Bug #117: Adding support for ~ in AtomClass
First implementation of entities
Better testing for entities
Initial implementation of entity finder for no-seqres files
Full implementation of entity finder
Fixing entity problem with nucleotide sequences
A few important improvements: identity matrix and gap coverage checking
Redone implementation of entity finder with simple res number alignment
Some more fixes for entity finder implementation
Some cleanup and a minor interface change in Compound
Bug fix for last commit, plus more minor interface changes and removed
some deprecations
Fixed a few imporant issues with Compound mmCIF parsing
Finally compound parsing working properly in mmcif parsing
- TestLongPdbVsMmCifParsing passes for 1000 random entries
Another change of interface in compound, redid pdb parsing accordingly
Merged entity heuristics stuff into the existing Compound code
Merge pull request #215 from josemduarte/master

I'll merge since there were no complaints
First implementation of interface clustering based on contact overlap
Fixed bug in demo (nmr structures would null point)
Adding more docs, removed 1 warning
Adding cluster id and sorting by average areas