Merge pull request #1546 from RosettaCommons/jadolfbr/ab_numbering_converter
Antibody numbering conversion
Description
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* Add a mover and app for converting antibody structures from one numbering scheme to another.
* Change numbering_scheme option to input_ab_scheme
* Implement output_ab_scheme to every app that outputs antibodies, so users can use any scheme as input and get any scheme as output in antibody apps, including antibody.cc (well, at least for output).
*Fix public app code_template.
- [x] Add Mover to inter-convert numbering schemes: ```AntibodyNumberingConverterMover```
- [x] Add app that does the conversion: ```antibody_numbering_converter```
- [x] Add integration test for app
- [x] Add RosettaScript Integration
- [x] Test with structures numbered in AHo and convert to Chothia! Woohoo! Reload the Chothia antibody in Rosetta, test clustering, CDRs, etc.
- [x] Update intra-cdr numbering database file manually using 2001 AHo numbering paper and the numbering scheme atlas.
- [x] Test crazy H3 antibodies and thoroughly write unit tests to interconvert all schemes and load back in.
Requested:
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- [x] Change input flag from ```-numbering_scheme_``` to``` _-input_ab_numbering_```
- [x] Change output flag from ```-output_numbering_scheme``` to ```-output_ab_numbering```.
- [x] Remove ```_Scheme``` suffix for numbering schemes - at least in terms of string parsing.
Current Use
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Just add the option, ```-output_ab_scheme``` to any antibody app that writes PDBs or the converter app.
Note that the option ```-input_ab_scheme``` instructs which numbering scheme the current input pdb is (and that ```-numbering_scheme``` option has been deprecated in favor of this option).