Rosetta
Functions
numeric::kinematic_closure::radians Namespace Reference

Functions

void triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 3 > &calpha, utility::fixedsizearray1< Real, 3 > &salpha)
 
void triangle (const utility::fixedsizearray1< Real, 3 > &vbond, utility::fixedsizearray1< Real, 4 > &calpha, utility::fixedsizearray1< Real, 4 > &salpha)
 
void sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 3 > &cosine, utility::fixedsizearray1< Real, 3 > &sine)
 
void sincos (const utility::fixedsizearray1< Real, 3 > &theta, const int flag, utility::fixedsizearray1< Real, 4 > &cosine, utility::fixedsizearray1< Real, 4 > &sine)
 
void triaxialCoefficients (const utility::fixedsizearray1< Real, 3 > &vb, const utility::fixedsizearray1< Real, 3 > &xi, const utility::fixedsizearray1< Real, 3 > &eta, const utility::fixedsizearray1< Real, 3 > &delta, const utility::fixedsizearray1< Real, 3 > &theta, const utility::vector1< int > &order, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &A, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &B, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &C, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &D, utility::fixedsizearray1< Real, 3 > &cal, utility::fixedsizearray1< Real, 3 > &sal, bool &feasible_triangle)
 
void cross (const utility::fixedsizearray1< Real, 3 > &L, const utility::fixedsizearray1< Real, 3 > &r0, utility::fixedsizearray1< Real, 3 > &r)
 
void frame (const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &R, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &U)
 
Real eucDistance (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b)
 
Real scpn (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)
 
Real bondangle (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c)
 
Real torsion (const utility::fixedsizearray1< Real, 3 > &a, const utility::fixedsizearray1< Real, 3 > &b, const utility::fixedsizearray1< Real, 3 > &c, const utility::fixedsizearray1< Real, 3 > &d)
 
void chainParams (const int &n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, Real &vbond, Real &xi, Real &eta, Real &delta, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)
 
void chainXYZ (const int &n, const utility::vector1< Real > &b_len1, const utility::vector1< Real > &b_ang1, const utility::vector1< Real > &t_ang1, const bool space, const utility::fixedsizearray1< Real, 3 > &R0, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &Q, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)
 
void chainXYZ (const int &n, const utility::vector1< Real > &b_len, const utility::vector1< Real > &b_ang, const utility::vector1< Real > &t_ang, utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms)
 
void chainTORS (const int n, const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, utility::vector1< Real > &t_ang, utility::vector1< Real > &b_ang, utility::vector1< Real > &b_len, utility::fixedsizearray1< Real, 3 > &R0, utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &Q)
 
void rotateX (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rx)
 
void rotateY (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Ry)
 
void rotateZ (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &R, const Real &c, const Real &s, utility::vector1< utility::fixedsizearray1< Real, 3 > > &Rz)
 
void to_radians (utility::vector1< Real > &degrees)
 
void to_degrees (utility::vector1< Real > &radians)
 
void bridge_objects (const utility::vector1< utility::fixedsizearray1< Real, 3 > > &atoms, const utility::vector1< Real > &dt, const utility::vector1< Real > &da, const utility::vector1< Real > &db, const utility::vector1< int > &pivots, const utility::vector1< int > &order, utility::vector1< utility::vector1< Real > > &t_ang, utility::vector1< utility::vector1< Real > > &b_ang, utility::vector1< utility::vector1< Real > > &b_len, int &nsol)
 Solve the triaxial loop closure problem for a system of atoms. More...
 
void chainXYZ (const int &n, const utility::vector1< numeric::Real > &b_len, const utility::vector1< numeric::Real > &b_ang, const utility::vector1< numeric::Real > &t_ang, const bool space, const utility::fixedsizearray1< numeric::Real, 3 > &R0, const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &Q, utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &atoms)
 

Function Documentation

◆ bondangle()

numeric::Real numeric::kinematic_closure::radians::bondangle ( const utility::fixedsizearray1< Real, 3 > &  a,
const utility::fixedsizearray1< Real, 3 > &  b,
const utility::fixedsizearray1< Real, 3 > &  c 
)
Returns
the bond angle between the given vectors in radians.

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, eucDistance(), create_a3b_hbs::r, and scpn().

Referenced by chainParams(), and chainTORS().

◆ bridge_objects()

void numeric::kinematic_closure::radians::bridge_objects ( const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  atoms,
const utility::vector1< Real > &  dt,
const utility::vector1< Real > &  da,
const utility::vector1< Real > &  db,
const utility::vector1< int > &  pivots,
const utility::vector1< int > &  order,
utility::vector1< utility::vector1< Real > > &  t_ang,
utility::vector1< utility::vector1< Real > > &  b_ang,
utility::vector1< utility::vector1< Real > > &  b_len,
int &  nsol 
)

Solve the triaxial loop closure problem for a system of atoms.

