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

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

#include <SSPairPotential.hh>

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

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...
	~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 (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

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

(

)

default constructor

References load_dotscore_bins(), and load_phi_theta_bins().

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

overridedefault

default destructor

destructor

Member Function Documentation

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

private

return dot score

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

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

References rsigma_dot_.

Referenced by score().

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

private

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

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

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

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

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

References protocols::fldsgn::topology::SS_Info2::bb_pos(), calc_dotscore(), calc_phithetascore(), calc_rsigmascore(), 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::chemical::ResidueType::is_upper_terminus(), lowstrand_, pair_dp(), 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(), 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::topology::DimerPairing::valid().

Member Data Documentation

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

private

Referenced by score().

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

private

Referenced by calc_dotscore(), and load_dotscore_bins().

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

private

Referenced by score().

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

private

Referenced by calc_phithetascore(), and load_phi_theta_bins().

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

private

Referenced by calc_rsigmascore().

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

private

Referenced by score().

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

• src/protocols/fldsgn/potentials/sspot/SSPairPotential.hh
• src/protocols/fldsgn/potentials/sspot/SSPairPotential.cc