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Rosetta
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#include <basic/database/open.hh>#include <basic/options/keys/edensity.OptionKeys.gen.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/parser.OptionKeys.gen.hh>#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>#include <basic/options/keys/willmatch.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/options/util.hh>#include <basic/Tracer.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 <core/import_pose/import_pose.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/MoveMap.hh>#include <core/kinematics/Stub.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/symmetry/util.hh>#include <core/pose/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/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 <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/simple_moves/FragmentMover.hh>#include <protocols/electron_density/util.hh>#include <protocols/flxbb/DesignLayerOperation.fwd.hh>#include <protocols/flxbb/DesignLayerOperation.hh>#include <protocols/flxbb/FlxbbDesign.hh>#include <protocols/jobdist/standard_mains.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/scoring/ImplicitFastClashCheck.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 | myoptH (Pose &pose, ScoreFunctionOP sf) |
| void | run () |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("genmatch_d6_bpy") |
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, basic::init(), and run().
| void myoptH | ( | Pose & | pose, |
| ScoreFunctionOP | sf | ||
| ) |
References beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.
| void run | ( | ) |
References a, orn_macrocycle::ala, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, angle_degrees(), compute_difference::b, CB, CD, CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), count, numeric::xyzVector< T >::cross(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::conversions::degrees(), numeric::xyzVector< T >::distance(), numeric::xyzVector< T >::distance_squared(), numeric::xyzVector< T >::dot(), test.T009_Exceptions::e, utility::file_basename(), h, create_a3b_hbs::i, basic::options::OptionKeys::in::in, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, basic::options::OptionKeys::willmatch::max_ang_metal, basic::options::OptionKeys::willmatch::max_dis_metal, surface_app::native, create_a3b_hbs::nres, basic::options::OptionKeys::out::file::o, basic::options::option, adapt_rotamers::ori, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), residue, basic::options::OptionKeys::willmatch::residues, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::sf, ObjexxFCL::string_of(), stub(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.
Referenced by main().
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static |
1.9.1