Open-Source Computational Structural Biology Framework. “This project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested method developers in the field of structural bioinformatics.”

• v 1.9 installed
• https://openstructure.org/
• recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt

OpenStructure relies on these applications and Python 2.7.15. All applications including Python need to compiled with –enable-share in the configuration step. A step by step process is listed below.

-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   python
--   unit_test_framework
--   filesystem
--   system
--   iostreams
--   program_options
--   regex
--   thread
-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
-- Numpy headers found
-- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
-- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")


====== Compilations ======

Use ''gcc'' => 4.5

<code>

export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH

export PATH=/share/apps/CENTOS6/cmake/3.12.1/bin:$PATH

tar zxvf ../Python-2.7.15.tgz                                                                                                       
cd Python-2.7.15/ 
./configure --prefix=/share/apps/CENTOS6/python/2.7.15 --enable-shared                                                              
export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
python ../get-pip.py                                                                                                                
pip install numpy scipy 

wget https://dl.bintray.com/boostorg/release/1.68.0/source/boost_1_68_0.tar.gz`
./bootstrap.sh --prefix=/share/apps/CENTOS6/boost/1.68.0 \
--with-python=/share/apps/CENTOS6/python/2.7.15/bin/python \
--with-python-root=/share/apps/CENTOS6/python/2.7.15
./b2 install
export LD_LIBRARY_PATH=/share/apps/CENTOS6/boost/1.68.0/lib:$LD_LIBRARY_PATH

wget http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz
mv ../3.2.10.tar.gz ../eigen-3.2.10.tar.gz
tar zxvf ../eigen-3.2.10.tar.gz
cd eigen-eigen-b9cd8366d4e8/
mkdir build
cd build
cmake ..  -DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/eigen/3.2.10
make blas
make install
scp -rp ./* /share/apps/CENTOS6/eigen/3.2.10/

wget http://fftw.org/fftw-3.3.8.tar.gz
tar zxvf ../fftw-3.3.8.tar.gz
cd fftw-3.3.8/
mkdir -p /share/apps/CENTOS6/fftw/3.3.8-enable-single
./configure --enable-shared --enable-single --prefix=/share/apps/CENTOS6/fftw/3.3.8-enable-single
make
make install
export PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib:$LD_LIBRARY_PATH

tar zxvf ../zlib-1.2.11.tar.gz
cd zlib-1.2.11/
./configure --prefix=/share/apps/CENTOS6/zlib/1.2.11
make
make install
export LD_LIBRARY_PATH=/share/apps/CENTOS6/zlib/1.2.11/lib:$LD_LIBRARY_PATH

tar -zxvf ../libpng-1.6.37.tar.gz
cd libpng-1.6.37/
./configure --prefix=/share/apps/CENTOS6/lpng/1.6.37
make
make install
export PATH=/share/apps/CENTOS6/lpng/1.6.37/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/lpng/1.6.37/lib:$LD_LIBRARY_PATH

tar xvfz ../tiff-4.0.9.tar.gz
cd tiff-4.0.9/
./configure --prefix=/share/apps/CENTOS6/tiff/4.0.9
make
make install
export PATH=/share/apps/CENTOS6/tiff/4.0.9/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/tiff/4.0.9/lib:$LD_LIBRARY_PATH



git clone https://git.scicore.unibas.ch/schwede/openstructure.git openstructure-1.9
cd openstructure-1.9/
cd /share/apps/CENTOS6/boost/1.68.0//lib
# fix for boost to find libs
cp -p libboost_python27.a libboost_python.a
cp -p libboost_python27.so.1.68.0 libboost_python.so

rm -f cmakelog; cmake \
-DCMAKE_INSTALL_PREFIX=/share/apps/CENTOS6/openstructure/1.9 \
          -DBOOST_ROOT=/share/apps/CENTOS6/boost/1.68.0 \
         -DPYTHON_ROOT=/share/apps/CENTOS6/python/2.7.15 \
  -DEIGEN3_INCLUDE_DIR=/share/apps/CENTOS6/eigen/3.2.10 \
        -DFFTW_LIBRARY=/share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so \
    -DFFTW_INCLUDE_DIR=/share/apps/CENTOS6/fftw/3.3.8-enable-single/include \
        -DZLIB_LIBRARY=/share/apps/CENTOS6/zlib/1.2.11/lib/libz.so \
    -DZLIB_INCLUDE_DIR=/share/apps/CENTOS6/zlib/1.2.11/include \
         -DPNG_LIBRARY=/share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so \
     -DPNG_INCLUDE_DIR=/share/apps/CENTOS6/lpng/1.6.37/include \
        -DTIFF_LIBRARY=/share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so \
    -DTIFF_INCLUDE_DIR=/share/apps/CENTOS6/tiff/4.0.9/include \
-DENABLE_GUI=OFF -DENABLE_GFX=OFF -DENABLE_INFO=OFF \
-DUSE_NUMPY=ON -DENABLE_MM=OFF \
-DENABLE_STATIC=OFF | tee cmake.log

make
make install
# [100%] Built target actions
export PATH=/share/apps/CENTOS6/openstructure/1.9/bin:$PATH
export LD_LIBRARY_PATH=/share/apps/CENTOS6/openstructure/1.9/lib64:$LD_LIBRARY_PATH

# setup the environment egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt

ost –help Usage:

  ost [ost options] [script to execute] [script parameters]

or

  ost [action name] [action options]

</code>

Remarkably complex compilations.