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Classes | Typedefs | Functions
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< Realcalc_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 
)

◆ 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 
)

◆ 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 
)

◆ 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 
)

◆ 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