Module _numeric_crick_equations_

ALPHA( (float)r0, (float)omega0, (float)P_omega0) -> float :
    Calculates alpha, the tilt angle of the minor helix.
    

    C++ signature :
        double ALPHA(double,double,double)

COSFXN( (float)t, (float)omega, (float)delta_omega) -> float :
    Calculates cos(omega*t+delta_omega)
    

    C++ signature :
        double COSFXN(double,double,double)

PP( (float)r0, (float)omega0, (float)z1, (bool)failed) -> float :
    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.
    

    C++ signature :
        double PP(double,double,double,bool {lvalue})

P_omega0( (float)r0, (float)omega0, (float)z1, (bool)failed) -> float :
    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.
    

    C++ signature :
        double P_omega0(double,double,double,bool {lvalue})

SINFXN( (float)t, (float)omega, (float)delta_omega) -> float :
    Calculates sin(omega*t+delta_omega)
    

    C++ signature :
        double SINFXN(double,double,double)

XYZ_BUNDLE( (float)t, (float)r0, (float)omega0, (float)delta_omega0, (float)r1, (float)omega1, (float)z1, (float)delta_omega1, (float)delta_z1, (bool)failed) -> xyzVector_Real :
    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.
    

    C++ signature :
        numeric::xyzVector<double> XYZ_BUNDLE(double,double,double,double,double,double,double,double,double,bool {lvalue})

X_BUNDLE( (float)t, (float)r0, (float)omega0, (float)delta_omega0, (float)r1, (float)omega1, (float)z1, (float)delta_omega1, (float)delta_z1, (bool)failed) -> float :
    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.
    

    C++ signature :
        double X_BUNDLE(double,double,double,double,double,double,double,double,double,bool {lvalue})

Y_BUNDLE( (float)t, (float)r0, (float)omega0, (float)delta_omega0, (float)r1, (float)omega1, (float)z1, (float)delta_omega1, (float)delta_z1, (bool)failed) -> float :
    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.
    

    C++ signature :
        double Y_BUNDLE(double,double,double,double,double,double,double,double,double,bool {lvalue})

Z_BUNDLE( (float)t, (float)r0, (float)omega0, (float)delta_omega0, (float)r1, (float)omega1, (float)z1, (float)delta_omega1, (float)delta_z1, (bool)failed) -> float :
    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.
    

    C++ signature :
        double Z_BUNDLE(double,double,double,double,double,double,double,double,double,bool {lvalue})

dx_ddelta_omega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dx_ddelta_omega1(double,double,double,double,double,double)

dx_ddelta_z1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dx_ddelta_z1(double,double,double,double,double,double)

dx_ddz1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dx_ddz1(double,double,double,double,double,double)

dx_domega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dx_domega1(double,double,double,double,double,double)

dx_dr1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dx_dr1(double,double,double,double,double,double)

dy_ddelta_omega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dy_ddelta_omega1(double,double,double,double,double,double)

dy_ddelta_z1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dy_ddelta_z1(double,double,double,double,double,double)

dy_ddz1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dy_ddz1(double,double,double,double,double,double)

dy_domega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dy_domega1(double,double,double,double,double,double)

dy_dr1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dy_dr1(double,double,double,double,double,double)

dz_ddelta_omega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dz_ddelta_omega1(double,double,double,double,double,double)

dz_ddelta_z1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dz_ddelta_z1(double,double,double,double,double,double)

dz_ddz1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dz_ddz1(double,double,double,double,double,double)

dz_domega1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dz_domega1(double,double,double,double,double,double)

dz_dr1( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    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.
    

    C++ signature :
        double dz_dr1(double,double,double,double,double,double)

gradnorm( (float)r0, (float)omega0, (float)Pomega0, (float)s0, (float)c0) -> float :
    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.
    

    C++ signature :
        double gradnorm(double,double,double,double,double)

x( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    Returns the x-coordinate of a point on a helix given r1, omega1, and t.
    Note that this is not translated or rotated.
    

    C++ signature :
        double x(double,double,double,double,double,double)

xyz( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> xyzVector_Real :
    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.
    

    C++ signature :
        numeric::xyzVector<double> xyz(double,double,double,double,double,double)

y( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    Returns the y-coordinate of a point on a helix given r1, omega1, and t.
    Note that this is not translated or rotated.
    

    C++ signature :
        double y(double,double,double,double,double,double)

z( (float)r1, (float)omega1, (float)t, (float)dz1, (float)delta_omega1, (float)delta_z1) -> float :
    Returns the z-coordinate of a point on a helix given r1, omega1, and t.
    Note that this is not translated or rotated.
    

    C++ signature :
        double z(double,double,double,double,double,double)