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protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential Class Reference

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

#include <NatbiasStrandPairPotential.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
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...
 
virtual ~NatbiasStrandPairPotential ()
 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 (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 (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_
 
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

Definition at line 45 of file NatbiasStrandPairPotential.hh.

Member Typedef Documentation

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

Definition at line 54 of file NatbiasStrandPairPotential.hh.

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

Definition at line 56 of file NatbiasStrandPairPotential.hh.

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

Definition at line 60 of file NatbiasStrandPairPotential.hh.

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

Definition at line 61 of file NatbiasStrandPairPotential.hh.

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

Definition at line 62 of file NatbiasStrandPairPotential.hh.

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

Definition at line 53 of file NatbiasStrandPairPotential.hh.

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

Definition at line 51 of file NatbiasStrandPairPotential.hh.

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

Definition at line 50 of file NatbiasStrandPairPotential.hh.

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

Definition at line 55 of file NatbiasStrandPairPotential.hh.

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

Definition at line 58 of file NatbiasStrandPairPotential.hh.

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

Definition at line 57 of file NatbiasStrandPairPotential.hh.

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

Definition at line 49 of file NatbiasStrandPairPotential.hh.

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

Definition at line 52 of file NatbiasStrandPairPotential.hh.

Constructor & Destructor Documentation

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

default constructor

Definition at line 65 of file NatbiasStrandPairPotential.cc.

References load_dotscore_bins(), and load_phi_theta_bins().

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

default constructor

value constructor

Definition at line 77 of file NatbiasStrandPairPotential.cc.

References load_dotscore_bins(), and load_phi_theta_bins().

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

default destructor

destructor

Definition at line 89 of file NatbiasStrandPairPotential.cc.

Member Function Documentation

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

return dot score

Definition at line 119 of file NatbiasStrandPairPotential.cc.

References dotscore_.

Referenced by score().

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

return score of phitheta

Definition at line 100 of file NatbiasStrandPairPotential.cc.

References phithetascore_.

Referenced by score().

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

return rsigma score

Definition at line 142 of file NatbiasStrandPairPotential.cc.

References rsigma_dot_.

Referenced by score().

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

Definition at line 425 of file NatbiasStrandPairPotential.cc.

References dotscore_.

Referenced by NatbiasStrandPairPotential().

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

Definition at line 380 of file NatbiasStrandPairPotential.cc.

References phithetascore_.

Referenced by NatbiasStrandPairPotential().

void protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::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 175 of file NatbiasStrandPairPotential.cc.

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

Referenced by score().

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

Definition at line 464 of file NatbiasStrandPairPotential.cc.

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

score secondary structure

Definition at line 237 of file NatbiasStrandPairPotential.cc.

References protocols::fldsgn::topology::SS_Info2::bb_pos(), calc_dotscore(), calc_phithetascore(), calc_rsigmascore(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::graph::Edge::get_node(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::is_upper_terminus(), native_spairset_, pair_dp(), protocols::swa::phi(), core::pose::Pose::residue_type(), protocols::fldsgn::potentials::sspot::spherical(), strand_dist_cutoff_, protocols::fldsgn::topology::SS_Info2::strand_id(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::potentials::TR().

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

Definition at line 94 of file NatbiasStrandPairPotential.cc.

References native_spairset_.

Member Data Documentation

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

Definition at line 146 of file NatbiasStrandPairPotential.hh.

Referenced by calc_dotscore(), and load_dotscore_bins().

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

Definition at line 151 of file NatbiasStrandPairPotential.hh.

Referenced by score(), and set_native_spairset().

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

Definition at line 144 of file NatbiasStrandPairPotential.hh.

Referenced by calc_phithetascore(), and load_phi_theta_bins().

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

Definition at line 148 of file NatbiasStrandPairPotential.hh.

Referenced by calc_rsigmascore().

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

Definition at line 142 of file NatbiasStrandPairPotential.hh.

Referenced by score().

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