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

#include <SecondaryStructurePotential.hh>

Inheritance diagram for core::scoring::SecondaryStructurePotential:

Collaboration diagram for core::scoring::SecondaryStructurePotential:

Public Types
typedef ObjexxFCL::FArray1D< Real >	FArray1D_real

typedef ObjexxFCL::FArray2D< Real >	FArray2D_real

typedef ObjexxFCL::FArray4D< Real >	FArray4D_real

typedef ObjexxFCL::FArray1< Real >	FArray1_real

typedef ObjexxFCL::FArray1A< Real >	FArray1A_real

typedef ObjexxFCL::FArray1D< int >	FArray1D_int

typedef conformation::symmetry::SymmetricConformation	SymmetricConformation

typedef conformation::symmetry::SymmetryInfoCOP	SymmetryInfoCOP

Public Member Functions
	SecondaryStructurePotential ()
	default constructor More...

	~SecondaryStructurePotential ()
	default destructor More...

void	setup_for_scoring (pose::Pose &pose) const

void	score (pose::Pose const &pose, SecondaryStructureWeights const &weights, Real &hs_score, Real &ss_score, Real &rsigma_score, Real &sheet_score) const
	score secondary structure More...

Private Member Functions
void	hspair (pose::Pose const &pose, Real &hs_score) const
	score hspair More...

void	sspair (pose::Pose const &pose, SecondaryStructureWeights const &weights, Real &ss_score, Real &rsigma_score) const
	score sspair More...

float	hairpin_killing_score (pose::Pose const &pose, Size const &pos1, Size const &pos2, Real const &theta, float const &ss_score) const

Real	sheets_from_dimers (pose::Pose const &pose) const
	This function takes a set of dimer neighbors, and determines how many sheets there, and how many strands are in each sheet This information is then used to calculate the "poker hand" score, which reflects to probability of that distribution of strands and sheets. More...

void	identify_ss (pose::Pose const &pose, Helices &helices, Strands &strands) const
	identifies secondary structure at the start of scoring and loads the Strands/Helices data More...

void	helix_end (int 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, the endpoints of the axis through an alpha-helix More...

void	pair_dp (int const &ss1, int const &ss2, BB_Pos const &bb_pos, Real &dp, Vector const &vdist, int &sign1, int &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 More...

int	get_foldtree_seqsep (pose::Pose const &pose, int pos1, int pos2, int gap_size=10) const
	identifies the sequence separation along the fold tree add the gap_size (default 10 ) into seqsep when there is chain break between pos1 and pos2 More...

void	load_phi_theta_bins (std::string const &hs_filename="scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth", std::string const &ss_filename="scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth")
	load phi/theta bins for use in secondary structure scoring More...

Static Private Member Functions
static void	dist_pair (Vector const &a1, Vector const &a2, Vector const &a3, Vector const &a4, Real &dist, Vector &cen1, Vector &cen2, Vector &v21)
	find the vector connecting the midpoints of two line segments defined by a1,a2 and a3,a4 More...

static void	spherical (Vector const &a2, Vector const &a4, Real &phi, Real &theta, Vector const &cen1, Vector const &cen2, Vector const &v21)
	find the angle (theta) between two vectors v1 and v2 and the angle (phi) by which v2 is rotated out of the plane defined by v1 and v21 around v1 (ie v1 is the z-axis) More...

static void	sigma (Vector const &a2, Vector const &cen1, Vector const &v21, Real &sig)
	find angle sigma between vectors cen1->a2 and v21 More...

static void	idsn_initializer (FArray1D_int &idsn)

static void	ids_initializer (FArray1D_int &ids)

static void	ssdist_initializer (FArray2D_real &ssdist)

static void	hs_dp_initializer (FArray1D_real &hs_dp)

static void	rsigma_dot_initializer (FArray4D_real &rsigma_dot)

static void	m_term_initializer (FArray1D_real &m_term)

static void	ss_penalty_initializer (FArray1D_real &SS_penalty)
	Penalty for pairing strand dimers that are close in sequence. More...

