core::pack::dunbrack::cenrot::CentroidRotamerSampleData Class Reference

Simple class storing all the data for one centroid-rotamer well. More...

#include <SingleResidueCenrotLibrary.hh>

Public Types
typedef utility::fixedsizearray1< Real, 3 >	DOF3

Public Member Functions
	CentroidRotamerSampleData ()
	normalization factor sigma=sqrt(2pi) More...
	CentroidRotamerSampleData (Real p, Real d, Real a, Real w, Real vd, Real va, Real vw)
	CentroidRotamerSampleData (const CentroidRotamerSampleData &cs)
	~CentroidRotamerSampleData ()
Real	distance () const
Real	angle () const
Real	dihedral () const
Real	sd_dis () const
Real	sd_ang () const
Real	sd_dih () const
Real	prob () const
Real	energy () const
Real	norm_factor () const
void	set_distance (Real d)
void	set_angle (Real a)
void	set_dihedral (Real w)
void	set_prob (Real p)
void	set_sd_dis (Real s)
void	set_sd_ang (Real s)
void	set_sd_dih (Real s)
void	private_data_to_public_array ()
void	public_array_to_private_data ()
Real	cal_distance (const DOF3 &sample, bool use_xyz=false) const
Real	cal_distance_squared (const DOF3 &sample, bool use_xyz=false) const
Real	cal_distance_squared (const conformation::Residue &rsd) const
Real	cal_delta_internal_coordinates_squared (const conformation::Residue &rsd, Real &d_sq, Real &a_sq, Real &w_sq) const
	return the value of angle (in rad) More...
Real	cal_delta_internal_coordinates (const conformation::Residue &rsd, Real &delta_d, Real &delta_a, Real &delta_w) const
void	assign_random_rotamer (DOF3 &sample, numeric::random::RandomGenerator &RG) const
	generate a random rot inside the well More...
void	assign_best_rotamer (DOF3 &sample) const
	generate the best rot (mean of the well) More...

Public Attributes
Real *	data_
Real *	deriv_phi_
Real *	deriv_psi_

Private Attributes
Real	prob_
Real	distance_
	probability for sidechain showing in this well More...
Real	angle_
	CEN-CB bond length. More...
Real	dihedral_
	CEN-CB-CA bond angle. More...
Real	sd_dis_
	CEN-CB-CA-N dihedral angle chi1. More...
Real	sd_ang_
	standard deviation of dis More...
Real	sd_dih_
	standard deviation of ang More...
Real	energy_
	standard deviation of dih More...
Real	norm_factor_
	-ln(P) More...

Static Private Attributes
static Size const	NUMBER_OF_PARAMS = 7

Detailed Description

Simple class storing all the data for one centroid-rotamer well.

Member Typedef Documentation

typedef utility::fixedsizearray1< Real, 3 > core::pack::dunbrack::cenrot::CentroidRotamerSampleData::DOF3

Constructor & Destructor Documentation

core::pack::dunbrack::cenrot::CentroidRotamerSampleData::CentroidRotamerSampleData ( )

inline

normalization factor sigma=sqrt(2pi)

References data_, deriv_phi_, deriv_psi_, and NUMBER_OF_PARAMS.

core::pack::dunbrack::cenrot::CentroidRotamerSampleData::CentroidRotamerSampleData ( Real  p, Real  d, Real  a, Real  w, Real  vd, Real  va, Real  vw  )

inline

References data_, deriv_phi_, deriv_psi_, energy_, norm_factor_, and NUMBER_OF_PARAMS.

core::pack::dunbrack::cenrot::CentroidRotamerSampleData::CentroidRotamerSampleData ( const CentroidRotamerSampleData &  cs )

inline

References angle(), angle_, data_, deriv_phi_, deriv_psi_, dihedral(), dihedral_, distance(), distance_, energy(), energy_, norm_factor(), norm_factor_, NUMBER_OF_PARAMS, prob(), prob_, sd_ang(), sd_ang_, sd_dih(), sd_dih_, sd_dis(), and sd_dis_.

core::pack::dunbrack::cenrot::CentroidRotamerSampleData::~CentroidRotamerSampleData ( )

inline

References data_, deriv_phi_, and deriv_psi_.

Member Function Documentation

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::angle ( ) const

inline

References angle_.

Referenced by CentroidRotamerSampleData().

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::assign_best_rotamer

(

DOF3 &

sample

)

const

generate the best rot (mean of the well)

References angle_, dihedral_, and distance_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::assign_random_rotamer	(	DOF3 &	sample,
		numeric::random::RandomGenerator &	RG
	)		const

generate a random rot inside the well

References angle_, dihedral_, and distance_.

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates	(	const conformation::Residue &	rsd,
		Real &	delta_d,
		Real &	delta_a,
		Real &	delta_w
	)		const

References core::pose::motif::a(), angle_, core::conformation::Residue::atom(), protocols::match::upstream::b, core::pack::dunbrack::c, dihedral_, distance_, and core::conformation::Atom::xyz().

Referenced by cal_delta_internal_coordinates_squared(), and core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates_squared	(	const conformation::Residue &	rsd,
		Real &	d_sq,
		Real &	a_sq,
		Real &	w_sq
	)		const

return the value of angle (in rad)

CentroidRotamerSampleData.

