add some tests for the thermodynamics module
Merge branch 'master' of github.com:pele-python/pele
improve TSGraph connected compents algorithm
update setup.py with new test directories

also remove application module
fix the gui connect to database action

it was not recognizing that the QString filename returned by the pop up
window was a string.
turn off -march=native by default

valgrind reports an unrecognized instruction when compiled with
-march=native
add example potential using fortran and iso_c_bindings

fortran with iso_c_bindings is called from python through cython

there appears to be something wrong with the example c_potential not
sure what it is
fix the example c potential

It was completely broken, I don't know how it got originally submitted
in such a broken state
folder with files to test openmm and its integration with PELE
OpenMM 6 installation instructuctions
Tested after installing openmm6. Works fine. Edited paths in main to point to input files in examples.
Tests OpenMMAmberPotential class in pele.amber.openmm_potential. Tested OK.
chechking in coords.pdb. used by multiple test scripts.
fixed some paths in main. timestamped and commented one edit in constructor
after fixing minimization error with Cpp lbfgs
fixed return types of energy and gradient to make it work with Cpp minimizer
changes to get_potential.
added test for connect runs
Added a copy of fortran_iso_c_bindings so that I can work on including
the AMBER 12 interface.
Merge branch 'master' of ssh://git@github.com/pele-python/pele.git