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Functions
numeric::crick_equations Namespace Reference

Functions

Real PP (Real const &r0, Real const &omega0, Real const &z1, bool &failed)
 Calculates P, the repeat distance of the major helix in the z-direction. More...
 
Real P_omega0 (Real const &r0, Real const &omega0, Real const &z1, bool const epsilon_equals_one, Real const &dr0_dt, bool &failed)
 Calculates P*omega0 (the repeat distance of the major helix in the z-direction times the major helix turn per residue). More...
 
Real ALPHA (Real const &r0, Real const &omega0, Real const &Pomega0)
 Calculates alpha, the tilt angle of the minor helix. More...
 
Real COSFXN (Real const &t, Real const &omega, Real const &delta_omega)
 Calculates cos(omega*t+delta_omega) More...
 
Real gradnorm (Real const &r0, Real const &omega0, Real const &Pomega0, Real const &s0, Real const &c0)
 Calculates the norm of the gradient vector. More...
 
Real SINFXN (Real const &t, Real const &omega, Real const &delta_omega)
 Calculates sin(omega*t+delta_omega) More...
 
Real X_BUNDLE (Real const &t, Real const &r0, Real const &omega0, Real const &delta_omega0, Real const &r1, Real const &omega1, Real const &z1, Real const &delta_omega1, Real const &delta_z1, Real const &epsilon, Real const &dr0prime_dt, bool &failed)
 Calculates the x-position on the helix of helices given the Crick parameters for the bundle. More...
 
Real Y_BUNDLE (Real const &t, Real const &r0, Real const &omega0, Real const &delta_omega0, Real const &r1, Real const &omega1, Real const &z1, Real const &delta_omega1, Real const &delta_z1, Real const &epsilon, Real const &dr0prime_dt, bool &failed)
 Calculates the y-position on the helix of helices given the Crick parameters for the bundle. More...
 
Real Z_BUNDLE (Real const &t, Real const &r0, Real const &omega0, Real const &delta_omega0, Real const &r1, Real const &omega1, Real const &z1, Real const &delta_omega1, Real const &delta_z1, Real const &epsilon, Real const &dr0prime_dt, bool &failed)
 Calculates the z-position on the helix of helices given the Crick parameters for the bundle. More...
 
xyzVector< RealXYZ_BUNDLE (Real const &t, Real const &r0, Real const &omega0, Real const &delta_omega0, Real const &r1, Real const &omega1, Real const &z1, Real const &delta_omega1, Real const &delta_z1, Real const &epsilon, bool &failed)
 Calculate the x,y,z coordinates of a point on the helix of helices given the Crick parameters for the bundle. More...
 
Real x (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the x-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real y (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the y-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real z (Real const &, Real const &, Real const &t, Real const &dz1, Real const &, Real const &delta_z1)
 Returns the z-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated. More...
 
xyzVector< Realxyz (Real const &r1, Real const &omega1, Real const &t, Real const &dz1, Real const &delta_omega1, Real const &delta_z1)
 Returns the x-, y-, and z-coordinates of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dx_dr1 (Real const &, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of x with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dy_dr1 (Real const &, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of y with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dz_dr1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of z with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dx_domega1 (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of x with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dy_domega1 (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of y with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dz_domega1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of z with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dx_ddz1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of x with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dy_ddz1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of y with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dz_ddz1 (Real const &, Real const &, Real const &t, Real const &, Real const &, Real const &)
 Returns the derivative of z with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dx_ddelta_omega1 (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of x with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dy_ddelta_omega1 (Real const &r1, Real const &omega1, Real const &t, Real const &, Real const &delta_omega1, Real const &)
 Returns the derivative of y with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dz_ddelta_omega1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of z with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dx_ddelta_z1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of x with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dy_ddelta_z1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of y with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 
Real dz_ddelta_z1 (Real const &, Real const &, Real const &, Real const &, Real const &, Real const &)
 Returns the derivative of z with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated. More...
 

