core::kinematics::inverse Namespace Reference

Classes
struct	AlignmentAtom
	this class has the duty of logging atoms and their desired positions More...
struct	AlignmentAtomArray
	This class contains the 3 AlignmentAtoms that we want to use to define the new jump value. More...
struct	InternalCoordAtoms
struct	InternalCoordGeometry

Typedefs
using	XYZ = numeric::xyzVector< core::Real >

Functions
static basic::Tracer	TR ("core.kinematics.inverse.jump")
Jump	calculate_new_jump (conformation::Conformation const &conformation, core::Size const jump_id, AlignmentAtomArray const &atoms)
	Update a desired jump in the conformation to place the atoms in the AlignmentAtomArray to the desired position. More...
static basic::Tracer	TR ("core.kinematics.inverse.jump_from_internal_coords")
Jump	jump_from_internal_coords (conformation::Conformation const &conf, InternalCoordAtoms const &fixed_atoms, InternalCoordAtoms const &moving_atoms, InternalCoordGeometry geom, Size const jump_id)
	Utility function for calculating jumps by knowing desired internal coordinates of arbitrary atoms. More...
numeric::xyzVector< Real >	calc_new_atom_location (numeric::xyzVector< Real > const &greatgrandparent, numeric::xyzVector< Real > const &grandparent, numeric::xyzVector< Real > const &parent, Real const dist, Real const bond_angle, Real const torsion_angle)
	Given internal coordinates and XYZs of the parents, calculate XYZ of a child. More...
static basic::Tracer	TR ("core.kinematics.inverse.util")
void	assert_atoms_are_downstream_of_jump (conformation::Conformation const &conformation, core::Size const jump_id, AlignmentAtomArray const &atom_arr)
void	assert_atoms_are_upstream_of_jump (conformation::Conformation const &conformation, core::Size const jump_id, AlignmentAtomArray const &atom_arr)

Typedef Documentation

XYZ

typedef numeric::xyzVector< Real > core::kinematics::inverse::XYZ

Function Documentation

assert_atoms_are_downstream_of_jump()

void core::kinematics::inverse::assert_atoms_are_downstream_of_jump	(	conformation::Conformation const &	conformation,
		core::Size const	jump_id,
		AlignmentAtomArray const &	atom_arr
	)

References protocols::cluster::calibur::aa, core::kinematics::inverse::AlignmentAtomArray::atoms, core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::partition_by_jump(), core::kinematics::Edge::stop(), and core::id::to_string().

Referenced by calculate_new_jump(), and jump_from_internal_coords().

assert_atoms_are_upstream_of_jump()

void core::kinematics::inverse::assert_atoms_are_upstream_of_jump	(	conformation::Conformation const &	conformation,
		core::Size const	jump_id,
		AlignmentAtomArray const &	atom_arr
	)

References protocols::cluster::calibur::aa, core::kinematics::inverse::AlignmentAtomArray::atoms, core::conformation::Conformation::fold_tree(), core::kinematics::FoldTree::jump_edge(), core::kinematics::FoldTree::partition_by_jump(), core::kinematics::Edge::start(), and core::id::to_string().

Referenced by jump_from_internal_coords().

calc_new_atom_location()

numeric::xyzVector< Real > core::kinematics::inverse::calc_new_atom_location	(	numeric::xyzVector< Real > const &	greatgrandparent,
		numeric::xyzVector< Real > const &	grandparent,
		numeric::xyzVector< Real > const &	parent,
		Real const	dist,
		Real const	bond_angle,
		Real const	torsion_angle
	)

Given internal coordinates and XYZs of the parents, calculate XYZ of a child.

References core::id::D, core::id::PHI, and core::id::THETA.

Referenced by jump_from_internal_coords().

calculate_new_jump()

Jump core::kinematics::inverse::calculate_new_jump	(	conformation::Conformation const &	conformation,
		core::Size const	jump_id,
		AlignmentAtomArray const &	atoms
	)

Update a desired jump in the conformation to place the atoms in the AlignmentAtomArray to the desired position.

protocol is described as comments in the body of the code.

Author

Jack Maguire

References assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::AlignmentAtomArray::create_destination_stub(), core::kinematics::inverse::AlignmentAtomArray::create_stub_from_atom_ids(), core::conformation::Conformation::downstream_jump_stub(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), core::conformation::Conformation::jump(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), and core::conformation::Conformation::upstream_jump_stub().

Referenced by jump_from_internal_coords().

jump_from_internal_coords()

Jump core::kinematics::inverse::jump_from_internal_coords	(	conformation::Conformation const &	conf,
		InternalCoordAtoms const &	fixed_atoms,
		InternalCoordAtoms const &	moving_atoms,
		InternalCoordGeometry	geom,
		Size const	jump_id
	)

Utility function for calculating jumps by knowing desired internal coordinates of arbitrary atoms.

fixed_atoms (A/B/C) are upstream of the jump, moving_atoms (D/E/F) are downstream. The user provides distances, angles, and dihedral angles for the relationship between the two sets and the number of the jump the user wants to change. Rosetta then calculates the new value of this jump.

References core::kinematics::inverse::InternalCoordGeometry::A_B_C_D_torsion_angle_rad, assert_atoms_are_downstream_of_jump(), assert_atoms_are_upstream_of_jump(), core::kinematics::inverse::AlignmentAtomArray::atoms, core::chemical::element::B, core::kinematics::inverse::InternalCoordGeometry::B_C_D_bond_angle_rad, core::kinematics::inverse::InternalCoordGeometry::B_C_D_E_torsion_angle_rad, core::chemical::element::C, core::kinematics::inverse::InternalCoordGeometry::C_D_dist_Ang, core::kinematics::inverse::InternalCoordGeometry::C_D_E_bond_angle_rad, core::kinematics::inverse::InternalCoordGeometry::C_D_E_F_torsion_angle_rad, calc_new_atom_location(), calculate_new_jump(), core::kinematics::inverse::InternalCoordAtoms::child, core::id::D, core::chemical::element::F, core::kinematics::inverse::InternalCoordAtoms::grandparent, core::kinematics::inverse::InternalCoordAtoms::parent, and core::conformation::Conformation::xyz().

TR() [1/3]

static basic::Tracer core::kinematics::inverse::TR ( "core.kinematics.inverse.jump"  )

static

TR() [2/3]

static basic::Tracer core::kinematics::inverse::TR ( "core.kinematics.inverse.jump_from_internal_coords"  )

static

TR() [3/3]

static basic::Tracer core::kinematics::inverse::TR ( "core.kinematics.inverse.util"  )

static