hi,

OK, this issue is solved. Now, everything (anaconda, rdkit, ipython notebook 
jupiter) runs fine.
I documented the installation process.  In case anyone is interested here is my 
installation script. I did not run it a last time, but it should be at least a 
good start to install and run rdkit in a python notebook within an anaconda 
environment.

regards
Soren


 rdkit_anaconda_install.sh ---
#!/bin/bash

sourcedir=/tmp/install_modeling_env
mkdir /tmp/install_modeling_env
cd /tmp/install_modeling_env

install_prefix=/path/to/target/dir

#Check target exists
if [ -d $install_prefix  ] ;then
echo "Please create target directory first"
exit 1
fi

export PATH=$PATH:$install_prefix/bin

yum -y install wget tar bzip2 git gcc-c++ patch python-qt4 @development-tools 
boost\
   boost-devel cmake bison python-devel tk-devel readline-devel\
   zlib-devel bzip2-devel sqlite-devel

wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
chmod +x Miniconda-latest-Linux-x86_64.sh
$sourcedir/Miniconda-latest-Linux-x86_64.sh -b -p $install_prefix
git clone https://github.com/rdkit/conda-rdkit.git conda-rdkit

conda update conda
conda update --all
conda install --yes pip
conda install --yes numpy
conda install --yes scipy
conda install --yes matplotlib
conda install --yes ipython
conda install --yes pil
conda install --yes scikit-learn
conda install --yes scikit-image
conda install --yes pandas
conda install --yes requests
conda install --yes conda-build
conda install --yes patchelf
conda install --yes jinja2
conda install --yes pyzmq
conda install --yes tornado
conda install --yes jsonschema
conda install --yes xwpython
conda update --all

cd $sourcedir/conda-rdkit && conda build boost
cd $sourcedir/conda-rdkit && conda build rdkit

cd $sourcedir
conda create --use-local -n env rdkit ipython matplotlib requests pyzmq pyqt 
jinja2 tornado jsonschema pil scikit-learn pandas wxpython

rm -r $sourcedir

source activate env

echo "NOTE Remember to add 'export PATH=\$PATH:$install_prefix/bin' to you PATH"

echo "NOTE Start the notebook with 'source activate env ; ipython notebook ; 
source deactivate '


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[Rdkit-discuss] https://sourceforge.net

[Soren Wacker]

Hi,

rdkit has moved to github, but there is still the repository on sourceforge.net.
However, if you google 'rdkit bugs' the sourceforge page comes up first. 
I find that confusing. Is there a reason to keep the sourceforge.net stuff?
If not, why don't you remove the sourceforge repository?

kind regards
Soren
--
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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 
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[Rdkit-discuss] building RDKit on Cygwin: rdBase not linked?

[Michal Krompiec]

Hello,
I am struggling to build RDKit on Cygwin, under 32-bit Windows 7,
using gcc 4.9.2, boost 1.55 and python 2.7.8, with the standard
options:
cmake .. && make && make install

The building itself did not raise any errors, but the python tests
fail, for example:

$ python -v -c 'from rdkit import Chem'
...
import rdkit.Chem # precompiled from /home/m/RDKit/rdkit/Chem/__init__.pyc
Traceback (most recent call last):
  File "", line 1, in 
  File "/home/m/RDKit/rdkit/Chem/__init__.py", line 18, in 
from rdkit import rdBase
ImportError: cannot import name rdBase

$RDBASE and $RDBASE/lib are in the PATH and PYTHONPATH. To be sure the
dlls are found, I even copied them to /bin. I am pretty sure that
paths are OK.

There is, however, no rdBase.so or anything like that present in $RDBASE/rdkit:
$ ls ~/RDKit/rdkit
__init__.py   _py2_pickle.py   Avalon  CMakeLists.txt  DataStructs
DistanceGeometry  ForceField  MLrdBase.pyd   RDConfig.pyc
RDPaths.py   SimDivFilters  six.pyc  test_list.py   utils
__init__.pyc  _py2_pickle.pyc  ChemDataManip   Dbase
epydoc.config GeometryNumerics  RDConfig.py  RDLogger.py
RDRandom.py  six.py spingTestRunner.py  VLib

$ ls ~/RDKit/build/rdkit/
Chem  cmake_install.cmake  CMakeFiles  CTestTestfile.cmake  DataManip
DataStructs  DistanceGeometry  ForceField  Geometry  Makefile  ML
Numerics  rdBase.pyd  RDPaths.py  SimDivFilters

$ locate rdBase
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/cmake_clean.cmake
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/CXX.includecache
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.internal
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend.make
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/flags.make
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/link.txt
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/progress.make
/home/m/RDKit/build/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o
/home/m/RDKit/build/rdkit/rdBase.pyd
/home/m/RDKit/rdkit/rdBase.pyd

What else could be wrong?

Thanks,
Michal

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[Rdkit-discuss] A small tutorial for RDKit and emscripten

[Giuseppe Marco Randazzo]

Hello world,

based on the post of Noel >> 
http://baoilleach.blogspot.ch/2015/02/cheminformaticsjs-rdkit.html

i wrote a more complete tutorial to embed rdkit with js.

http://gmrand.blogspot.ch/2015/03/howto-install-rdkit-and-emscripten-on.html 



Maybe some one will enjoy this post.

Have a nice day.


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