crick_equations

Bindings for numeric::crick_equations namespace

pyrosetta.rosetta.numeric.crick_equations.ALPHA(r0: float, omega0: float, P_omega0: float) → float

Calculates alpha, the tilt angle of the minor helix.

C++: numeric::crick_equations::ALPHA(const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.COSFXN(t: float, omega: float, delta_omega: float) → float

Calculates cos(omega*t+delta_omega)

C++: numeric::crick_equations::COSFXN(const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.PP(r0: float, omega0: float, z1: float, failed: bool) → 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++: numeric::crick_equations::PP(const double &, const double &, const double &, bool &) –> double

pyrosetta.rosetta.numeric.crick_equations.P_omega0(r0: float, omega0: float, z1: float, epsilon_equals_one: bool, dr0_dt: float, failed: bool) → 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++: numeric::crick_equations::P_omega0(const double &, const double &, const double &, const bool, const double &, bool &) –> double

pyrosetta.rosetta.numeric.crick_equations.SINFXN(t: float, omega: float, delta_omega: float) → float

Calculates sin(omega*t+delta_omega)

C++: numeric::crick_equations::SINFXN(const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.XYZ_BUNDLE(t: float, r0: float, omega0: float, delta_omega0: float, r1: float, omega1: float, z1: float, delta_omega1: float, delta_z1: float, epsilon: float, failed: bool) → pyrosetta.rosetta.numeric.xyzVector_double_t

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++: numeric::crick_equations::XYZ_BUNDLE(const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, bool &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.numeric.crick_equations.X_BUNDLE(t: float, r0: float, omega0: float, delta_omega0: float, r1: float, omega1: float, z1: float, delta_omega1: float, delta_z1: float, epsilon: float, dr0prime_dt: float, failed: bool) → 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++: numeric::crick_equations::X_BUNDLE(const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, bool &) –> double

pyrosetta.rosetta.numeric.crick_equations.Y_BUNDLE(t: float, r0: float, omega0: float, delta_omega0: float, r1: float, omega1: float, z1: float, delta_omega1: float, delta_z1: float, epsilon: float, dr0prime_dt: float, failed: bool) → 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++: numeric::crick_equations::Y_BUNDLE(const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, bool &) –> double

pyrosetta.rosetta.numeric.crick_equations.Z_BUNDLE(t: float, r0: float, omega0: float, delta_omega0: float, r1: float, omega1: float, z1: float, delta_omega1: float, delta_z1: float, epsilon: float, dr0prime_dt: float, failed: bool) → 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++: numeric::crick_equations::Z_BUNDLE(const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const double &, bool &) –> double

pyrosetta.rosetta.numeric.crick_equations.dx_ddelta_omega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dx_ddelta_omega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dx_ddelta_z1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dx_ddelta_z1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dx_ddz1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dx_ddz1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dx_domega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dx_domega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dx_dr1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dx_dr1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dy_ddelta_omega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dy_ddelta_omega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dy_ddelta_z1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dy_ddelta_z1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dy_ddz1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dy_ddz1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dy_domega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dy_domega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dy_dr1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dy_dr1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dz_ddelta_omega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dz_ddelta_omega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dz_ddelta_z1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dz_ddelta_z1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dz_ddz1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dz_ddz1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dz_domega1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dz_domega1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.dz_dr1(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::dz_dr1(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.gradnorm(r0: float, omega0: float, Pomega0: float, s0: float, c0: float) → 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++: numeric::crick_equations::gradnorm(const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.x(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::x(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.xyz(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

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++: numeric::crick_equations::xyz(const double &, const double &, const double &, const double &, const double &, const double &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.numeric.crick_equations.y(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::y(const double &, const double &, const double &, const double &, const double &, const double &) –> double

pyrosetta.rosetta.numeric.crick_equations.z(r1: float, omega1: float, t: float, dz1: float, delta_omega1: float, delta_z1: float) → 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++: numeric::crick_equations::z(const double &, const double &, const double &, const double &, const double &, const double &) –> double