Merge pull request #961 from RosettaCommons/aleaverfay/manual_serialization
Merging branch aleaverfay/manual_serialization into master.
Preliminary work on bringing serialization code into master as progress toward JD3.
This branch builds on pull request #751, making several large changes to the implementation of constraints and to the way Poses can be copied.
300 some classes now have serialization routines -- basically, Pose, and everything that can be cached inside of a Pose can be serialized.
Separately, there is code in the tools repository to ensure that all classes with serialization routines serialize all of their data members.
ResidueSelectors now define an XSD to describe the format in which they may be specified in XML files.
Constraints comparison semantics have been improved, and a bug in the way ConstraintSets are cloned and remapped has been fixed. Func objects can now be compared. ConstraintSet copying should now be quite a bit faster, since the ResidueConstraints objects are more efficiently copied between ConstraintSets.
Significant integration test changes are likely the result of adding a new data member to class Residue; Residue now contains both a ResidueType const & and a ResidueTypeCOP. There were four integration test changes up to revision a06365a that were all explainable, and the only changes after that point that could have an impact on existing code was to have Residue hold this smart pointer. This will change inlining and lead to integration test trajectory changes.
Full documentation of the utility::tag::XMLSchema classes will arrive shortly.