Fixes #295
upgrade the py27 build to boost 1_55 + add java wrappers to py34
Merge pull request #309 from rvianello/travis-ci-2

travis-ci script update
Fixes #296
fix a deprecation warning
Fixes: #240
Merge remote-tracking branch 'origin/master'
initial pass at adding avalon fps to cartridge. needs more testing
do not default to building inchi and avalon code
Fixes #311
try adding cartridge to the travis build
that was not particularly successful; add boost as well
that did not work at all; try again another day
- fixed a bug which caused the MMFF parameterization code
  to segfault when a system not listed in the MMFFBndk
  table was found. THe Herschbach-Laurie fallback according
  to MMFF.V was implemented and a relevant test was added
  in testMMFFHelpers.cpp
cleanup some old debug printing
Fixes #313
NOTE: this still needs testing on machines with older versions of flex/bison
complete the fix for #313 by checking in a missed .cmake file and output using older versions of flex and bison (just to be sure)
ExplicitBitVect: Add +operator to concatenate two ExplicitBitVects
MolOps: Add function to get the number of atoms with a distinct property
ChemReactions: Extented functionality of chemical reactions

- Module to generate reaction fingerprints: structural FP for screening,
  difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
  to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now