Ubuntu (22.04.3) 安装openstructure

官方文档 https://openstructure.org/docs/2.8/install/

提前下载https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz

一、有sudo权限，可安装默认功能版本

sudo aptitude install openstructure
chemdict_tool create components.cif.gz compounds.chemlib

二、无sudo权限，安装编译版本

# 安装依赖 boost-1.76
wget https://archives.boost.io/release/1.76.0/source/boost_1_76_0.tar.gz
tar zxvf boost_1_76_0.tar.gz
cd boost_1_76_0

# 修改 bootstrap.sh PREFIX 和 PYTHON
# PREFIX=<BOOST DIR TO INSTALL>
# PYTHON=<SYSTEM PYTHON>
vim bootstrap.sh 

# build
./b2

# install to <BOOST DIR TO INSTALL>
./b2 install

# 安装QT5 for QT5Xml
git clone https://code.qt.io/qt/qtbase.git

cd qtbase

# select 5.15 version
git checkout -b 5.15 origin/5.15

# configure set <YOUR DIR to Install>
./configure --prefix=<YOUR DIR to Install>

gmake

gmake install

# 安装openmm
wget -c https://www.doxygen.nl/files/doxygen-1.12.0.linux.bin.tar.gz
tar zxvf doxygen-1.12.0.linux.bin.tar.gz
cd doxygen-1.12.0
# set INSTALL=<YOUR INSTALL DIR>
make


git clone git@github.com:openmm/openmm.git

cd openmm
cmake . -DCMAKE_INSTALL_PREFIX=<YOUR DIR>/installs/openmm8.1.2 -DDOXYGEN_EXECUTABLE=<YOUR DIR>/installs/doxygen_1.12.0/bin/doxygen

# 编译openstructure

git clone https://git.scicore.unibas.ch/schwede/openstructure.git
cd openstructure

cmake . -DCOMPOUND_LIB=<YOUR DIR>/compounds.chemlib -DCMAKE_INSTALL_PREFIX=<YOUR DIR>/installs/openstructure -DUSE_RPATH=ON -DUSE_SHADER=ON -DENABLE_MM=ON -DCOMPILE_TMTOOLS=ON -DCOMPILE_TMTOOLS=ON -DOPEN_MM_PLUGIN_DIR=<YOUR DIR>/installs/openmm8.1.2/lib/plugins -DEIGEN3_INCLUDE_DIR=<YOUR DIR>/installs/eigen3.4/include/eigen3 -DOPEN_MM_INCLUDE_DIR=<YOUR DIR>/installs/openmm8.1.2/include -DOPEN_MM_LIBRARY=<YOUR DIR>/installs/openmm8.1.2/lib

# 输出以下配置信息

'''
   Install Prefix                        (-DPREFIX) : <YOUR DIR>/installs/openstructure
   RPath in install                   (-DUSE_RPATH) : ON
   Info support                     (-DENABLE_INFO) : ON
   Graphical interface               (-DENABLE_GUI) : ON
   OpenGL support                    (-DENABLE_GFX) : ON
   Shader support                    (-DUSE_SHADER) : ON
   SpaceNav Device support         (-DENABLE_SPNAV) : OFF
   OpenMM support                     (-DENABLE_MM) : ON
   OpenMM plugins            (-DOPEN_MM_PLUGIN_DIR) : <YOUR DIR>/installs/openmm8.1.2/lib/plugins
   Parasail alignment library   (-DENABLE_PARASAIL) : OFF
   Optimize                            (-DOPTIMIZE) : OFF
   Profiling support                    (-DPROFILE) : OFF
   Double Precision        (-DUSE_DOUBLE_PRECISION) : OFF
   Compound Lib                    (-DCOMPOUND_LIB) : <YOUR DIR>/compounds.chemlib
   TMAlign and TMScore          (-DCOMPILE_TMTOOLS) : ON
   Static Libraries               (-DENABLE_STATIC) : OFF
   Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : OFF
   Hidden object visibility  (-DHIDDEN_VISIBILITY) : OFF
'''