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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>Classes | |
| struct | MyRT |
Functions | |
| std::string | SAN1 ("CB") |
| std::string | SAN2 ("CA") |
| std::string | SAN3 ("N") |
| void | alncys (core::pose::Pose &pose, Real c1, Real c2, Real c3) |
| void | get_cys_rts (utility::vector1< utility::vector1< core::Real > > &CHI, utility::vector1< Stub > &STs, utility::vector1< utility::vector1< MyRT > > &RTs) |
| void | run_sf4h () |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("sf4_hash") |
| void alncys | ( | core::pose::Pose & | pose, |
| Real | c1, | ||
| Real | c2, | ||
| Real | c3 | ||
| ) |
References alignaxis(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::dihedral_degrees(), beta_nonlocal::pose, rot_pose(), and trans_pose().
Referenced by get_cys_rts().
| void get_cys_rts | ( | utility::vector1< utility::vector1< core::Real > > & | CHI, |
| utility::vector1< Stub > & | STs, | ||
| utility::vector1< utility::vector1< MyRT > > & | RTs | ||
| ) |
References alignaxis(), alncys(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, CHI1, CHI2, CHI3, clash(), utility::io::oc::cout, numeric::dihedral_degrees(), ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, rot_pose(), SAN1(), SAN2(), SAN3(), TR, trans_pose(), numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().
Referenced by run_sf4h().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, test.T009_Exceptions::e, basic::init(), and run_sf4h().
| void run_sf4h | ( | ) |
References alignaxis(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, CHI1, CHI2, CHI3, numeric::dihedral_degrees(), numeric::xyzVector< T >::dot(), utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_cys_rts(), create_a3b_hbs::i, create_a3b_hbs::j, numeric::xyzVector< T >::max(), numeric::xyzVector< T >::normalized(), basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, rot_pose(), basic::options::OptionKeys::in::file::s, SAN1(), SAN2(), SAN3(), ObjexxFCL::string_of(), predPRE::t, basic::options::TR, MyRT::trans, trans, trans_pose(), utility_exit_with_message, w, MyRT::w, x, MyRT::x, predPRE::y, MyRT::y, predPRE::z, and MyRT::z.
Referenced by main().
| std::string SAN1 | ( | "CB" | ) |
Referenced by get_cys_rts(), and run_sf4h().
| std::string SAN2 | ( | "CA" | ) |
Referenced by get_cys_rts(), and run_sf4h().
| std::string SAN3 | ( | "N" | ) |
Referenced by get_cys_rts(), and run_sf4h().
|
static |
Referenced by get_cys_rts().
1.9.1