Gromacs wrapper

[tomnewport]

The gromacs wrapper should abstract making process calls to GROMACS. Several existing tools have been considered but rejected mainly due to their experimental status, difficulty of installation and including several tools which aren't required.

The only way to call gromacs presently is via text-based subprocess calls.

It is also important to be able to control the working directory in which processes are run. The API should behave as follows when complete:

gromacs = GromacsWrapper()
gromacs.cd("/tmp/test")
gromacs.mdrun(deffnm="em")

gromacs = GromacsWrapper("/usr/local/gromacs/bin/gmx")

Tasks:

• [x] Create basic container with a folder and ability to use bash
• [x] Generate prefix/suffix based on gromacs binaries directory
• [x] Make bash calls
• [x] With arguments
• [x] Capturing stdout
• [x] Capturing stderr
• [x] Gracefully capturing exceptions
• [x] Automatically taking unfamiliar gromacs.gwhatever(...) and running gmx whatever
• [x] Deleting that stupid GROMACS header
• [x] Including additional defaults for mdrun to make debugging easier
• [x] Providing callbacks and progress updates for mdrun steps