Parameters
[in]atoms- matrix of cartesian coordinates of N-CA-C atoms indexed as atoms[atom][dimension]
[in]dt- desired torsions for each atom (radians)
[in]da- desired bond angle for each atom (radians)
[in]db- desired bond length for each atom (radians)
[in]pivots- 3 indices (base 1) of atoms to be used as loop closure pivots
[in]order- length 3 vector giving order to solve for the tau parameters (use 1,2,3 if unsure)
[out]t_ang- matrix giving torsion angles for each atom for each solution, indexed as t_ang[solution][atom] (radians)
[out]b_ang- matrix giving bond angles for each atom for each solution, indexed as b_ang[solution][atom] (radians)
[out]b_len- matrix giving bond lengths for each atom for each solution, indexed as b_len[solution][atom] (radians)
[out]nsol- number of solutions found
Global Read:
Global Write:
Returns
Remarks
dt, da, and db are cast to Real precision when placed in t_ang1,2, b_ang1,2 and b_len1,2. Solution is carried out in Real precision. Solutions are cast back to Reals when placed into t_ang.
References:
Author
Evangelos A. Coutsias
Daniel J. Mandell

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, atoms, C, local::chain1, local::chain2, chainParams(), chainXYZ(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::options::OptionKeys::out::path::db, numeric::kinematic_closure::dixon_eig(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kk, test.G201_Module_Structure::l1, internal_coordinates::loop, numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, N, run_backbone::pivots, predPRE::R2, rotateX(), rotateZ(), torsion(), and triaxialCoefficients().

◆ chainParams()

void numeric::kinematic_closure::radians::chainParams ( const int &  n,
const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  atoms,
Real &  vbond,
Real &  xi,
Real &  eta,
Real &  delta,
utility::fixedsizearray1< Real, 3 > &  R0,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  Q 
)

References atoms, bondangle(), eucDistance(), frame(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::Q, and torsion().

Referenced by bridge_objects().

◆ chainTORS()

void numeric::kinematic_closure::radians::chainTORS ( const int  n,
const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  atoms,
utility::vector1< Real > &  t_ang,
utility::vector1< Real > &  b_ang,
utility::vector1< Real > &  b_len,
utility::fixedsizearray1< Real, 3 > &  R0,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  Q 
)

References atoms, bondangle(), eucDistance(), frame(), create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::Q, and torsion().

◆ chainXYZ() [1/3]

void numeric::kinematic_closure::radians::chainXYZ ( const int &  n,
const utility::vector1< numeric::Real > &  b_len,
const utility::vector1< numeric::Real > &  b_ang,
const utility::vector1< numeric::Real > &  t_ang,
const bool  space,
const utility::fixedsizearray1< numeric::Real, 3 > &  R0,
const utility::fixedsizearray1< utility::fixedsizearray1< numeric::Real, 3 >, 3 > &  Q,
utility::vector1< utility::fixedsizearray1< numeric::Real, 3 > > &  atoms 
)

◆ chainXYZ() [2/3]

void numeric::kinematic_closure::radians::chainXYZ ( const int &  n,
const utility::vector1< Real > &  b_len,
const utility::vector1< Real > &  b_ang,
const utility::vector1< Real > &  t_ang,
utility::vector1< utility::fixedsizearray1< Real, 3 > > &  atoms 
)

References atoms, chainXYZ(), and kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

◆ chainXYZ() [3/3]

void numeric::kinematic_closure::radians::chainXYZ ( const int &  n,
const utility::vector1< Real > &  b_len1,
const utility::vector1< Real > &  b_ang1,
const utility::vector1< Real > &  t_ang1,
const bool  space,
const utility::fixedsizearray1< Real, 3 > &  R0,
const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  Q,
utility::vector1< utility::fixedsizearray1< Real, 3 > > &  atoms 
)

References atoms, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, docking::Q, docking::s, sign::space, docking::U, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by bridge_objects(), and chainXYZ().

◆ cross()

void numeric::kinematic_closure::radians::cross ( const utility::fixedsizearray1< Real, 3 > &  L,
const utility::fixedsizearray1< Real, 3 > &  r0,
utility::fixedsizearray1< Real, 3 > &  r 
)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::L, and create_a3b_hbs::r.

Referenced by frame(), and torsion().

◆ eucDistance()

Real numeric::kinematic_closure::radians::eucDistance ( const utility::fixedsizearray1< Real, 3 > &  a,
const utility::fixedsizearray1< Real, 3 > &  b 
)

References a, compute_difference::b, and ObjexxFCL::pow().

Referenced by bondangle(), chainParams(), and chainTORS().

◆ frame()

void numeric::kinematic_closure::radians::frame ( const utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  R,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  U 
)

References cross(), create_a3b_hbs::i, docking::R, and docking::U.

Referenced by chainParams(), and chainTORS().

