Im trying to minimise a ligand library to do virtual screening. To do this, I have installed OpenBabel 2.4.1 as the latest version does not seem to be compatible with the program I want to use for virtual screening (VSpipe). I downloaded the 2.4.1 version and then followed these instructions.
Install cairo library and libpython-dev sudo apt-get install libpython-dev sudo apt-get install libcairo2-dev 3. There are some requirements specified in the INSTALL file in OpenBabel
Even though there are some that are optional, here we are going to explain
how to install them all:
3.1. CMake 2.4.8 or later
sudo apt-get install cmake 3.2. Eigen 3.0 or later (optional)
sudo apt-get install libeigen3-dev 3.3. libxml2 (optional)
sudo apt-get install libxml2-dev 3.4. zlib (optional)
sudo apt-get install zlib1g-dev 3.5. wxWidgets 2.8 (optional, needed to build GUI)
sudo apt-get install libwxgtk3.0-dev 4. Follow OpenBabel installation. Here we only add the basic installation.
If you want an advanced installation, check their INSTALL file
The following instructions assume that the Open Babel source distribution is in
the directory ~/Applications/openbabel-2.4.1.
4.1. Create a 'build' directory:
cd ~/Applications/openbabel-2.4.1 mkdir build cd build 4.2. Configure the build system. You can specify additional build
options at this time (see below):
cmake .. 4.3. Compile:
make -j2 4.4. Test (optional):
make test 4.5. Install:
sudo make install
Everything seems to work swell until I get to the make test stage. This returns this message.
98% tests passed, 4 tests failed out of 160
Total Test time (real) = 88.24 sec
The following tests FAILED: 157 - pytest_pdbformat (Failed) 158 - pybindtest_bindings (Failed) 159 - pybindtest__pybel (Failed) 160 - pybindtest_example (Failed) Errors while running CTest make: * [test] Error 8
Does anyone know what I can do to get around this?
I tried following the suggestion raised on this following issue, but could not figure out how to download and apply the suggested patch.
https://github.com/harryjubb/openbabel_python_docker/issues/1
Can anyone help?
