Updated compiled doc.

doc/html/container/index.html

doc/html/container/singularity.html

doc/html/contributing.html

doc/html/core/geometry.html

doc/html/core/graph_minimizer.html

doc/html/core/helper.html

doc/html/core/index.html

doc/html/core/pm3argparse.html

doc/html/core/runtime_profiling.html

doc/html/core/setcompoundschemlib.html

doc/html/dev_setup.html

doc/html/developers.html

doc/html/genindex.html

doc/html/gettingstarted.html

doc/html/index.html

doc/html/license.html

doc/html/loop/all_atom.html

doc/html/loop/backbone.html

doc/html/loop/index.html

doc/html/loop/load_loop_objects.html