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Rosetta
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Stub class – an object of orthogonal coordinate frame. More...
#include <Stub.hh>
Public Types | |
| typedef numeric::xyzMatrix< Real > | Matrix |
| typedef numeric::xyzVector< Real > | Vector |
Public Member Functions | |
| Stub () | |
| constructor – sets to "default" stub More... | |
| Stub (Matrix const &M_in, Vector const &v_in) | |
| copy constructor More... | |
| Stub (RT const &rt) | |
| constructor from RT object More... | |
| Stub (Vector const ¢er, Vector const &a, Vector const &b, Vector const &c) | |
| constructor by four points More... | |
| Stub (Vector const &a, Vector const &b, Vector const &c) | |
| constructor by three points More... | |
| void | from_four_points (Vector const ¢er, Vector const &a, Vector const &b, Vector const &c) |
| build a stub from a center and other three points a, b, c More... | |
| bool | is_orthogonal (core::Real const &tolerance) const |
| check if the stub is orthogonal under the tolerance cutoff More... | |
| Vector | global2local (Vector const &xyz) const |
| convert a global reference (lab) frame vector to our local (stub) frame More... | |
| Vector | local2global (Vector const &xyz) const |
| convert a local reference (stub) frame vector to the global (lab) frame More... | |
| Vector | spherical (Real const phi, Real const theta, Real const d) const |
| Build a vector in the global lab frame from the spherical coords used in the atomtree. More... | |
| Vector | build_fake_xyz (Size const index) const |
| Build stubatom coords that would yield this stub. More... | |
| Vector | build_fake_xyz (Size const index, Real const length1, Real const length2, Real const angle_degrees) const |
| Build stubatom coords that would yield this stub. More... | |
| bool | operator== (Stub const &rhs) const |
| Matrix | rotation () const |
| Coordinate frame rotation matrix. More... | |
| Vector | center () const |
| Coordinate frame center. More... | |
Static Public Member Functions | |
| static Stub | create_orthogonal (Vector const &a, Vector const &b, Vector const &c) |
| constructor by three points Like the three-point constructor, but adjust things to make sure the stub is orthoganal More... | |
Public Attributes | |
| Matrix | M |
| coord frame by 3x3 matrix, each column is a unit vector More... | |
| Vector | v |
| center point by a vector More... | |
Stub class – an object of orthogonal coordinate frame.
an orthogonal coord frame M (matrix) centered at point V (vector), defined by four points, one is for the center and the other three for calculating the orthogonal frame. For example, a stub can be derived from a backbone triplet N-CA-C centered at CA.
See AtomTree overview and concepts for details.
| typedef numeric::xyzMatrix< Real > core::kinematics::Stub::Matrix |
| typedef numeric::xyzVector< Real > core::kinematics::Stub::Vector |
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constructor – sets to "default" stub
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constructor by four points
first point is the center (V) and the rest three are used to construct the coord frame (M). see member function from_four_points(...) construct a stub centered at v_in, as would come from building c then b then a
References core::pose::motif::a(), protocols::match::upstream::b, and from_four_points().
constructor by three points
first point is the center (V) and all the three are used to construct the coord frame (M). see member function from_four_points(...) construct a stub as would come from building c then b then a
References core::pose::motif::a(), protocols::match::upstream::b, and from_four_points().
Build stubatom coords that would yield this stub.
Referenced by protocols::simple_filters::JumpEvaluator::apply(), and core::scoring::constraints::RTConstraint::fill_f1_f2().
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Coordinate frame center.
References v.
Referenced by from_four_points(), and core::energy_methods::RNA_StubCoordinateEnergy::residue_pair_energy().
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constructor by three points Like the three-point constructor, but adjust things to make sure the stub is orthoganal
References core::pose::motif::a(), protocols::match::upstream::b, and is_orthogonal().
Referenced by core::chemical::MutableICoorRecord::build(), core::chemical::AtomICoor::build(), and core::chemical::fill_ideal_xyz_from_icoor().
| void core::kinematics::Stub::from_four_points | ( | Vector const & | center, |
| Vector const & | a, | ||
| Vector const & | b, | ||
| Vector const & | c | ||
| ) |
build a stub from a center and other three points a, b, c
build a stub from a center points and other three points a, b, c
orthogonal coord frame M contains three unit vectors by column, the first one is the unit vector from b pointing to a, the second one is the unit vector which is in the plane defined by vector b->a and b->c and perpendicular to b->a, the third one is the cross product of the first two.
