Rosetta  2021.16
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_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.

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.

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

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 )
 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.

Referenced by XYZ_BUNDLE().