Function Documentation

Real numeric::crick_equations::ALPHA ( Real const &  r0,
Real const &  omega0,
Real const &  Pomega0 
)

Calculates alpha, the tilt angle of the minor helix.

References numeric::constants::d::pi_2.

Referenced by X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

Real numeric::crick_equations::COSFXN ( Real const &  t,
Real const &  omega,
Real const &  delta_omega 
)

Calculates cos(omega*t+delta_omega)

Referenced by X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

Real numeric::crick_equations::dx_ddelta_omega1 ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of x with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dx_ddelta_z1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of x with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dx_ddz1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of x with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dx_domega1 ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of x with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dx_dr1 ( Real const &  ,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of x with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dy_ddelta_omega1 ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of y with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dy_ddelta_z1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of y with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dy_ddz1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of y with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dy_domega1 ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of y with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dy_dr1 ( Real const &  ,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the derivative of y with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dz_ddelta_omega1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of z with respect to delta_omega1 (omega-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dz_ddelta_z1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of z with respect to delta_z1 (z-offset) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dz_ddz1 ( Real const &  ,
Real const &  ,
Real const &  t,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of z with respect to dz1 (rise per residue) for a given value of r1, omega1, and t. Note that this is not translated or rotated.

References basic::options::OptionKeys::in::file::t.

Real numeric::crick_equations::dz_domega1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of z with respect to omega1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::dz_dr1 ( Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &  ,
Real const &   
)

Returns the derivative of z with respect to r1 for a given value of r1, omega1, and t. Note that this is not translated or rotated.

Real numeric::crick_equations::gradnorm ( Real const &  r0,
Real const &  omega0,
Real const &  Pomega0,
Real const &  s0,
Real const &  c0 
)

Calculates the norm of the gradient vector.

Needed for adding the small delta_z1 offsets, which are in the direction of (dx/dt, dy/dt, dz/dt) of the major helix.

References numeric::constants::d::pi_2, and ObjexxFCL::pow().

Referenced by X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

Real numeric::crick_equations::P_omega0 ( Real const &  r0,
Real const &  omega0,
Real const &  z1,
bool const  epsilon_equals_one,
Real const &  dr0_dt,
bool failed 
)

Calculates P*omega0 (the repeat distance of the major helix in the z-direction times the major helix turn per residue).

Sets "failed" to TRUE if and only if the value of P*omega0 could not be calculated.

References numeric::constants::d::pi_2, and ObjexxFCL::pow().

Referenced by X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

Real numeric::crick_equations::PP ( Real const &  r0,
Real const &  omega0,
Real const &  z1,
bool failed 
)

Calculates P, the repeat distance of the major helix in the z-direction.

Sets "failed" to TRUE if and only if the value of P could not be calculated.

References numeric::constants::d::pi_2, and ObjexxFCL::pow().

Real numeric::crick_equations::SINFXN ( Real const &  t,
Real const &  omega,
Real const &  delta_omega 
)

Calculates sin(omega*t+delta_omega)

Referenced by X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

Real numeric::crick_equations::x ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the x-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated.