References core::pose::motif::a(), protocols::match::upstream::b, center(), M, core::id::to_string(), and v.
Referenced by protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_residue_helper(), protocols::features::SaltBridgeFeatures::report_features(), protocols::hotspot_hashing::StubGenerator::residueStubCentroidFrame(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::store_target(), Stub(), and protocols::hotspot_hashing::stub_from_points().
convert a global reference (lab) frame vector to our local (stub) frame
References M, v, and protocols::kinmatch::xyz().
Referenced by protocols::rna::movers::RNA_Decoarsify::apply(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::rna::denovo::create_rna_vall_torsions(), core::scoring::constraints::LocalCoordinateConstraint::dist(), protocols::stepwise::sampler::protein::do_set_xyz(), protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb(), core::io::silent::RNA_SilentStruct::fill_struct(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz(), core::kinematics::AtomTree::get_frag_descendant_local_xyz(), core::kinematics::AtomTree::get_frag_parent_local_xyz(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), protocols::loops::loop_closure::ccd::get_overlap_pos(), protocols::sewing::hashing::LigandBindingResPlacer::identify_possible_binders(), protocols::hotspot_hashing::SearchPatternRotSetOp::increase_packer_residue_radius(), core::kinematics::AtomTree::insert_fragment(), protocols::hotspot_hashing::StubGenerator::moveFromStubFrame(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::fibril::reorient_extended_fibril(), protocols::features::SaltBridgeFeatures::report_features(), core::energy_methods::RNA_StubCoordinateEnergy::residue_pair_energy(), protocols::toolbox::sample_around::rotate_into_nucleobase_frame(), protocols::toolbox::sample_around::rotate_into_phosphate_frame(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::set_xyz_target(), core::scoring::constraints::LocalCoordinateConstraint::steal_def(), protocols::sic_dock::xform_pose_rev(), and protocols::kinmatch::xform_rsd_gl2().
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check if the stub is orthogonal under the tolerance cutoff
References M.
Referenced by core::conformation::Conformation::check_valid_membrane(), create_orthogonal(), core::kinematics::Jump::from_bond_cst(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_internal_coords(), core::kinematics::tree::BondedAtom::update_xyz_coords(), and core::kinematics::tree::JumpAtom::update_xyz_coords().
convert a local reference (stub) frame vector to the global (lab) frame
References M, v, and protocols::kinmatch::xyz().
Referenced by protocols::rna::movers::RNA_Decoarsify::apply(), core::scoring::lkball::WaterBuilder::build(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), core::pack::rotamer_set::create_oriented_water_rotamer(), core::scoring::lkball::WaterBuilder::derivatives(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz(), core::kinematics::AtomTree::get_frag_descendant_local_xyz(), core::kinematics::AtomTree::get_frag_parent_local_xyz(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions(), protocols::loops::loop_closure::ccd::get_overlap_pos(), core::kinematics::AtomTree::insert_single_fragment(), protocols::magnesium::instantiate_water_at_octahedral_vertex(), protocols::hotspot_hashing::StubGenerator::moveIntoStubFrame(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), core::pose::rna::prepare_scratch_residue(), protocols::fibril::reorient_extended_fibril(), protocols::hotspot_hashing::SICPatternAtTransform::Searchpoints(), spherical(), protocols::hotspot_hashing::stub_to_points(), core::fragment::xform_pose(), protocols::sic_dock::xform_pose(), and core::scoring::constraints::LocalCoordinateConstraint::xyz_target().
| bool core::kinematics::Stub::operator== | ( | Stub const & | rhs | ) | const |
Floating point comparison is notoriously fickle. Perform the same series of rotations and translations with ever so slightly different code, and you will produce two different stubs. The comparison operator is looking for exact matches. The only reason to expect that stub A and stub B are the same is because A was copied from B; if neither have changed since the copy, then you will have the same stub.
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Coordinate frame rotation matrix.
References M.
Referenced by core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::get_f1_f2().
