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Rosetta
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#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/match.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/Tracer.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/util.hh>#include <core/conformation/Residue.hh>#include <core/import_pose/import_pose.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/kinematics/Stub.hh>#include <core/kinematics/MoveMap.hh>#include <utility/graph/Graph.hh>#include <core/pack/packer_neighbors.hh>#include <core/pack/rotamer_set/RotamerSetFactory.hh>#include <core/pack/rotamer_set/RotamerSet.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/scoring/Energies.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/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/constraints/CoordinateConstraint.hh>#include <core/io/silent/ScoreFileSilentStruct.hh>#include <core/io/silent/SilentFileData.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/scoring/ImplicitFastClashCheck.hh>#include <protocols/minimization_packing/PackRotamersMover.hh>#include <protocols/minimization_packing/MinMover.hh>#include <numeric/kinematic_closure/bridgeObjects.hh>#include <sstream>#include <utility/io/izstream.hh>#include <utility/io/ozstream.hh>#include <numeric/NumericTraits.hh>#include <utility/vector0.hh>#include <utility/vector1.hh>#include <platform/types.hh>#include <core/pose/init_id_map.hh>#include <apps/pilot/will/will_util.ihh>#include <algorithm>#include <cassert>#include <cmath>#include <complex>#include <cstddef>#include <cstdio>#include <cstdlib>#include <execinfo.h>#include <fstream>#include <iomanip>#include <iosfwd>#include <iostream>#include <istream>#include <limits>#include <list>#include <map>#include <ostream>#include <set>#include <string>#include <typeinfo>#include <utility>#include <vector>#include <boost/algorithm/string/erase.hpp>#include <boost/unordered/unordered_map.hpp>#include <zlib/zlib.h>#include <zlib/zutil.h>Classes | |
| struct | Hit |
Typedefs | |
| typedef utility::vector1< core::Real > | Reals |
| typedef utility::vector1< core::Size > | Sizes |
| typedef numeric::xyzVector< Real > | Vec |
| typedef numeric::xyzMatrix< Real > | Mat |
| typedef utility::vector1< Vec > | Vecs |
| typedef utility::pointer::shared_ptr< Hit > | HitOP |
Functions | |
| vector1< Reals > | vecs2vv (Vecs const &v) |
| vector1< Vec > | vv2vecs (vector1< Reals > const &vv) |
| Real | ik_arg_glu_frnt (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| Real | ik_arg_glu_side (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| Real | ik_arg_asp_frnt (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| Real | ik_arg_asp_side (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| void | ik_lys_ctp_asp (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| void | ik_lys_ctp_glu (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp) |
| void | repack (Pose &arg) |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("test_ikrs") |
| core::io::silent::SilentFileData | sfd |
| typedef numeric::xyzMatrix<Real> Mat |
| typedef utility::vector1<core::Real> Reals |
| typedef utility::vector1<core::Size> Sizes |
| typedef numeric::xyzVector<Real> Vec |
| typedef utility::vector1<Vec> Vecs |
| Real ik_arg_asp_frnt | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().
Referenced by main().
| Real ik_arg_asp_side | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().
Referenced by main().
| Real ik_arg_glu_frnt | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), CA, numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().
Referenced by main().
| Real ik_arg_glu_side | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), CA, numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().
Referenced by main().
| void ik_lys_ctp_asp | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::distance_squared(), h, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), run_backbone::pivots, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, vecs2vv(), and vv2vecs().
Referenced by main().
| void ik_lys_ctp_glu | ( | Pose & | pose, |
| Size | rsd1, | ||
| Size | rsd2, | ||
| ImplicitFastClashCheck & | ifc, | ||
| vector1< HitOP > & | hits, | ||
| Pose | ctp | ||
| ) |
References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::distance_squared(), h, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), run_backbone::pivots, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, vecs2vv(), and vv2vecs().
Referenced by main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References orn_macrocycle::ala, numeric::alignVectorSets(), numeric::angle_degrees(), Hit::apply(), arg(), argv, clash(), basic::options::OptionKeys::constraints::constraints, numeric::xyzVector< T >::distance_squared(), test.T009_Exceptions::e, utility::file_basename(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, Hit::frnt, create_a3b_hbs::i, ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), basic::options::OptionKeys::in::in, basic::init(), enumerate_junctions::int, max(), numeric::xyzVector< T >::max(), min(), basic::options::OptionKeys::in::file::movemap, natoms(), Hit::nego, basic::options::option, PI, numeric::NumericTraits< T >::pi(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, repack(), rot_pose(), Hit::rsd1, Hit::rsd2, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::match::scaffold_active_site_residues, basic::options::OptionKeys::out::sf, sfd, ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), Hit::stub, basic::options::TR, trans_pose(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().
| void repack | ( | Pose & | arg | ) |
References arg(), basic::options::OptionKeys::out::sf, and vancomycin::task.
Referenced by main().
References create_a3b_hbs::i, create_a3b_hbs::r, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.
Referenced by ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), and ik_lys_ctp_glu().
References create_a3b_hbs::i, and create_a3b_hbs::r.
Referenced by ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), and ik_lys_ctp_glu().
| core::io::silent::SilentFileData sfd |
Referenced by main().
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static |
1.9.1