Merging vmullig/metals into master. This updates the handling of metalloproteins in a number of important ways:
--Adds option of automatic detection of covalent bonds to metals on PDB load.
--Adds option of automatic setup of atom_pair and angle constraints between metals and metal-binding residues on PDB load.
--Adds METALBINDING property to residue types.
--Adds METAL property to residue types.
--Adds METAL_BINDING_ATOMS line to params files.
--Adds automatic removal of protons that overlap with metal ions.
--Adds flags controlling behaviour of automatic metal setup.
--Adds Cu and Co (residue types and atom types).
--Allows automatic identification of metals: " ZN", "ZN ", "ZN1", and "ZN2" are all interpreted as ZN.
--Alters unit and integration tests that used a ZN1.params file; these now use ZNx.params.
All of these changes are documented on the Gollum wiki ("Metals" section of "Rosetta Basics").
Unit test status: Pass (with some unit tests' ZN1.params files changed to ZNx.params).
Integration test status: Many changed tests, but all for expected reasons:
1. Trivial output changes due to addition of Cu2p and Co2p atom types.
2. Trivial output changes due to addition of CU.params and CO.params (on by default -- adds 2 new residue types).
3. Specific integration tests now use ZNx.params instead of ZN1.params; their output now says "ZNx" wherever it used to say "ZN1".
4. The usual numerical instabilities.
modified: database/chemical/atom_type_sets/fa_standard/atom_properties.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/NACCESS_sasa_radii.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/atom_orbital_hybridization.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/facts_born_params.epm1.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/gen_born_params.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/memb_fa_params.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/reduce_sasa_radii.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/sasa_radii_legacy.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/soft_rep_params.txt
modified: database/chemical/atom_type_sets/fa_standard/extras/std_charges.txt
modified: database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt
modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASP.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYS.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYV.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYZ.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/GLU.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS_D.params
new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_binding_ncaa/BPY.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CA.params
new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CO.params
new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CU.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE2.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/K.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MG.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MN.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/NA.params
modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/ZN.params
new file: source/src/apps/pilot/vmullig/MetalNotes.txt
new file: source/src/apps/pilot/vmullig/metals_notes.txt
new file: source/src/apps/pilot/vmullig/test_metalloproteins.cc
modified: source/src/basic/options/keys/OptionKeys.cc.gen0.hh
modified: source/src/basic/options/keys/in.OptionKeys.gen.hh
modified: source/src/basic/options/keys/inout.OptionKeys.gen.hh
modified: source/src/basic/options/option.cc.gen.hh
modified: source/src/basic/options/options_rosetta.py
modified: source/src/core.3.src.settings
modified: source/src/core/chemical/ResidueType.cc
modified: source/src/core/chemical/ResidueType.hh
modified: source/src/core/chemical/residue_io.cc
modified: source/src/core/conformation/Residue.hh
modified: source/src/core/import_pose/import_pose.cc
modified: source/src/core/import_pose/import_pose_options.cc
modified: source/src/core/import_pose/import_pose_options.hh
modified: source/src/core/io/pdb/file_data.cc
modified: source/src/core/io/pdb/file_data_fixup.cc
modified: source/src/core/io/pdb/pose_io.cc
modified: source/src/core/pose/Pose.cc
new file: source/src/core/pose/metalloproteins/util.cc
new file: source/src/core/pose/metalloproteins/util.hh
modified: source/src/core/pose/util.cc
modified: source/src/core/pose/util.hh
modified: source/src/core/scoring/ScoreFunctionFactory.cc
