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Rosetta 3.5
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Rosetta 3.5
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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) | |
| ctor 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 (double 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... | |
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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| core::kinematics::Stub::Stub | ( | RT const & | rt) |
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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 functon from_four_points(...)
Definition at line 88 of file Stub.hh.
References 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 functon from_four_points(...)
Definition at line 106 of file Stub.hh.
References from_four_points().
Build stubatom coords that would yield this stub.
Definition at line 76 of file Stub.cc.
Referenced by protocols::simple_filters::JumpEvaluator::apply().
| 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.
Definition at line 56 of file Stub.cc.
Referenced by protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::features::SaltBridgeFeatures::report_features(), protocols::hotspot_hashing::StubGenerator::residueStubCentroidFrame(), Stub(), and protocols::hotspot_hashing::stub_from_points().
convert a global reference (lab) frame vector to our local (stub) frame
Definition at line 138 of file Stub.hh.
Referenced by core::pack::rotamer_set::create_oriented_water_rotamer(), protocols::swa::protein::do_set_xyz(), protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb(), core::kinematics::AtomTree::get_frag_descendant_local_xyz(), core::kinematics::AtomTree::get_frag_parent_local_xyz(), protocols::sic_dock::get_xform_stats(), protocols::hotspot_hashing::SearchPatternRotSetOp::increase_packer_residue_radius(), core::kinematics::AtomTree::insert_fragment(), protocols::hotspot_hashing::StubGenerator::moveFromStubFrame(), core::conformation::orient_residue_for_ideal_bond(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::sic_dock::refine_mindis_with_xyzHash(), protocols::fibril::reorient_extended_fibril(), protocols::features::SaltBridgeFeatures::report_features(), protocols::sic_dock::XfoxmScore::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), 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
Definition at line 128 of file Stub.hh.
References M.
Referenced by core::kinematics::Jump::from_bond_cst(), core::kinematics::tree::JumpAtom::update_internal_coords(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::kinematics::tree::JumpAtom::update_xyz_coords(), and core::kinematics::tree::BondedAtom::update_xyz_coords().
convert a local reference (stub) frame vector to the global (lab) frame
Definition at line 145 of file Stub.hh.
Referenced by core::pack::rotamer_set::create_oriented_water_rotamer(), core::kinematics::AtomTree::get_frag_descendant_local_xyz(), core::kinematics::AtomTree::get_frag_parent_local_xyz(), core::kinematics::AtomTree::insert_single_fragment(), protocols::hotspot_hashing::StubGenerator::moveIntoStubFrame(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), protocols::fibril::reorient_extended_fibril(), protocols::sic_dock::CBScore::score(), protocols::sic_dock::SICFast::slide_into_contact(), spherical(), protocols::hotspot_hashing::stub_to_points(), protocols::sic_dock::vec3_to_stub(), protocols::sic_dock::xform_pose(), and core::fragment::xform_pose().
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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
Definition at line 159 of file Stub.hh.
References local2global().
Referenced by core::chemical::orbitals::ICoorOrbitalData::build(), core::scoring::methods::build_optimal_water_Os_on_acceptor(), core::pack::rotamer_set::build_optimal_water_Os_on_acceptor(), core::conformation::Conformation::fill_missing_atoms(), core::kinematics::Jump::from_bond_cst(), core::chemical::ResidueDatabaseIO::read_residue_type_icoor(), and core::chemical::read_topology_file().
| Matrix core::kinematics::Stub::M |
coord frame by 3x3 matrix, each column is a unit vector
Definition at line 175 of file Stub.hh.
Referenced by protocols::rna::bases_are_coplanar(), build_fake_xyz(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_base_pairing(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_stack_base(), core::kinematics::distance(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::hackaro::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::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), protocols::rna::figure_out_base_pair_orientation(), core::kinematics::find_stub_transform(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), from_four_points(), core::kinematics::RT::from_stubs(), protocols::swa::rna::get_atom_coordinates(), core::scoring::dna::get_base_pair_params_old(), core::scoring::dna::get_base_step_params(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), core::scoring::dna::get_midstep_stub(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub(), protocols::swa::rna::get_specific_atom_coordinate(), core::scoring::dna::get_stub_stub_params(), protocols::sic_dock::get_xform_stats(), protocols::simple_moves::BBConRotMover::get_xyz(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), protocols::sic_dock::invstub(), protocols::swa::rna::Is_base_pair(), protocols::swa::rna::Is_base_stack(), is_orthogonal(), local2global(), protocols::rna::make_coarse_pose(), core::kinematics::RT::make_jump(), protocols::sic_dock::multstubs(), core::kinematics::operator<<(), protocols::sic_dock::refine_mindis_with_xyzHash(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy_aro_aro(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), core::kinematics::Jump::rotation_by_matrix(), core::kinematics::Jump::set_rb_center(), core::kinematics::Jump::translation_along_axis(), protocols::rna::MultipleDomainMover::try_to_slide_into_contact(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), core::kinematics::tree::BondedAtom::update_stub(), and core::kinematics::tree::BondedAtom::update_xyz_coords().
| Vector core::kinematics::Stub::v |
center point by a vector
Definition at line 177 of file Stub.hh.
Referenced by build_fake_xyz(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_base_pairing(), protocols::swa::rna::StepWiseRNA_BaseCentroidScreener::check_stack_base(), core::kinematics::distance(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::kinematics::find_stub_transform(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), from_four_points(), core::kinematics::RT::from_stubs(), protocols::swa::rna::get_atom_coordinates(), core::scoring::dna::get_base_pair_params_old(), core::scoring::dna::get_base_step_params(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), core::kinematics::tree::BondedAtom::get_dof_axis_and_end_pos(), core::scoring::dna::get_midstep_stub(), protocols::swa::rna::StepWiseRNA_ResidueSampler::get_reference_stub(), protocols::swa::rna::get_specific_atom_coordinate(), core::scoring::dna::get_stub_stub_params(), protocols::sic_dock::get_xform_stats(), protocols::simple_moves::BBConRotMover::get_xyz(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), protocols::sic_dock::invstub(), protocols::swa::rna::Is_base_pair(), protocols::swa::rna::Is_base_stack(), local2global(), core::kinematics::RT::make_jump(), protocols::sic_dock::multstubs(), core::kinematics::operator<<(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), core::kinematics::Jump::rotation_by_matrix(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), protocols::sic_dock::XfoxmScore::score(), core::kinematics::Jump::set_rb_center(), protocols::sic_dock::slide_into_contact_and_score(), core::kinematics::tree::BondedAtom::update_internal_coords(), and core::kinematics::tree::BondedAtom::update_xyz_coords().
1.8.4