Merge branch 'master' into develop
moved from inheritance to wrapping of mdtraj trajectory and topology
moved from inheritance to wrapping of mdtraj trajectory and topology
Merge branch 'mdtraj_wrap' into develop
removed id_to_idx mapping in atom list and bond list generators; changed behavior of n_atoms to exclude ports
Merge branch 'develop' of https://github.com/sallai/mbuild into develop
moved opls work to new branch
cleanup/docs
cleanup/docs, additional test, renamed post_remove to _remove
new unit tests
oplsaa wip
added some test cases for opls_validation
opls validation wip
cleanup/organization of oplsaa; factored out neighbor checking function
simplified outer loop in opls, docs
fixed bug in dihedral finding that would identify 3-membered rings as a dihedral
function to create compound from .top/.pdb and extract opls_types; added GROMACS molecule & liquid database
Added opls_149. Added testing/debug output to opls validation. test_opls.py does not do anything with py.test but if run directly, provides useful debugging information for all molecules in the validation test set.
Added opls_148. Added benzene test case. Added option to only run one particular molecule.
Added biphenyl and benzene tests.