protocols::fldsgn::potentials::sspot::HSPairPotential Class Reference

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

#include <HSPairPotential.hh>

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

Collaboration diagram for protocols::fldsgn::potentials::sspot::HSPairPotential:

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::BB_Pos	BB_Pos
typedef protocols::fldsgn::topology::SS_Info2	SS_Info2
typedef ObjexxFCL::FArray1D< int >	FArray1D_int
typedef ObjexxFCL::FArray1D< Real >	FArray1D_real
typedef ObjexxFCL::FArray4D< Real >	FArray4D_real

Public Member Functions
	HSPairPotential ()
	default constructor More...
virtual	~HSPairPotential ()
	default destructor More...
void	score (Pose const &pose, SS_Info2 const &ss_info, Real &hs_score) const
	score secondary structure More...

Private Member Functions
Real	calc_phithetascore (Size const strand_seqsep, Real const phi, Real const theta) const
void	helix_end (Size const &pos1, BB_Pos const &bb_pos, Vector &p1, Vector &p2) const
	function reads in two points in sequence and returns two points in space, More...
void	load_phi_theta_bins (String const &ss_filename="scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth")
	load phi/theta bins for use in secondary structure scoring More...

Private Attributes
Real	dist_cutoff_
FArray4D_real	phithetascore_

Detailed Description

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

Definition at line 45 of file HSPairPotential.hh.

Member Typedef Documentation

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

Definition at line 55 of file HSPairPotential.hh.

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

Definition at line 54 of file HSPairPotential.hh.

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

Definition at line 58 of file HSPairPotential.hh.

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

Definition at line 59 of file HSPairPotential.hh.

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

Definition at line 60 of file HSPairPotential.hh.

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

Definition at line 53 of file HSPairPotential.hh.

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

Definition at line 51 of file HSPairPotential.hh.

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

Definition at line 50 of file HSPairPotential.hh.

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

Definition at line 56 of file HSPairPotential.hh.

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

Definition at line 49 of file HSPairPotential.hh.

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

Definition at line 52 of file HSPairPotential.hh.

Constructor & Destructor Documentation

protocols::fldsgn::potentials::sspot::HSPairPotential::HSPairPotential

(

)

default constructor

Definition at line 56 of file HSPairPotential.cc.

References load_phi_theta_bins().

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

virtual

default destructor

Definition at line 64 of file HSPairPotential.cc.

Member Function Documentation

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

private

Definition at line 69 of file HSPairPotential.cc.

References phithetascore_.

Referenced by score().

void protocols::fldsgn::potentials::sspot::HSPairPotential::helix_end ( Size const &  pos1, BB_Pos const &  bb_pos, Vector &  p1, Vector &  p2  ) const

private

function reads in two points in sequence and returns two points in space,

the endpoints of the axis through an alpha-helix

Definition at line 100 of file HSPairPotential.cc.

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

Referenced by score().

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

private

load phi/theta bins for use in secondary structure scoring

Definition at line 206 of file HSPairPotential.cc.

References phithetascore_.

Referenced by HSPairPotential().

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

score secondary structure

Definition at line 125 of file HSPairPotential.cc.

References protocols::fldsgn::topology::SS_Info2::bb_pos(), calc_phithetascore(), core::graph::Node::const_edge_list_end(), dist_cutoff_, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::graph::Edge::get_node(), protocols::fldsgn::topology::SS_Info2::helices(), helix_end(), core::chemical::ResidueType::is_upper_terminus(), protocols::swa::phi(), core::pose::Pose::residue_type(), protocols::fldsgn::potentials::sspot::spherical(), protocols::fldsgn::topology::SS_Info2::strand_id(), and protocols::fldsgn::topology::SS_Info2::strands().

Member Data Documentation

Real protocols::fldsgn::potentials::sspot::HSPairPotential::dist_cutoff_

private

Definition at line 102 of file HSPairPotential.hh.

Referenced by score().

FArray4D_real protocols::fldsgn::potentials::sspot::HSPairPotential::phithetascore_

private

Definition at line 105 of file HSPairPotential.hh.

Referenced by calc_phithetascore(), and load_phi_theta_bins().

---

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

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