Merge pull request #883 from RosettaCommons/kimdn/master_sew
[what has been updated for beta-sandwich_analysis]
* Add a more rule so that two parallel short strands can be "sheet" for Tim-barrel
[what has been updated for SEWING]
* [model generation update]
- sewing::hash_tag_only_terminal_Es is possible
- User can provide an option (generate_five_ss_model) so that 'db -> node (model)' can generate '3_or_5_secondary_structure_based models'
- added unit test (SewingHasherTests.cxxtest) for "db -> node (model/substructure) can generate 5_secondary_structure_based models"
* [Model_trimmer update]
- becomes little faster (don't care rest trimming steps if any preceding trimming decides to erase the model)
- can do 'leave_models_with_E_terminal_ss'
- can do 'leave_parallel_way_H_bonded_models_by_terminal_strands_only'
- can do 'leave_antiparallel_way_H_bonded_models_by_terminal_strands_only'
- can do 'model_should_have_at_least_one_E'
- can do 'model_should_have_at_least_one_E_at_terminal_segment'
* [hashing update] node (model) -> edge (score) can handle 'any number of
secondary_structure' based models
* [model assembly update]
- User can choose between 27 and 125 boxes for neighborhood_lookup
(-sewing:box_length), both scoring and assembly should use same box numbers
* [ExhaustiveAssemblyMover newly added]
- Enumerate every possible assembly exhaustively
- User can choose 'dump_every_model_for_devel_purpose' option
* [MonteCarloAssemblyMover update]
- User can choose not to stick to best_score if specified 'min_assembly_score' as an option in parser
- User can choose 'offset_bump_dsq' as an option
[beautified some other's files]
beautified except
File utility/json_spirit/json_spirit_writer_template.h could not be beautified
File utility/json_spirit/json_spirit_error_position.h could not be beautified
File utility/json_spirit/json_spirit_writer_options.h could not be beautified