modified: source/test/apps.test.settings
modified: source/test/apps/public/ligand_docking/7cpa_7cpa_input.pdb
modified: source/test/apps/public/ligand_docking/7cpa_7cpa_native.pdb
renamed: source/test/apps/public/ligand_docking/ZN1.params -> source/test/apps/public/ligand_docking/ZNx.params
modified: source/test/apps/public/ligand_docking/ligand_dock.cxxtest.hh
modified: source/test/apps/public/ligand_docking/silent.out.ref
modified: source/test/protocols.test.settings
modified: source/test/protocols/ligand_docking/7cpa_7cpa_native.pdb
modified: source/test/protocols/ligand_docking/ResidueTorsionRestraints.cxxtest.hh
renamed: source/test/protocols/ligand_docking/ZN1.params -> source/test/protocols/ligand_docking/ZNx.params
renamed: tests/integration/tests/contactMap/input/ZN1.params -> tests/integration/tests/contactMap/input/ZNx.params
modified: tests/integration/tests/database_jd2_compact_io/7cpa_7cpa_input.pdb.gz
renamed: tests/integration/tests/database_jd2_compact_io/ZN1.params -> tests/integration/tests/database_jd2_compact_io/ZNx.params
modified: tests/integration/tests/database_jd2_compact_io/test_input.flags
modified: tests/integration/tests/database_jd2_compact_io/test_output.flags
modified: tests/integration/tests/grid_scores_features/flags
modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_input.pdb.gz
modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_native.pdb.gz
modified: tests/integration/tests/grid_scores_features/inputs/7cpa_confs.pdb.gz
deleted: tests/integration/tests/grid_scores_features/inputs/ZN1.params
new file: tests/integration/tests/grid_scores_features/inputs/ZNx.params
modified: tests/integration/tests/kinemage_grid_output/flags
modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_input.pdb.gz
modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_native.pdb.gz
modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_confs.pdb.gz
deleted: tests/integration/tests/kinemage_grid_output/inputs/ZN1.params
new file: tests/integration/tests/kinemage_grid_output/inputs/ZNx.params
modified: tests/integration/tests/ligand_database_io/flags_param_output
modified: tests/integration/tests/ligand_database_io/inputs/7cpa_confs.pdb.gz
modified: tests/integration/tests/ligand_database_io/inputs/7cpa_input.pdb.gz
modified: tests/integration/tests/ligand_database_io/inputs/7cpa_native.pdb.gz
deleted: tests/integration/tests/ligand_database_io/inputs/ZN1.params
new file: tests/integration/tests/ligand_database_io/inputs/ZNx.params
modified: tests/integration/tests/ligand_dock_7cpa/flags
modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_input.pdb.gz
modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_native.pdb.gz
modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_confs.pdb.gz
deleted: tests/integration/tests/ligand_dock_7cpa/inputs/ZN1.params
new file: tests/integration/tests/ligand_dock_7cpa/inputs/ZNx.params
modified: tests/integration/tests/ligand_dock_grid/flags
modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_input.pdb.gz
modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_native.pdb.gz
modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_confs.pdb.gz
deleted: tests/integration/tests/ligand_dock_grid/inputs/ZN1.params
new file: tests/integration/tests/ligand_dock_grid/inputs/ZNx.params
modified: tests/integration/tests/ligand_dock_script/flags
modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_confs.pdb.gz
modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_input.pdb.gz
modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_native.pdb.gz
deleted: tests/integration/tests/ligand_dock_script/inputs/ZN1.params
new file: tests/integration/tests/ligand_dock_script/inputs/ZNx.params
modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_input.pdb.gz
modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_native.pdb.gz
modified: tests/integration/tests/startfrom_file/inputs/7cpa_confs.pdb.gz
deleted: tests/integration/tests/startfrom_file/inputs/ZN1.params
new file: tests/integration/tests/startfrom_file/inputs/ZNx.params
modified: tests/integration/tests/startfrom_file/mover_flags
modified: tests/integration/tests/startfrom_file/startfrom_flags
modified: tests/integration/tests/write_mol_file/flags
modified: tests/integration/tests/write_mol_file/inputs/7cpa_confs.pdb.gz
modified: tests/integration/tests/write_mol_file/inputs/7cpa_input.pdb.gz
deleted: tests/integration/tests/write_mol_file/inputs/ZN1.params
new file: tests/integration/tests/write_mol_file/inputs/ZNx.params