PyRosetta. Fixing monolith build imports order.

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add NetBeans IDE template class files.

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Fix CA_rmsd warning message Meiler lab Powercoding with Alyssa Lokits Make it such that CA_rmsd(pose1,pose2) doesn't print a warning message for missing CA atom (e.g. ligand residues or virtual residues). Explicit range CA_rmsd will still print a warning. Also fix/remove bb_rmsd_*() functions, which weren't actually using all their parameters. Fixes bug 0000337 Integration test changes expected as warnings are no longer printed: membrane_relax relax_w_allatom_cst mr_protocols hybridization density_refine metalloprotein_abrelax density_refine_symm readin_dna_rna_protein

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Add a cxx_ver option to test/run.py Also remove the default for cxx, so hopefully Mac users will now be able to better autodetect that they're using clang. This fixes bug 0000335 No test changes expected

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Add some API docs on the nb_list minimizer option. Specifically, I added doxygen comments to certain methods of MinMover and MinimizerOptions. I wrote these comments because I just had to read a bunch of code to figure out what nb_list did. I'm not an expert on the minimizer, so these comments may not be perfectly complete or accurate. But I don't think they're totally off-the-mark.

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merge master into local

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Add support for passing additional arguments to profile tests

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Clean up source/ide/ directory from old xcode items The new way of doing xcode is in source/xcode/ If you were still using the old xcode setup, see https://wiki.rosettacommons.org/index.php/Tools:XCode for details on the new way, or email the developers list for help.

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Fix warnings in BuriedUnsatisfiedPolarsCalculator2

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[update of SandwichFeatures] - much better (accurate and catching more) 'fnIII' topology identification - should not change any integration tests other than (expected) features and features_database_schema (if any)

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removing undefined function to restore Pyrosetta build.

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fix to unit tests for hbond_type_manager.

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pilot_apps.src.settings.all change and make_ctags script

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Adding a pilot app

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Merge of several important changes from personal branch: (1) fix to geom_sol derivatives, needed for RNA, (2) removal of 'incorrect_deriv' options from hbonds, not in use anymore, (3) code to allow parsing of residue chains and numbers from tags like 'A:5-20', used now in stepwise assembly/monte carlo to read in 'conventional' chains and numbering from FASTA files, (4) cleanup of directory structure in protocols/stepwise/, including combination of all legacy/ subdirs into one subdir. Integration tests checked, and only RNA and swa/swm tests change, except maybe for order of tracer output from match tests.

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[typo corrected at ProteinResidueConformationFeatures] [update of SandwichFeatures] - change from 'fn3' to 'fnIII' because 'fnIII' seems more correct according to '2008_Manipulating the stability of fibronectin type III domains by protein engineering' - should not change any integration tests other than (expected) features and features_database_schema (if any)

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