Rosetta
Public Types | Public Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential Class Reference

secondary structure scoring cut from classic rosetta structure.h/structure.cc More...

#include <NatbiasStrandPairPotential.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential:
Inheritance graph
[legend]

Public Types

typedef std::string String
 
typedef core::Size Size
 
typedef core::Real Real
 
typedef core::Vector Vector
 
typedef core::pose::Pose Pose
 
typedef protocols::fldsgn::topology::BB_Pos BB_Pos
 
typedef protocols::fldsgn::topology::SS_Info2 SS_Info2
 
typedef protocols::fldsgn::topology::DimerPairings DimerPairings
 
typedef protocols::fldsgn::topology::StrandPairingSetOP StrandPairingSetOP
 
typedef protocols::fldsgn::topology::StrandPairingSetCOP StrandPairingSetCOP
 
typedef ObjexxFCL::FArray1D< int > FArray1D_int
 
typedef ObjexxFCL::FArray1D< Real > FArray1D_real
 
typedef ObjexxFCL::FArray4D< Real > FArray4D_real
 

Public Member Functions

 NatbiasStrandPairPotential ()
 default constructor More...
 
 NatbiasStrandPairPotential (StrandPairingSetOP const spairset)
 default constructor More...
 
 ~NatbiasStrandPairPotential () override
 default destructor More...
 
void score (Pose const &pose, SS_Info2 const &ss_info, Real &ss_score) const
 score secondary structure More...
 
void set_native_spairset (StrandPairingSetOP const spairset)
 

Private Member Functions

void pair_dp (core::Size const &ss1, core::Size const &ss2, BB_Pos const &bb_pos, Real &dp, Vector const &mid_vector, core::Size &sign1, core::Size &sign2) const
 calculate sum of dot product of the co vectors of strand dimers ss1 and ss2 More...
 
Real calc_phithetascore (Real const phi, Real const theta) const
 return score of phitheta More...
 
Real calc_dotscore (Real const dpall) const
 return dot score More...
 
Real calc_rsigmascore (Real sig, Real dist, core::Size const sign1, core::Size const sign2) const
 return rsigma score More...
 
void load_phi_theta_bins (String const &ss_filename="scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth")
 load phi/theta bins for use in secondary structure scoring More...
 
void load_dotscore_bins ()
 

Static Private Member Functions

static void rsigma_dot_initializer (FArray4D_real &rsigma_dot)
 

Private Attributes

Real strand_dist_cutoff_
 
FArray4D_real phithetascore_
 
FArray1D_real dotscore_
 
FArray4D_real rsigma_dot_
 
StrandPairingSetOP native_spairset_
 

Detailed Description

secondary structure scoring cut from classic rosetta structure.h/structure.cc

Member Typedef Documentation

◆ BB_Pos

typedef protocols::fldsgn::topology::BB_Pos protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::BB_Pos

◆ DimerPairings

typedef protocols::fldsgn::topology::DimerPairings protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::DimerPairings

◆ FArray1D_int

typedef ObjexxFCL::FArray1D< int > protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::FArray1D_int

◆ FArray1D_real

typedef ObjexxFCL::FArray1D< Real > protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::FArray1D_real

◆ FArray4D_real

typedef ObjexxFCL::FArray4D< Real > protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::FArray4D_real

◆ Pose

typedef core::pose::Pose protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::Pose

◆ Real

typedef core::Real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::Real

◆ Size

typedef core::Size protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::Size

◆ SS_Info2

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::SS_Info2

◆ StrandPairingSetCOP

typedef protocols::fldsgn::topology::StrandPairingSetCOP protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::StrandPairingSetCOP

◆ StrandPairingSetOP

typedef protocols::fldsgn::topology::StrandPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::StrandPairingSetOP

◆ String

typedef std::string protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::String

◆ Vector

typedef core::Vector protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::Vector

Constructor & Destructor Documentation

◆ NatbiasStrandPairPotential() [1/2]

protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::NatbiasStrandPairPotential ( )

default constructor

References load_dotscore_bins(), and load_phi_theta_bins().

