GitLab

Added unittest and 1 system tests. Includes 1 bugfix to resolving a circular import and 1 bugfix where dms wasn't creating the topology correctly when the water was specified in different chains

Create system from Desmond files

add getByAtomicNumber to element.

ATOM lines should be 80 chars

Fix bug in gromacs top file parser

Look for gromacs include directory in a more flexible way

Documentation updates for 5.2

Reference implementation of CustomIntegrator did not initialize the random number seed correctly

Include a comment at the top of PDB files

PdbStructure records MODRES records

Added option to increase hydrogen mass

In rare situations, _matchResidue() would take a very long time to return

Fixes to adding hydrogens to RNA