wtorek, 10 czerwca 2014

Notes on Open Babel compiling and local install...

Installing openbabel locally sometimes is not as straightforward as it could be. Here are some notes on compiling it on the system without root permissions.

Compiling OB from sources


Fetching / updating sources from git repositories. Please notice the patching eem charges model with eem_fix.patch (optional).

#!/bin/bash

# for the first time use:
#mkdir -p openbabel
# cd openbabel
#git clone git://github.com/openbabel/openbabel.git

cd openbabel
git pull
cd ..

# optional for patching EEM
# echo patching....
# patch openbabel/src/charges/eem.cpp < eem_fix.patch

if [ -d build ]; then
    echo "********* Please delete build dir"
    exit
fi

mkdir build
cd build
cmake ../openbabel -DPYTHON_BINDINGS=ON -DRUN_SWIG=ON \
    -DPYTHON_INCLUDE_DIR=/usr/include/python2.6 \
    -DPYTHON_LIBRARY=/usr/lib/python2.6/config/libpython2.6.so \
    -DCMAKE_INSTALL_PREFIX=~/bin/openbabel-install

make -j14

make test

After successful compilation you should have a complete openbabel structure under your bin/openbabel-install:

~/bin/openbabel-install/
   |-bin
   |-include
   |---inchi
   |---openbabel-2.0
   |-----openbabel
   |-------json
   |-------math
   |-------stereo
   |-lib
   |---cmake
   |-----openbabel2
   |---openbabel
   |-----2.3.90
   |---pkgconfig
   |---python2.6
   |-----site-packages
   |-share
   |---man
   |-----man1
   |---openbabel
   |-----2.3.90


Compiling align-it


Fetch the newest version of silicos align-it, extract it to directory of your choice (eg. align-it-1.0.4). Then you can use following script to setup environmental variables and compile the program:

#!/bin/bash

export BABEL_LIBDIR=/home/fstefaniak/bin/openbabel-install/lib/ 
export BABEL_INCLUDEDIR=/home/fstefaniak/bin/openbabel-install/include/openbabel-2.0/openbabel/
export BABEL_DATADIR=/home/fstefaniak/bin/openbabel-install/share/openbabel/2.3.90/

cd align-it-1.0.4

mkdir build
cd build
cmake ..
make


To be continued


Some more notes


Update 2017/12/01


compiling the older version of OpenBabel (2.3.1), I get the error

Scanning dependencies of target openbabel
[  0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o
In file included from /home/fstefaniak/sources/openbabel/openbabel-2.3.1/include/openbabel/alias.h:19:0,
                 from /home/fstefaniak/sources/openbabel/openbabel-2.3.1/src/alias.cpp:17:
/home/fstefaniak/sources/openbabel/openbabel-2.3.1/include/openbabel/shared_ptr.h:27:14: error: ‘std::tr1’ has not been declared
   using std::tr1::shared_ptr;
              ^
src/CMakeFiles/openbabel.dir/build.make:62: recipe for target 'src/CMakeFiles/openbabel.dir/alias.o' failed
make[2]: *** [src/CMakeFiles/openbabel.dir/alias.o] Error 1
CMakeFiles/Makefile2:1232: recipe for target 'src/CMakeFiles/openbabel.dir/all' failed
make[1]: *** [src/CMakeFiles/openbabel.dir/all] Error 2
Makefile:138: recipe for target 'all' failed
make: *** [all] Error 2

Thanks to https://diane-be-unique.com/2016/10/19/openbabel-error-in-installing/ the solution is: in openbabel-2.3.1/include/openbabel/shared_ptr.h add:

#include <tr1/memory>

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