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core::kinematics::Stub Class Reference

Stub class – an object of orthogonal coordinate frame. More...

#include <Stub.hh>

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Public Types

typedef numeric::xyzMatrix< RealMatrix
 
typedef numeric::xyzVector< RealVector
 

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 &center, 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 &center, 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...
 

Detailed Description

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.

Member Typedef Documentation

Constructor & Destructor Documentation

core::kinematics::Stub::Stub ( )
inline

constructor – sets to "default" stub

core::kinematics::Stub::Stub ( Matrix const &  M_in,
Vector const &  v_in 
)
inline

copy constructor

core::kinematics::Stub::Stub ( RT const &  rt)

ctor from RT object

core::kinematics::Stub::Stub ( Vector const &  center,
Vector const &  a,
Vector const &  b,
Vector const &  c 
)
inline

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(...)

References from_four_points().

core::kinematics::Stub::Stub ( Vector const &  a,
Vector const &  b,
Vector const &  c 
)
inline

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(...)

References from_four_points().

Member Function Documentation

Vector core::kinematics::Stub::build_fake_xyz ( Size const  index) const

Build stubatom coords that would yield this stub.

References M, and v.

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.

References M, and v.

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().

Vector core::kinematics::Stub::global2local ( Vector const &  xyz) const
inline
bool core::kinematics::Stub::is_orthogonal ( double const &  tolerance) const
inline
Vector core::kinematics::Stub::local2global ( Vector const &  xyz) const
inline
Vector core::kinematics::Stub::spherical ( Real const  phi,
Real const  theta,
Real const  d 
) const
inline

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

Note
These are non-standard in the choice of axis for historical reasons –PB

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().

Member Data Documentation

Matrix core::kinematics::Stub::M

coord frame by 3x3 matrix, each column is a unit vector

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

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().


The documentation for this class was generated from the following files: