Merge pull request #135 from peastman/master

Minor code cleanup
Merge pull request #137 from peastman/master

Fixed some errors in definitions of hydrogens
Merge pull request #138 from peastman/master

Fixes to adding hydrogens to RNA
Merge pull request #140 from peastman/master

In rare situations, _matchResidue() would take a very long time to return
Merge pull request #141 from peastman/master

Added option to increase hydrogen mass
Merge pull request #142 from peastman/master

PdbStructure records MODRES records
Merge pull request #143 from peastman/master

Include a comment at the top of PDB files
Merge pull request #144 from peastman/master

Reference implementation of CustomIntegrator did not initialize the random number seed correctly
Merge pull request #145 from peastman/master

Documentation updates for 5.2
Look for gromacs include directory in a more flexible way
Fix bug in gromacs top file parser where #else preprocessor directives were not being followed
Fix typo
Add an elseStack
Merge pull request #149 from rmcgibbo/gmxpath

Look for gromacs include directory in a more flexible way
Merge pull request #150 from rmcgibbo/gmxbug

Fix bug in gromacs top file parser
ATOM lines should be 80 chars
add get_by_atomic_number to element
Move left by one column
Remove the module-level function
Merge pull request #152 from rmcgibbo/pdbbug

ATOM lines should be 80 chars