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Rosetta
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#include <basic/database/open.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>#include <basic/options/keys/abinitio.OptionKeys.gen.hh>#include <basic/options/keys/frags.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/options/option_macros.hh>#include <basic/options/util.hh>#include <basic/Tracer.hh>#include <core/chemical/AtomType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/util.hh>#include <core/chemical/VariantType.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/symmetry/SymDof.hh>#include <core/conformation/symmetry/SymmData.hh>#include <core/conformation/symmetry/SymmetricConformation.hh>#include <core/conformation/symmetry/SymmetryInfo.hh>#include <core/conformation/symmetry/util.hh>#include <core/conformation/symmetry/VirtualCoordinate.hh>#include <core/fragment/BBTorsionSRFD.hh>#include <core/fragment/ConstantLengthFragSet.hh>#include <core/fragment/FragData.hh>#include <core/fragment/FragmentIO.hh>#include <core/fragment/FragSet.hh>#include <devel/init.hh>#include <core/import_pose/import_pose.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/io/silent/ScoreFileSilentStruct.hh>#include <core/io/silent/SilentFileData.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/MoveMap.hh>#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>#include <core/pack/optimizeH.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pose/annotated_sequence.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/pose/symmetry/util.hh>#include <core/scoring/constraints/AmbiguousConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/func/CircularHarmonicFunc.hh>#include <core/scoring/constraints/MultiConstraint.hh>#include <core/scoring/constraints/util.hh>#include <core/scoring/func/XYZ_Func.hh>#include <core/scoring/dssp/Dssp.hh>#include <core/scoring/electron_density/util.hh>#include <core/scoring/Energies.hh>#include <core/scoring/packstat/compute_sasa.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/sasa.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/symmetry/SymmetricScoreFunction.hh>#include <core/util/SwitchResidueTypeSet.hh>#include <numeric/model_quality/rms.hh>#include <numeric/random/random.hh>#include <numeric/xyz.functions.hh>#include <numeric/xyz.io.hh>#include <ObjexxFCL/FArray2D.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <protocols/abinitio/AbrelaxMover.hh>#include <protocols/abinitio/ClassicAbinitio.hh>#include <protocols/simple_moves/FragmentMover.hh>#include <protocols/electron_density/util.hh>#include <protocols/flxbb/FlxbbDesign.hh>#include <protocols/jd2/JobDistributor.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/rigid/RigidBodyMover.hh>#include <protocols/symmetry/SetupForSymmetryMover.hh>#include <protocols/minimization_packing/symmetry/SymMinMover.hh>#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/relax/FastRelax.hh>#include <protocols/symmetry/SymDockingInitialPerturbation.hh>#include <protocols/symmetric_docking/SymDockingLowRes.hh>#include <protocols/viewer/viewers.hh>#include <sstream>#include <utility/io/izstream.hh>#include <utility/io/ozstream.hh>#include <apps/pilot/will/will_util.ihh>#include <apps/pilot/will/mynamespaces.ihh>Functions | |
| void | register_options () |
| Vec | center_ca (Pose const &p, Size st=1, Size nres=0) |
| Vec | center_heavy (Pose const &p, Size st=1, Size nres=0) |
| void | calc_c3_rmsd (Size const nres, Pose p, Pose const &native, Vec const &natcom, Vec const &natcomca, Real &carmsd, Real &aarmsd) |
| int | main (int argc, char *argv[]) |
Variables | |
| static core::io::silent::SilentFileData | sfd |
| void calc_c3_rmsd | ( | Size const | nres, |
| Pose | p, | ||
| Pose const & | native, | ||
| Vec const & | natcom, | ||
| Vec const & | natcomca, | ||
| Real & | carmsd, | ||
| Real & | aarmsd | ||
| ) |
References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, center_ca(), center_heavy(), utility::io::oc::cout, numeric::dihedral_degrees(), surface_app::native, create_a3b_hbs::nres, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, rot_pose(), str(), trans_pose(), utility_exit_with_message, and numeric::xyzVector< T >::z().
Referenced by main().
References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.
Referenced by calc_c3_rmsd(), and main().
References create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.
Referenced by calc_c3_rmsd(), and main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References basic::options::OptionKeys::frags::annotate, argv, calc_c3_rmsd(), center_ca(), center_heavy(), pyrosetta::create_score_function, test.T009_Exceptions::e, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::file::frag3, basic::options::OptionKeys::in::file::frag9, test.T020_Pose_Bindings::ft, basic::init(), basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, surface_app::native, basic::options::OptionKeys::in::file::native, basic::options::OptionKeys::frags::nr_large_copies, create_a3b_hbs::nres, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, basic::options::OptionKeys::out::file::o, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, pyrosetta.distributed.io::pose_from_file, register_options(), basic::options::OptionKeys::frags::scoring::scoring, beta_sc_scan::seq, sfd, basic::options::OptionKeys::out::file::silent, str(), erraser_analysis::temp, numeric::random::uniform(), basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.
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static |
Referenced by main().
1.9.1