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Build a vector in the global lab frame from the spherical coords used in the atomtree.
theta is the angle between the postive x and the vector (0<=theta<=pi), phi is the angle between the y-z plane projection of the vector and the positive y (0<=theta<=2*pi), d is the length of the vector
References local2global().
Referenced by core::chemical::MutableICoorRecord::build(), core::chemical::orbitals::ICoorOrbitalData::build(), core::chemical::AtomICoor::build(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::scoring::lkball::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::build_optimal_water_Os_on_acceptor(), core::conformation::Conformation::fill_missing_atoms(), protocols::pockets::PocketGrid::findExemplars(), core::kinematics::Jump::from_bond_cst(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), and protocols::loops::loop_closure::ccd::get_overlap_pos().
| Matrix core::kinematics::Stub::M |
coord frame by 3x3 matrix, each column is a unit vector
Referenced by protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::UniformRotationMover::apply(), core::pose::rna::bases_are_coplanar(), build_fake_xyz(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_pair(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::classify_base_pairs(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::HackAroEnergy::eval_atom_derivative_aro_aro(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator::evaluate(), core::pose::rna::figure_out_base_pair_orientation(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::kinematics::find_stub_transform(), from_four_points(), core::kinematics::RT::from_stubs(), core::scoring::rna::RNA_LowResolutionPotential::get_base_backbone(), protocols::toolbox::rigid_body::get_base_centroid_and_rotation_matrix(), core::scoring::dna::get_base_step_params(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub(), core::pose::rna::get_stub_stub(), core::scoring::dna::get_stub_stub_params(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), protocols::simple_moves::BBConRotMover::get_xyz(), protocols::sic_dock::getxform(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), is_orthogonal(), local2global(), core::import_pose::make_coarse_pose(), core::kinematics::Jump::make_jump(), core::kinematics::RT::make_jump(), operator==(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), core::energy_methods::HackAroEnergy::residue_pair_energy_aro_aro(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), rotation(), core::kinematics::Jump::rotation_by_matrix(), core::kinematics::Jump::set_rb_center(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker(), protocols::rna::denovo::coarse::MultipleDomainMover::slide_back_to_origin(), protocols::sic_dock::slide_into_contact_and_score_DEPRICATED(), protocols::sic_dock::SICFast::slide_into_contact_DEPRICATED(), core::kinematics::Jump::translation_along_axis(), protocols::rna::denovo::coarse::MultipleDomainMover::try_to_slide_into_contact(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_internal_coords(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), core::kinematics::tree::JumpAtom::update_stub(), core::kinematics::tree::BondedAtom::update_stub(), core::kinematics::tree::BondedAtom::update_xyz_coords(), core::kinematics::tree::JumpAtom::update_xyz_coords(), and protocols::backbone_moves::local_backbone_mover::xyz_from_internal_coords().
| Vector core::kinematics::Stub::v |
center point by a vector
Referenced by protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::UniformTranslationMover::apply(), build_fake_xyz(), center(), protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_pair(), protocols::stepwise::screener::StubDistanceScreener::check_screen(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::kinematics::find_stub_transform(), from_four_points(), core::kinematics::RT::from_stubs(), core::scoring::dna::get_base_step_params(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), protocols::toolbox::rigid_body::get_specific_atom_coordinate(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub(), core::scoring::dna::get_stub_stub_params(), protocols::simple_moves::BBConRotMover::get_xyz(), protocols::sic_dock::getxform(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), local2global(), core::kinematics::RT::make_jump(), operator==(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::kinematics::Jump::rotation_by_matrix(), protocols::hotspot_hashing::SICPatternAtTransform::Searchpoints(), core::kinematics::Jump::set_rb_center(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::setup_VDW_bin_checker(), protocols::sic_dock::slide_into_contact_and_score_DEPRICATED(), protocols::sic_dock::SICFast::slide_into_contact_DEPRICATED(), core::kinematics::tree::BondedAtom::update_internal_coords(), protocols::environment::CoMTrackerCM::update_tracking_residue(), core::kinematics::tree::BondedAtom::update_xyz_coords(), core::kinematics::tree::JumpAtom::update_xyz_coords(), and protocols::backbone_moves::local_backbone_mover::xyz_from_internal_coords().
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