◆ NatbiasStrandPairPotential() [2/2]

protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::NatbiasStrandPairPotential ( StrandPairingSetOP const  spairset)

default constructor

value constructor

References load_dotscore_bins(), and load_phi_theta_bins().

◆ ~NatbiasStrandPairPotential()

protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::~NatbiasStrandPairPotential ( )
overridedefault

default destructor

destructor

Member Function Documentation

◆ calc_dotscore()

core::Real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::calc_dotscore ( Real const  dpall) const
private

return dot score

References dotscore_.

Referenced by score().

◆ calc_phithetascore()

core::Real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::calc_phithetascore ( Real const  phi,
Real const  theta 
) const
private

return score of phitheta

References phithetascore_.

Referenced by score().

◆ calc_rsigmascore()

core::Real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::calc_rsigmascore ( Real  sig,
Real  dist,
core::Size const  sign1,
core::Size const  sign2 
) const
private

return rsigma score

References rsigma_dot_.

Referenced by score().

◆ load_dotscore_bins()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::load_dotscore_bins ( )
private

References dotscore_.

Referenced by NatbiasStrandPairPotential().

◆ load_phi_theta_bins()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::load_phi_theta_bins ( String const &  ss_filename = "scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth")
private

load phi/theta bins for use in secondary structure scoring

References phithetascore_.

Referenced by NatbiasStrandPairPotential().

◆ pair_dp()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::pair_dp ( core::Size const &  ss1,
core::Size const &  ss2,
BB_Pos const &  bb_pos,
Real &  dp,
Vector const &  mid_vector,
core::Size &  sign1,
core::Size &  sign2 
) const
private

calculate sum of dot product of the co vectors of strand dimers ss1 and ss2

with the vector connecting the midpoints of the dimer vectors (vdist)

also determine return the sign of the dot products for each dimer

to determine which direction the CO groups point

References protocols::fldsgn::topology::BB_Pos::C(), and protocols::fldsgn::topology::BB_Pos::O().

Referenced by score().

◆ rsigma_dot_initializer()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::rsigma_dot_initializer ( FArray4D_real &  rsigma_dot)
staticprivate

References core::scoring::SecondaryStructurePotential::rsigma_dot_initializer().

◆ score()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score ( Pose const &  pose,
SS_Info2 const &  ss_info,
Real &  ss_score 
) const

score secondary structure

References protocols::fldsgn::topology::SS_Info2::bb_pos(), protocols::fldsgn::topology::BB_Pos::C(), calc_dotscore(), calc_phithetascore(), calc_rsigmascore(), core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::is_upper_terminus(), protocols::fldsgn::topology::BB_Pos::N(), native_spairset_, pair_dp(), core::pose::Pose::residue_type(), protocols::fldsgn::potentials::sspot::spherical(), protocols::loops::loop_closure::ccd::strand, strand_dist_cutoff_, protocols::fldsgn::topology::SS_Info2::strand_id(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::potentials::TR().

◆ set_native_spairset()

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::set_native_spairset ( StrandPairingSetOP const  spairset)

References native_spairset_.

Member Data Documentation

◆ dotscore_

FArray1D_real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::dotscore_
private

Referenced by calc_dotscore(), and load_dotscore_bins().

◆ native_spairset_

StrandPairingSetOP protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::native_spairset_
private

Referenced by score(), and set_native_spairset().

◆ phithetascore_

FArray4D_real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::phithetascore_
private

Referenced by calc_phithetascore(), and load_phi_theta_bins().

◆ rsigma_dot_

FArray4D_real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::rsigma_dot_
private

Referenced by calc_rsigmascore().

◆ strand_dist_cutoff_

Real protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::strand_dist_cutoff_
private

Referenced by score().

The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 10:57:25 for Rosetta by doxygen 1.9.1