Referenced by PyMOL-RosettaServer.Matrix::__init__(), numeric::interpolation::catmull_rom_interpolate_basic(), numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), correct_dunbrack(), correct_rama(), correlation_coefficient(), ObjexxFCL::cross(), ObjexxFCL::cross_product(), ObjexxFCL::cube(), numeric::cube(), DockFragmentsMover::cut_from_map(), numeric::statistics::Dawson(), numeric::interpolation::spline::TricubicSpline::dFdx(), numeric::interpolation::spline::BicubicSpline::dFdx(), numeric::interpolation::spline::TricubicSpline::dFdy(), numeric::interpolation::spline::BicubicSpline::dFdy(), numeric::interpolation::spline::TricubicSpline::dFdz(), numeric::deriv::dihedral_p1_cosine_deriv(), numeric::deriv::dihedral_p2_cosine_deriv(), numeric::dihedral_radians(), numeric::random::do_recursion(), numeric::statistics::errf(), numeric::statistics::errfc(), numeric::statistics::errfcx(), basic::sampling::orientations::Quaternion::euler(), numeric::expand_xforms(), numeric::interpolation::spline::TricubicSpline::F(), numeric::interpolation::spline::BicubicSpline::F(), ObjexxFCL::format::F(), numeric::FArray_to_vector_of_xyzvectors(), numeric::interpolation::spline::BicubicSpline::FdF(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), numeric::interpolation::spline::SplineGenerator::get_interpolator(), zinc1_homodimer_design::gridsearch_rollmove_angles(), numeric::kinematic_closure::hyper_tan(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::init(), numeric::inplace_product(), numeric::inplace_transpose_product(), numeric::xyzMatrix< T >::left_multiply_by(), numeric::xyzMatrix< T >::left_multiply_by_transpose(), numeric::nls::lm_lmdif(), main(), make_fragments(), numeric::kinematic_closure::modrf(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), basic::sampling::orientations::Quaternion::Normalize(), nucleobase_probe_score_test(), numeric::XformHash32::operator()(), numeric::XformHash64::operator()(), numeric::xyzMatrix< T >::operator*=(), numeric::deriv::p1_theta_deriv(), basic::periodic_range(), utility::libsvm::Svm_rosetta::predict(), utility::libsvm::Svm_rosetta::predict_probability(), basic::sampling::orientations::Quaternion::Print(), numeric::linear_algebra::qzvec(), numeric::read_row(), numeric::xyzMatrix< T >::right_multiply_by(), numeric::xyzMatrix< T >::right_multiply_by_transpose(), numeric::rotation_axis(), basic::sampling::orientations::Quaternion::rotation_matrix(), run_pep_prep(), numeric::serialize(), pyrosetta.PyMOLRosettaServer::set_spectrum(), PyMOL-RosettaServer::set_spectrum(), numeric::VoxelGrid< typename >::SetupGrid(), numeric::sin_cos_range(), numeric::statistics::sinc(), numeric::statistics::sinh_taylor(), numeric::interpolation::spline::spline_interpolate(), numeric::interpolation::spline::sqr(), numeric::interpolation::spline::CubicSpline::sqr(), sqr(), numeric::interpolation::spline::BicubicSpline::sqr(), numeric::statistics::sqr(), ObjexxFCL::square(), numeric::square(), ObjexxFCL::CArray< typename >::square(), ObjexxFCL::CArrayP< typename >::square(), ObjexxFCL::ChunkVector< typename >::square(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_train(), swap(), utility::sys_sleep(), numeric::UniformRotationSampler::UniformRotationSampler(), numeric::vector_of_xyzvectors_to_FArray(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit_lax(), numeric::statistics::w(), numeric::statistics::w_im(), numeric::statistics::w_im_y100(), xyz(), and rosetta_binders::xyzVector_add_on_binder().

Real numeric::crick_equations::X_BUNDLE ( Real const &  t,
Real const &  r0,
Real const &  omega0,
Real const &  delta_omega0,
Real const &  r1,
Real const &  omega1,
Real const &  z1,
Real const &  delta_omega1,
Real const &  delta_z1,
Real const &  epsilon,
Real const &  dr0prime_dt,
bool failed 
)

Calculates the x-position on the helix of helices given the Crick parameters for the bundle.

Returns failed=true if calculation fails, failed=false otherwise.

References ALPHA(), COSFXN(), gradnorm(), P_omega0(), basic::options::OptionKeys::stepwise::s1, and SINFXN().

Referenced by XYZ_BUNDLE().

xyzVector< Real > numeric::crick_equations::xyz ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  dz1,
Real const &  delta_omega1,
Real const &  delta_z1 
)

Returns the x-, y-, and z-coordinates of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated.

