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< Real >	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. 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< Real >	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. 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

ALPHA()

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 apply_ideal_A_form_torsions(), apply_suite_torsions(), minimize_poses(), print_all_torsions_test(), rotamerize_structure(), save_torsions(), ConstraintConfig::show_cst_grids(), X_BUNDLE(), Y_BUNDLE(), and Z_BUNDLE().

COSFXN()

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

Calculates cos(omega*t+delta_omega)

References basic::options::OptionKeys::AnchoredDesign::filters::omega, and predPRE::t.

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

dx_ddelta_omega1()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

dx_ddelta_z1()

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.

dx_ddz1()

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.

dx_domega1()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

dx_dr1()

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.

References predPRE::t.

dy_ddelta_omega1()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

dy_ddelta_z1()

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.

dy_ddz1()

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.

dy_domega1()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

dy_dr1()

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.

References predPRE::t.

dz_ddelta_omega1()

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.

dz_ddelta_z1()

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.

dz_ddz1()

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 predPRE::t.

dz_domega1()

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.

dz_dr1()

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.

gradnorm()

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().

P_omega0()

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, ObjexxFCL::pow(), and basic::options::OptionKeys::motifs::z1.

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

PP()

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, ObjexxFCL::pow(), and basic::options::OptionKeys::motifs::z1.

SINFXN()

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

Calculates sin(omega*t+delta_omega)

References basic::options::OptionKeys::AnchoredDesign::filters::omega, and predPRE::t.

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

x()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

Referenced by xyz().

X_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.

References compute_difference::alpha, ALPHA(), COSFXN(), gradnorm(), P_omega0(), basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::stepwise::s1, SINFXN(), predPRE::t, and basic::options::OptionKeys::motifs::z1.

Referenced by XYZ_BUNDLE().

xyz()

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 basic::options::OptionKeys::motifs::r1, predPRE::t, x(), y(), and z().

Referenced by add_Cu_chains().

XYZ_BUNDLE()

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< T >::assign(), basic::options::OptionKeys::motifs::r1, predPRE::t, numeric::xyzVector< T >::x(), X_BUNDLE(), numeric::xyzVector< T >::y(), Y_BUNDLE(), numeric::xyzVector< T >::z(), basic::options::OptionKeys::motifs::z1, and Z_BUNDLE().

y()

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.

References basic::options::OptionKeys::motifs::r1, and predPRE::t.

Referenced by xyz().

Y_BUNDLE()

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 compute_difference::alpha, ALPHA(), COSFXN(), gradnorm(), P_omega0(), basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::stepwise::s1, SINFXN(), predPRE::t, and basic::options::OptionKeys::motifs::z1.

Referenced by XYZ_BUNDLE().

z()

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.

References predPRE::t.

Referenced by xyz().

Z_BUNDLE()

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 compute_difference::alpha, ALPHA(), COSFXN(), gradnorm(), P_omega0(), numeric::constants::d::pi_2, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::stepwise::s1, SINFXN(), predPRE::t, and basic::options::OptionKeys::motifs::z1.

Referenced by XYZ_BUNDLE().