References cal_delta_internal_coordinates().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance	(	const DOF3 &	sample,
		bool	use_xyz = false
	)		const

DOF3 sample: (dis, ange, dih) calculate the distance between this rot and given CEN

References cal_distance_squared().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared	(	const DOF3 &	sample,
		bool	use_xyz = false
	)		const

References angle_, dihedral_, and distance_.

Referenced by cal_distance(), and cal_distance_squared().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared

(

const conformation::Residue &

rsd

)

const

References core::pose::motif::a(), core::conformation::Residue::atom(), protocols::match::upstream::b, core::pack::dunbrack::c, cal_distance_squared(), and core::conformation::Atom::xyz().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::dihedral ( ) const

inline

References dihedral_.

Referenced by CentroidRotamerSampleData().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::distance ( ) const

inline

References distance_.

Referenced by CentroidRotamerSampleData().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::energy ( ) const

inline

References energy_.

Referenced by CentroidRotamerSampleData().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::norm_factor ( ) const

inline

Referenced by CentroidRotamerSampleData().

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::private_data_to_public_array

(

)

References angle_, data_, dihedral_, distance_, prob_, sd_ang_, sd_dih_, and sd_dis_.

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::prob ( ) const

inline

References prob_.

Referenced by CentroidRotamerSampleData(), and core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv().

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::public_array_to_private_data

(

)

References angle_, data_, dihedral_, distance_, energy_, norm_factor_, prob_, sd_ang_, sd_dih_, and sd_dis_.

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_ang ( ) const

inline

References sd_ang_.

Referenced by CentroidRotamerSampleData(), and core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dih ( ) const

inline

References sd_dih_.

Referenced by CentroidRotamerSampleData(), and core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dis ( ) const

inline

References sd_dis_.

Referenced by CentroidRotamerSampleData(), and core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_deriv().

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_angle ( Real  a )

inline

References core::pose::motif::a(), and angle_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_dihedral ( Real  w )

inline

References dihedral_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_distance ( Real  d )

inline

References distance_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_prob ( Real  p )

inline

References energy_, and prob_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_ang ( Real  s )

inline

References sd_ang_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_dih ( Real  s )

inline

References sd_dih_.

void core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_sd_dis ( Real  s )

inline

References sd_dis_.

Member Data Documentation

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::angle_

private

CEN-CB bond length.

Referenced by angle(), assign_best_rotamer(), assign_random_rotamer(), cal_delta_internal_coordinates(), cal_distance_squared(), CentroidRotamerSampleData(), private_data_to_public_array(), public_array_to_private_data(), and set_angle().

Real* core::pack::dunbrack::cenrot::CentroidRotamerSampleData::data_

Referenced by CentroidRotamerSampleData(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv(), private_data_to_public_array(), public_array_to_private_data(), and ~CentroidRotamerSampleData().

Real* core::pack::dunbrack::cenrot::CentroidRotamerSampleData::deriv_phi_

Referenced by CentroidRotamerSampleData(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv(), and ~CentroidRotamerSampleData().

Real* core::pack::dunbrack::cenrot::CentroidRotamerSampleData::deriv_psi_

Referenced by CentroidRotamerSampleData(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::eval_rotameric_energy_bb_dof_deriv(), and ~CentroidRotamerSampleData().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::dihedral_

private

CEN-CB-CA bond angle.

Referenced by assign_best_rotamer(), assign_random_rotamer(), cal_delta_internal_coordinates(), cal_distance_squared(), CentroidRotamerSampleData(), dihedral(), private_data_to_public_array(), public_array_to_private_data(), and set_dihedral().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::distance_

private

probability for sidechain showing in this well

Referenced by assign_best_rotamer(), assign_random_rotamer(), cal_delta_internal_coordinates(), cal_distance_squared(), CentroidRotamerSampleData(), distance(), private_data_to_public_array(), public_array_to_private_data(), and set_distance().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::energy_

private

standard deviation of dih

Referenced by CentroidRotamerSampleData(), energy(), public_array_to_private_data(), and set_prob().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::norm_factor_

private

-ln(P)

Referenced by CentroidRotamerSampleData(), and public_array_to_private_data().

Size const core::pack::dunbrack::cenrot::CentroidRotamerSampleData::NUMBER_OF_PARAMS = 7

staticprivate

Referenced by CentroidRotamerSampleData().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::prob_

private

Referenced by CentroidRotamerSampleData(), private_data_to_public_array(), prob(), public_array_to_private_data(), and set_prob().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_ang_

private

standard deviation of dis

Referenced by CentroidRotamerSampleData(), private_data_to_public_array(), public_array_to_private_data(), sd_ang(), and set_sd_ang().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dih_

private

standard deviation of ang

Referenced by CentroidRotamerSampleData(), private_data_to_public_array(), public_array_to_private_data(), sd_dih(), and set_sd_dih().

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::sd_dis_

private

CEN-CB-CA-N dihedral angle chi1.

Referenced by CentroidRotamerSampleData(), private_data_to_public_array(), public_array_to_private_data(), sd_dis(), and set_sd_dis().

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

• src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.hh
• src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.cc