apbs

To build the latest branch, follow the instructions below...

Import submodules:

We are using Git submodules to manage various pieces of code. To build the master branch, after cloning it, you will need to do the following from within the root apbs-pdb2pqr directory:

• git submodule init
• git submodule update

Build flags for CMake

• cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_DOC=OFF -DBUILD_SHARED_LIBS=OFF <apbs src location>

Using geometric flow

If you want to use the geometric flow implementation, when invoking CMake, set ENABLE_GEOFLOW to ON, e.g., -DENABLE_GEOFLOW=ON.

Adding finite element support (fe-manual)

If you would like to use the FEM, you will need to be on OS X or Linux. To enable, when invoking CMake, set ENABLE_FETK to ON, e.g., -DENABLE_FETK=ON. On Linux the FETK shared libraries need to be locatable by the shared library loader. One way to do this is to update LD_LIBRARY_PATH to point at <build-dir>/fetk/lib, e.g., export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<build-dir>/fetk/lib.

Building the python libraries for pdb2pqr

• Install swig
• Build APBS with the following flag: -DENABLE_PYTHON=ON. If you are on linux you also need -DBUILD_SHARED_LIBS=OFF
• Add these libraries to your library path so pdb2pqr can find them.