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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

Realdata_
 
Realderiv_phi_
 
Realderiv_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

◆ DOF3

Constructor & Destructor Documentation

◆ CentroidRotamerSampleData() [1/3]

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

normalization factor sigma=sqrt(2pi)

References data_, deriv_phi_, deriv_psi_, and NUMBER_OF_PARAMS.

◆ CentroidRotamerSampleData() [2/3]

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

◆ CentroidRotamerSampleData() [3/3]

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

◆ ~CentroidRotamerSampleData()

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

References data_, deriv_phi_, and deriv_psi_.

Member Function Documentation

◆ angle()

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

References angle_.

Referenced by CentroidRotamerSampleData().

◆ assign_best_rotamer()

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_.

◆ assign_random_rotamer()

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_.

◆ cal_delta_internal_coordinates()

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

◆ cal_delta_internal_coordinates_squared()

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().

◆ cal_distance()

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().

◆ cal_distance_squared() [1/2]

Real core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared ( const conformation::Residue rsd) const

◆ cal_distance_squared() [2/2]

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().

◆ dihedral()

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

References dihedral_.

Referenced by CentroidRotamerSampleData().

◆ distance()

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

References distance_.

Referenced by CentroidRotamerSampleData().

◆ energy()

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

References energy_.

Referenced by CentroidRotamerSampleData().

◆ norm_factor()

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

◆ private_data_to_public_array()

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

◆ prob()

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

◆ public_array_to_private_data()

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

◆ sd_ang()

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

◆ sd_dih()

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

◆ sd_dis()

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

◆ set_angle()

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

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

◆ set_dihedral()

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

References dihedral_.

◆ set_distance()

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

References distance_.

◆ set_prob()

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

References energy_, and prob_.

◆ set_sd_ang()

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

References sd_ang_.

◆ set_sd_dih()

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

References sd_dih_.

◆ set_sd_dis()

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

References sd_dis_.

Member Data Documentation

◆ angle_

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

◆ data_

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

◆ deriv_phi_

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

◆ deriv_psi_

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

◆ dihedral_

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

◆ distance_

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

◆ energy_

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

standard deviation of dih

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

◆ norm_factor_

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

◆ NUMBER_OF_PARAMS

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

◆ prob_

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

◆ sd_ang_

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

◆ sd_dih_

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

◆ sd_dis_

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

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