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

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

#include <SSPairPotential.hh>

Inheritance diagram for protocols::fldsgn::potentials::sspot::SSPairPotential:
Inheritance graph

Public Types

typedef std::string String
typedef core::Size Size
typedef core::Real Real
typedef core::Vector Vector
typedef core::pose::Pose Pose
typedef core::scoring::EnergyGraph EnergyGraph
typedef protocols::fldsgn::topology::DimerPairing DimerPairing
typedef protocols::fldsgn::topology::BB_Pos BB_Pos
typedef protocols::fldsgn::topology::SS_Info2 SS_Info2
typedef protocols::fldsgn::topology::DimerPairings DimerPairings
typedef ObjexxFCL::FArray1D< int > FArray1D_int
typedef ObjexxFCL::FArray1D< RealFArray1D_real
typedef ObjexxFCL::FArray4D< RealFArray4D_real

Public Member Functions

 SSPairPotential ()
 default constructor More...
 ~SSPairPotential () override
 default destructor More...
void score (Pose const &pose, SS_Info2 const &ss_info, DimerPairings &dimer_pairs, Real &ss_score) const
 score secondary structure More...

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 (core::Size const strand_seqsep, 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_
core::Size dimer_seqsep_cutoff_
core::Size lowstrand_
FArray4D_real phithetascore_
FArray1D_real dotscore_
FArray4D_real rsigma_dot_

Detailed Description

secondary structure scoring cut from classic rosetta structure.h/

Member Typedef Documentation

◆ BB_Pos

◆ DimerPairing

◆ DimerPairings

◆ EnergyGraph

◆ FArray1D_int

◆ FArray1D_real

◆ FArray4D_real

◆ Pose

◆ Real

◆ Size

◆ SS_Info2

◆ String

◆ Vector

Constructor & Destructor Documentation

◆ SSPairPotential()

protocols::fldsgn::potentials::sspot::SSPairPotential::SSPairPotential ( )

default constructor

References load_dotscore_bins(), and load_phi_theta_bins().

◆ ~SSPairPotential()

protocols::fldsgn::potentials::sspot::SSPairPotential::~SSPairPotential ( )

default destructor


Member Function Documentation

◆ calc_dotscore()

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

return dot score

References dotscore_.

Referenced by score().

◆ calc_phithetascore()

core::Real protocols::fldsgn::potentials::sspot::SSPairPotential::calc_phithetascore ( core::Size const  strand_seqsep,
Real const  phi,
Real const  theta 
) const

return score of phitheta

References phithetascore_.

Referenced by score().

◆ calc_rsigmascore()

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

return rsigma score

References rsigma_dot_.

Referenced by score().

◆ load_dotscore_bins()

void protocols::fldsgn::potentials::sspot::SSPairPotential::load_dotscore_bins ( )

References dotscore_.

Referenced by SSPairPotential().

◆ load_phi_theta_bins()

void protocols::fldsgn::potentials::sspot::SSPairPotential::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

References phithetascore_.

Referenced by SSPairPotential().

◆ pair_dp()

void protocols::fldsgn::potentials::sspot::SSPairPotential::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

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::SSPairPotential::rsigma_dot_initializer ( FArray4D_real rsigma_dot)

◆ score()

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

Member Data Documentation

◆ dimer_seqsep_cutoff_

core::Size protocols::fldsgn::potentials::sspot::SSPairPotential::dimer_seqsep_cutoff_

Referenced by score().

◆ dotscore_

FArray1D_real protocols::fldsgn::potentials::sspot::SSPairPotential::dotscore_

◆ lowstrand_

core::Size protocols::fldsgn::potentials::sspot::SSPairPotential::lowstrand_

Referenced by score().

◆ phithetascore_

FArray4D_real protocols::fldsgn::potentials::sspot::SSPairPotential::phithetascore_

◆ rsigma_dot_

FArray4D_real protocols::fldsgn::potentials::sspot::SSPairPotential::rsigma_dot_

Referenced by calc_rsigmascore().

◆ strand_dist_cutoff_

Real protocols::fldsgn::potentials::sspot::SSPairPotential::strand_dist_cutoff_

Referenced by score().

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