◆ rotateX()

void numeric::kinematic_closure::radians::rotateX ( const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  R,
const Real &  c,
const Real &  s,
utility::vector1< utility::fixedsizearray1< Real, 3 > > &  Rx 
)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, docking::R, and docking::s.

Referenced by bridge_objects().

◆ rotateY()

void numeric::kinematic_closure::radians::rotateY ( const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  R,
const Real &  c,
const Real &  s,
utility::vector1< utility::fixedsizearray1< Real, 3 > > &  Ry 
)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, docking::R, and docking::s.

◆ rotateZ()

void numeric::kinematic_closure::radians::rotateZ ( const utility::vector1< utility::fixedsizearray1< Real, 3 > > &  R,
const Real &  c,
const Real &  s,
utility::vector1< utility::fixedsizearray1< Real, 3 > > &  Rz 
)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, create_a3b_hbs::i, docking::R, and docking::s.

Referenced by bridge_objects().

◆ scpn()

Real numeric::kinematic_closure::radians::scpn ( const utility::fixedsizearray1< Real, 3 > &  a,
const utility::fixedsizearray1< Real, 3 > &  b,
const utility::fixedsizearray1< Real, 3 > &  c 
)

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, and create_a3b_hbs::i.

Referenced by bondangle().

◆ sincos() [1/2]

void numeric::kinematic_closure::radians::sincos ( const utility::fixedsizearray1< Real, 3 > &  theta,
const int  flag,
utility::fixedsizearray1< Real, 3 > &  cosine,
utility::fixedsizearray1< Real, 3 > &  sine 
)

References a, docking::a1, aa, kmeans_adaptive_kernel_density_bb_dependent_rotlib::flag, and create_a3b_hbs::i.

Referenced by triaxialCoefficients().

◆ sincos() [2/2]

void numeric::kinematic_closure::radians::sincos ( const utility::fixedsizearray1< Real, 3 > &  theta,
const int  flag,
utility::fixedsizearray1< Real, 4 > &  cosine,
utility::fixedsizearray1< Real, 4 > &  sine 
)

References a, docking::a1, aa, kmeans_adaptive_kernel_density_bb_dependent_rotlib::flag, and create_a3b_hbs::i.

◆ to_degrees()

void numeric::kinematic_closure::radians::to_degrees ( utility::vector1< Real > &  radians)

References create_a3b_hbs::i, numeric::conversions::radians(), and numeric::conversions::to_degrees().

◆ to_radians()

void numeric::kinematic_closure::radians::to_radians ( utility::vector1< Real > &  degrees)

References numeric::conversions::degrees(), create_a3b_hbs::i, and numeric::conversions::to_radians().

◆ torsion()

numeric::Real numeric::kinematic_closure::radians::torsion ( const utility::fixedsizearray1< Real, 3 > &  a,
const utility::fixedsizearray1< Real, 3 > &  b,
const utility::fixedsizearray1< Real, 3 > &  c,
const utility::fixedsizearray1< Real, 3 > &  d 
)
Returns
the torsion angle between the given vectors in radians.

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, cross(), create_a3b_hbs::f, create_a3b_hbs::i, numeric::constants::r::pi, ObjexxFCL::pow(), create_a3b_hbs::r, docking::s, numeric::wrap_2pi(), predPRE::y, and predPRE::z.

Referenced by bridge_objects(), chainParams(), and chainTORS().

◆ triangle() [1/2]

void numeric::kinematic_closure::radians::triangle ( const utility::fixedsizearray1< Real, 3 > &  vbond,
utility::fixedsizearray1< Real, 3 > &  calpha,
utility::fixedsizearray1< Real, 3 > &  salpha 
)

Referenced by triaxialCoefficients().

◆ triangle() [2/2]

void numeric::kinematic_closure::radians::triangle ( const utility::fixedsizearray1< Real, 3 > &  vbond,
utility::fixedsizearray1< Real, 4 > &  calpha,
utility::fixedsizearray1< Real, 4 > &  salpha 
)

◆ triaxialCoefficients()

void numeric::kinematic_closure::radians::triaxialCoefficients ( const utility::fixedsizearray1< Real, 3 > &  vb,
const utility::fixedsizearray1< Real, 3 > &  xi,
const utility::fixedsizearray1< Real, 3 > &  eta,
const utility::fixedsizearray1< Real, 3 > &  delta,
const utility::fixedsizearray1< Real, 3 > &  theta,
const utility::vector1< int > &  order,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  A,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  B,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  C,
utility::fixedsizearray1< utility::fixedsizearray1< Real, 3 >, 3 > &  D,
utility::fixedsizearray1< Real, 3 > &  cal,
utility::fixedsizearray1< Real, 3 > &  sal,
bool &  feasible_triangle 
)

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, ObjexxFCL::abs(), compute_difference::b, C, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::L, N, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, sincos(), and triangle().

Referenced by bridge_objects().

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