References x(), y(), and z().

xyzVector< Real > numeric::crick_equations::XYZ_BUNDLE ( Real const &  t,
Real const &  r0,
Real const &  omega0,
Real const &  delta_omega0,
Real const &  r1,
Real const &  omega1,
Real const &  z1,
Real const &  delta_omega1,
Real const &  delta_z1,
Real const &  epsilon,
bool failed 
)

Calculate the x,y,z coordinates of a point on the helix of helices given the Crick parameters for the bundle.

Not quite as efficient as it could be, but it probably doesn't matter. (If I really wanted to optimize this, I'd make sure that c0, c1, s0, s1, and alpha were all calculated once rather than thrice.) Returns failed=true if calculation fails, failed=false otherwise.

References numeric::xyzVector< typename >::assign(), numeric::xyzVector< typename >::x(), X_BUNDLE(), numeric::xyzVector< typename >::y(), Y_BUNDLE(), numeric::xyzVector< typename >::z(), and Z_BUNDLE().

Real numeric::crick_equations::y ( Real const &  r1,
Real const &  omega1,
Real const &  t,
Real const &  ,
Real const &  delta_omega1,
Real const &   
)

Returns the y-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated.

Referenced by numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), correct_dunbrack(), correct_rama(), correlation_coefficient(), ObjexxFCL::cross(), ObjexxFCL::cross_product(), DockFragmentsMover::cut_from_map(), ObjexxFCL::date(), numeric::statistics::Dawson(), numeric::interpolation::Histogram< typename, typename >::derivative(), numeric::interpolation::spline::BicubicSpline::dFdx(), numeric::interpolation::spline::BicubicSpline::dFdy(), numeric::dihedral_radians(), numeric::statistics::errf(), numeric::statistics::errfc(), basic::sampling::orientations::Quaternion::euler(), numeric::interpolation::spline::BicubicSpline::F(), numeric::FArray_to_vector_of_xyzvectors(), numeric::interpolation::spline::BicubicSpline::FdF(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), numeric::interpolation::spline::SplineGenerator::get_interpolator(), zinc1_homodimer_design::gridsearch_rollmove_angles(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::init(), numeric::inplace_product(), numeric::inplace_transpose_product(), numeric::MathMatrix< float >::inverse_tridiagonal_matrix(), Kernel::k_function(), numeric::xyzMatrix< T >::left_multiply_by(), numeric::xyzMatrix< T >::left_multiply_by_transpose(), main(), max(), min(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), basic::sampling::orientations::Quaternion::Normalize(), nucleobase_probe_score_test(), numeric::xyzMatrix< T >::operator*=(), basic::sampling::orientations::Quaternion::Print(), numeric::linear_algebra::qzvec(), numeric::interpolation::Histogram< typename, typename >::read_from_db(), numeric::read_row(), numeric::xyzMatrix< T >::right_multiply_by(), numeric::xyzMatrix< T >::right_multiply_by_transpose(), numeric::rotation_axis(), basic::sampling::orientations::Quaternion::rotation_matrix(), run_pep_prep(), numeric::geometry::hashing::xyzStripeHash::sanity_check(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::sanity_check(), numeric::serialize(), numeric::VoxelGrid< typename >::SetupGrid(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), utility::string2uint(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), swap(), numeric::kinematic_closure::torsion(), numeric::kinematic_closure::radians::torsion(), numeric::UniformRotationSampler::UniformRotationSampler(), numeric::vector_of_xyzvectors_to_FArray(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit_lax(), numeric::statistics::w(), xyz(), and rosetta_binders::xyzVector_add_on_binder().

Real numeric::crick_equations::Y_BUNDLE ( Real const &  t,
Real const &  r0,
Real const &  omega0,
Real const &  delta_omega0,
Real const &  r1,
Real const &  omega1,
Real const &  z1,
Real const &  delta_omega1,
Real const &  delta_z1,
Real const &  epsilon,
Real const &  dr0prime_dt,
bool failed 
)

Calculates the y-position on the helix of helices given the Crick parameters for the bundle.

