core::kinematics::Stub Class Reference

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 &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...
Matrix	rotation () const
	Coordinate frame rotation matrix. More...
Vector	center () const
	Coordinate frame center. 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

typedef numeric::xyzMatrix< Real > core::kinematics::Stub::Matrix

typedef numeric::xyzVector< Real > core::kinematics::Stub::Vector

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

)

constructor 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 function from_four_points(...) construct a stub centered at v_in, as would come from building c then b then a

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(...) construct a stub as would come from building c then b then a

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 angle, length, M, numeric::conversions::radians(), utility_exit_with_message, and v.

Vector core::kinematics::Stub::center ( ) const

inline

Coordinate frame center.

References v.

Referenced by from_four_points().

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 center(), numeric::xyzMatrix< class >::col_x(), cross(), M, numeric::xyzVector< class >::normalize(), and v.

Referenced by Stub().

Vector core::kinematics::Stub::global2local ( Vector const &  xyz ) const

inline

convert a global reference (lab) frame vector to our local (stub) frame

References M, numeric::xyzMatrix< class >::transposed(), and v.

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_fragment(), core::conformation::orient_residue_for_ideal_bond(), and core::scoring::constraints::LocalCoordinateConstraint::score().

bool core::kinematics::Stub::is_orthogonal ( double const &  tolerance ) const

inline

check if the stub is orthogonal under the tolerance cutoff

References numeric::xyzMatrix< Real >::identity(), M, and numeric::xyzMatrix< class >::transposed().

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().

Vector core::kinematics::Stub::local2global ( Vector const &  xyz ) const

inline

convert a local reference (stub) frame vector to the global (lab) frame

References M, and v.

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(), spherical(), and core::fragment::xform_pose().

Matrix core::kinematics::Stub::rotation ( ) const

inline

Coordinate frame rotation matrix.

References M.

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::chemical::AtomICoor::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(), 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 core::pose::rna::bases_are_coplanar(), build_fake_xyz(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), 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(), core::pose::rna::figure_out_base_pair_orientation(), 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_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(), core::scoring::dna::get_stub_stub_params(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), is_orthogonal(), local2global(), core::kinematics::RT::make_jump(), core::kinematics::operator<<(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy_aro_aro(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_LowResolutionPotential::rna_base_backbone_pair_energy_one_way(), rotation(), core::kinematics::Jump::rotation_by_matrix(), core::kinematics::Jump::set_rb_center(), core::kinematics::Jump::translation_along_axis(), 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(), center(), core::kinematics::distance(), core::scoring::dna::DNA_BasePotential::eval_base_pair_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_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(), core::scoring::dna::get_stub_stub_params(), core::fragment::getxform(), global2local(), core::kinematics::AtomTree::insert_single_fragment(), local2global(), core::kinematics::RT::make_jump(), core::kinematics::operator<<(), core::kinematics::Jump::rotation_by_matrix(), core::kinematics::Jump::set_rb_center(), core::kinematics::tree::BondedAtom::update_internal_coords(), and core::kinematics::tree::BondedAtom::update_xyz_coords().

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

• src/core/kinematics/Stub.hh
• src/core/kinematics/Stub.cc