DisulfideBondEnergy Class Reference

Public Member Functions
	DisulfideBondEnergy (double, double, double)
double	probability (double ca_ca_sg, double cb_sg_sg_cb, double sg_cb_ca, double d)
double	probability (core::PointPosition cb1, core::PointPosition sg1, core::PointPosition sg2, core::PointPosition cb2)
bool	detectDisulfideBond (pose::Pose &pose, int cysId1, int cysId2)
double	evaluate (pose::Pose &pose, int cysId1, int cysId2)
bool	rebuildAndDetectDisulfideBond (pose::Pose &pose, int cysId1, double chi1, int cysId2, double chi2)
bool	rebuildAndDetectDisulfideBond (pose::Pose &pose, int cysId1, int cysId2)
double	tabulate (pose::Pose &pose, int cysId1, int cysId2)

Static Public Attributes
static double	energyBondCutoff = -0.3
static double	pseudocountsFraction = 0.000000001

Private Attributes
double *	stdevPos
double *	stdevNeg
double *	twoVarPos
double *	twoVarNeg

Static Private Attributes
static double	theta = 1.19426
static double	dist = 1.808
static double	meanPos [] = { 104.4, 93.6, 104.4, 2.055 }
static double	meanNeg [] = { 103.8, -85.89, 103.9, 2.055 }
static double	maxCBDistance = 4.5
static double	sqrtTwoPi = sqrt(M_PI * 2.0)

Constructor & Destructor Documentation

DisulfideBondEnergy()

DisulfideBondEnergy::DisulfideBondEnergy	(	double	planarWidthScaling,
		double	torsionWidthScaling,
		double	distanceWidthScaling
	)

Member Function Documentation

detectDisulfideBond()

bool DisulfideBondEnergy::detectDisulfideBond	(	pose::Pose &	pose,
		int	cysId1,
		int	cysId2
	)

evaluate()

double DisulfideBondEnergy::evaluate	(	pose::Pose &	pose,
		int	cysId1,
		int	cysId2
	)

References utility::io::oc::cout, numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and beta_nonlocal::pose.

Referenced by main().

probability() [1/2]

double DisulfideBondEnergy::probability	(	core::PointPosition	cb1,
		core::PointPosition	sg1,
		core::PointPosition	sg2,
		core::PointPosition	cb2
	)

References numeric::angle_radians(), numeric::dihedral_degrees(), and build_jacobian::distance.

probability() [2/2]

double DisulfideBondEnergy::probability	(	double	ca_ca_sg,
		double	cb_sg_sg_cb,
		double	sg_cb_ca,
		double	d
	)

References create_a3b_hbs::i, predPRE::t, and x.

rebuildAndDetectDisulfideBond() [1/2]

bool DisulfideBondEnergy::rebuildAndDetectDisulfideBond	(	pose::Pose &	pose,
		int	cysId1,
		double	chi1,
		int	cysId2,
		double	chi2
	)

References utility::io::oc::cout, dist(), numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, numeric::x_rotation_matrix_degrees(), and numeric::z_rotation_matrix_radians().

Referenced by main().

rebuildAndDetectDisulfideBond() [2/2]

bool DisulfideBondEnergy::rebuildAndDetectDisulfideBond	(	pose::Pose &	pose,
		int	cysId1,
		int	cysId2
	)

References dist(), build_jacobian::distance, numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, numeric::x_rotation_matrix_degrees(), and numeric::z_rotation_matrix_radians().

tabulate()

double DisulfideBondEnergy::tabulate	(	pose::Pose &	pose,
		int	cysId1,
		int	cysId2
	)

References utility::io::oc::cout, dist(), numeric::log(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, numeric::x_rotation_matrix_degrees(), and numeric::z_rotation_matrix_radians().

Member Data Documentation

dist

double DisulfideBondEnergy::dist = 1.808

staticprivate

energyBondCutoff

double DisulfideBondEnergy::energyBondCutoff = -0.3

static

maxCBDistance

double DisulfideBondEnergy::maxCBDistance = 4.5

staticprivate

meanNeg

double DisulfideBondEnergy::meanNeg = { 103.8, -85.89, 103.9, 2.055 }

staticprivate

meanPos

double DisulfideBondEnergy::meanPos = { 104.4, 93.6, 104.4, 2.055 }

staticprivate

pseudocountsFraction

double DisulfideBondEnergy::pseudocountsFraction = 0.000000001

static

sqrtTwoPi

double DisulfideBondEnergy::sqrtTwoPi = sqrt(M_PI * 2.0)

staticprivate

stdevNeg

double* DisulfideBondEnergy::stdevNeg

private

stdevPos

double* DisulfideBondEnergy::stdevPos

private

theta

double DisulfideBondEnergy::theta = 1.19426

staticprivate

twoVarNeg

double* DisulfideBondEnergy::twoVarNeg

private

twoVarPos

double* DisulfideBondEnergy::twoVarPos

private

---

The documentation for this class was generated from the following file:

• src/apps/pilot/dgront/experiments/DisulfideBondEnergy.cc