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protocols::fldsgn::potentials::sspot::SSPairPotential Class Reference

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

#include <SSPairPotential.hh>

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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< Real > FArray1D_real
 
typedef ObjexxFCL::FArray4D< Real > FArray4D_real
 

Public Member Functions

 SSPairPotential ()
 default constructor More...
 
virtual ~SSPairPotential ()
 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 (Size const &ss1, Size const &ss2, BB_Pos const &bb_pos, Real &dp, Vector const &mid_vector, Size &sign1, Size &sign2) const
 calculate sum of dot product of the co vectors of strand dimers ss1 and ss2 More...
 
Real calc_phithetascore (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, Size const sign1, 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_
 
Size dimer_seqsep_cutoff_
 
Size lowstrand_
 
FArray4D_real phithetascore_
 
FArray1D_real dotscore_
 
FArray4D_real rsigma_dot_
 

Detailed Description

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

Definition at line 46 of file SSPairPotential.hh.

Member Typedef Documentation

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

Definition at line 58 of file SSPairPotential.hh.

typedef protocols::fldsgn::topology::DimerPairing protocols::fldsgn::potentials::sspot::SSPairPotential::DimerPairing

Definition at line 57 of file SSPairPotential.hh.

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

Definition at line 60 of file SSPairPotential.hh.

typedef core::scoring::EnergyGraph protocols::fldsgn::potentials::sspot::SSPairPotential::EnergyGraph

Definition at line 55 of file SSPairPotential.hh.

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

Definition at line 62 of file SSPairPotential.hh.

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

Definition at line 63 of file SSPairPotential.hh.

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

Definition at line 64 of file SSPairPotential.hh.

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

Definition at line 54 of file SSPairPotential.hh.

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

Definition at line 52 of file SSPairPotential.hh.

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

Definition at line 51 of file SSPairPotential.hh.

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

Definition at line 59 of file SSPairPotential.hh.

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

Definition at line 50 of file SSPairPotential.hh.

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

Definition at line 53 of file SSPairPotential.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 60 of file SSPairPotential.cc.

References load_dotscore_bins(), and load_phi_theta_bins().

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

default destructor

destructor

Definition at line 73 of file SSPairPotential.cc.

Member Function Documentation

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

return dot score

Definition at line 107 of file SSPairPotential.cc.

References dotscore_.

Referenced by score().

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

return score of phitheta

Definition at line 78 of file SSPairPotential.cc.

References phithetascore_.

Referenced by score().

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

return rsigma score

Definition at line 130 of file SSPairPotential.cc.

References rsigma_dot_.

Referenced by score().

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

Definition at line 416 of file SSPairPotential.cc.

References dotscore_.

Referenced by SSPairPotential().

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

Definition at line 370 of file SSPairPotential.cc.

References phithetascore_.

Referenced by SSPairPotential().

void protocols::fldsgn::potentials::sspot::SSPairPotential::pair_dp ( Size const &  ss1,
Size const &  ss2,
BB_Pos const &  bb_pos,
Real &  dp,
Vector const &  mid_vector,
Size &  sign1,
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

Definition at line 163 of file SSPairPotential.cc.

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

Referenced by score().

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

Definition at line 454 of file SSPairPotential.cc.

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

score secondary structure

Definition at line 225 of file SSPairPotential.cc.

References protocols::fldsgn::topology::SS_Info2::bb_pos(), calc_dotscore(), calc_phithetascore(), calc_rsigmascore(), core::graph::Node::const_upper_edge_list_end(), dimer_seqsep_cutoff_, core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::fldsgn::topology::DimerPairings::finalize(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::graph::Edge::get_node(), core::chemical::ResidueType::is_upper_terminus(), lowstrand_, pair_dp(), protocols::swa::phi(), protocols::fldsgn::topology::DimerPairing::res1(), protocols::fldsgn::topology::DimerPairing::res2(), core::pose::Pose::residue_type(), protocols::fldsgn::topology::DimerPairing::score(), protocols::fldsgn::potentials::sspot::spherical(), strand_dist_cutoff_, protocols::fldsgn::topology::SS_Info2::strand_id(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::topology::DimerPairing::valid().

Member Data Documentation

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

Definition at line 138 of file SSPairPotential.hh.

Referenced by score().

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

Definition at line 144 of file SSPairPotential.hh.

Referenced by calc_dotscore(), and load_dotscore_bins().

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

Definition at line 140 of file SSPairPotential.hh.

Referenced by score().

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

Definition at line 142 of file SSPairPotential.hh.

Referenced by calc_phithetascore(), and load_phi_theta_bins().

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

Definition at line 146 of file SSPairPotential.hh.

Referenced by calc_rsigmascore().

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

Definition at line 136 of file SSPairPotential.hh.

Referenced by score().

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