Calculates the x-position on the helix of helices given the Crick parameters for the bundle.

Returns failed=true if calculation fails, failed=false otherwise.

References ALPHA(), COSFXN(), gradnorm(), P_omega0(), basic::options::OptionKeys::stepwise::s1, and SINFXN().

Referenced by XYZ_BUNDLE().

Real numeric::crick_equations::z ( Real const &  ,
Real const &  ,
Real const &  t,
Real const &  dz1,
Real const &  ,
Real const &  delta_z1 
)

Returns the z-coordinate of a point on a helix given r1, omega1, and t. Note that this is not translated or rotated.

Referenced by numeric::geometry::hashing::xyzStripeHash::clash(), numeric::geometry::hashing::xyzStripeHash::clash_amount(), numeric::geometry::hashing::xyzStripeHash::clash_check_ball(), numeric::geometry::hashing::xyzStripeHash::clash_not_resid(), numeric::geometry::hashing::xyzStripeHash::clash_raw(), ObjexxFCL::cross(), ObjexxFCL::cross_product(), DockFragmentsMover::cut_from_map(), numeric::model_quality::erfcc(), basic::sampling::orientations::Quaternion::euler(), numeric::FArray_to_vector_of_xyzvectors(), numeric::geometry::hashing::xyzStripeHash::fill_pairs(), numeric::VoxelGrid< typename >::GetNeighborsMultiDimensional(), zinc1_homodimer_design::gridsearch_rollmove_angles(), numeric::VoxelGrid< typename >::HasNeighborsMultiDimensional(), numeric::geometry::hashing::xyzStripeHash::init(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::init(), numeric::xyzMatrix< T >::left_multiply_by(), numeric::xyzMatrix< T >::left_multiply_by_transpose(), main(), numeric::geometry::hashing::xyzStripeHash::nbcount(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::nbcount(), numeric::geometry::hashing::xyzStripeHash::nbcount_raw(), basic::sampling::orientations::Quaternion::Normalize(), nucleobase_probe_score_test(), numeric::xyzMatrix< T >::operator*=(), basic::sampling::orientations::Quaternion::Print(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::read_row(), numeric::linear_algebra::rgg(), numeric::xyzMatrix< T >::right_multiply_by(), numeric::xyzMatrix< T >::right_multiply_by_transpose(), numeric::rotation_axis(), basic::sampling::orientations::Quaternion::rotation_matrix(), run_pep_prep(), numeric::geometry::hashing::xyzStripeHash::sanity_check(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::sanity_check(), numeric::serialize(), numeric::VoxelGrid< typename >::SetupGrid(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), numeric::kinematic_closure::torsion(), numeric::kinematic_closure::radians::torsion(), numeric::UniformRotationSampler::UniformRotationSampler(), numeric::vector_of_xyzvectors_to_FArray(), numeric::geometry::hashing::xyzStripeHash::visit(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit(), numeric::geometry::hashing::xyzStripeHash::visit_lax(), numeric::geometry::hashing::xyzStripeHashWithMeta< float >::visit_lax(), xyz(), and rosetta_binders::xyzVector_add_on_binder().

Real numeric::crick_equations::Z_BUNDLE ( Real const &  t,
Real const &  r0,
Real const &  omega0,
Real const &  delta_omega0,
Real const &  r1,
Real const &  omega1,
Real const &  z1,
Real const &  delta_omega1,
Real const &  delta_z1,
Real const &  epsilon,
Real const &  dr0prime_dt,
bool failed 
)

Calculates the z-position on the helix of helices given the Crick parameters for the bundle.

Calculates the x-position on the helix of helices given the Crick parameters for the bundle.

Returns failed=true if calculation fails, failed=false otherwise.

References ALPHA(), COSFXN(), gradnorm(), P_omega0(), numeric::constants::d::pi_2, basic::options::OptionKeys::stepwise::s1, and SINFXN().

Referenced by XYZ_BUNDLE().