Merge pull request #3797 from RosettaCommons/jadolfbr/sm_in_pyrosetta
This Address #3777 - getting SimpleMetrics to work seamlessly in PyRosetta
This PR makes `pose.scores` work by accessing the `ScoreMap` 'class' directly instead of individual extra scores functions. Unit tests for this functionality are added to the PyRosetta unit testing framework, as well as additional tests for SimpleMetrics in C++ testing framework. The `ScoreMap` itself is now unit tested to work with SMs and an additional clear function has been added to the `SimpleMetricData` class.
This PR also deprecates the old-style PyRosetta score file, which was ALWAYS bad and too different from C++ Rosetta scorefile output to be of much use in general protocols. If one tries to use the old-style format, we exit with a helpful message.