Private Attributes
FArray1D_int	iptsn_

FArray4D_real	pts_

FArray1D_real	ds_

FArray1D_int const	idsn_

FArray1D_int const	ids_

FArray2D_real const	ssdist_

FArray1D_real const	hs_dp_

FArray4D_real const	rsigma_dot_

FArray1D_real const	m_term_

Detailed Description

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

Definition at line 45 of file SecondaryStructurePotential.hh.

Member Typedef Documentation

typedef ObjexxFCL::FArray1< Real > core::scoring::SecondaryStructurePotential::FArray1_real

Definition at line 52 of file SecondaryStructurePotential.hh.

typedef ObjexxFCL::FArray1A< Real > core::scoring::SecondaryStructurePotential::FArray1A_real

Definition at line 53 of file SecondaryStructurePotential.hh.

typedef ObjexxFCL::FArray1D< int > core::scoring::SecondaryStructurePotential::FArray1D_int

Definition at line 54 of file SecondaryStructurePotential.hh.

typedef ObjexxFCL::FArray1D< Real > core::scoring::SecondaryStructurePotential::FArray1D_real

Definition at line 49 of file SecondaryStructurePotential.hh.

typedef ObjexxFCL::FArray2D< Real > core::scoring::SecondaryStructurePotential::FArray2D_real

Definition at line 50 of file SecondaryStructurePotential.hh.

typedef ObjexxFCL::FArray4D< Real > core::scoring::SecondaryStructurePotential::FArray4D_real

Definition at line 51 of file SecondaryStructurePotential.hh.

typedef conformation::symmetry::SymmetricConformation core::scoring::SecondaryStructurePotential::SymmetricConformation

Definition at line 56 of file SecondaryStructurePotential.hh.

typedef conformation::symmetry::SymmetryInfoCOP core::scoring::SecondaryStructurePotential::SymmetryInfoCOP

Definition at line 57 of file SecondaryStructurePotential.hh.

Constructor & Destructor Documentation

core::scoring::SecondaryStructurePotential::SecondaryStructurePotential ( )

default constructor

Definition at line 73 of file SecondaryStructurePotential.cc.

References load_phi_theta_bins().

core::scoring::SecondaryStructurePotential::~SecondaryStructurePotential ( )

inline

default destructor

Definition at line 66 of file SecondaryStructurePotential.hh.

Member Function Documentation

void core::scoring::SecondaryStructurePotential::dist_pair	(	Vector const &	a1,
		Vector const &	a2,
		Vector const &	a3,
		Vector const &	a4,
		Real &	dist,
		Vector &	cen1,
		Vector &	cen2,
		Vector &	v21
	)

staticprivate

find the vector connecting the midpoints of two line segments defined by a1,a2 and a3,a4

find the vector connecting the midpoints of two line segments

Parameters

[out]	dist	length of v21
[out]	v21	vector connecting midpoints

defined by a1,a2 and a3,a4

Parameters

[out]	dist	length of v21
[out]	v21	vector connecting midpoints

Definition at line 1456 of file SecondaryStructurePotential.cc.

Referenced by hspair(), and sspair().

int core::scoring::SecondaryStructurePotential::get_foldtree_seqsep	(	pose::Pose const &	pose,
		int	pos1,
		int	pos2,
		int	gap_size = `10`
	)		const

private

identifies the sequence separation along the fold tree add the gap_size (default 10 ) into seqsep when there is chain break between pos1 and pos2

identifies the sequence separation along the fold tree lin the old way to calculate the sequence separation takes an asumption of no-break chain lin when there is chain break between pos1 and pos2, we add a gap to make a correct calculation in ss energy

Definition at line 1423 of file SecondaryStructurePotential.cc.

References core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_simple_tree(), core::chemical::ResidueType::is_terminus(), and core::pose::Pose::residue_type().

Referenced by hspair(), and sspair().

float core::scoring::SecondaryStructurePotential::hairpin_killing_score	(	pose::Pose const &	pose,
		Size const &	pos1,
		Size const &	pos2,
		Real const &	theta,
		float const &	ss_score
	)		const

private

Definition at line 940 of file SecondaryStructurePotential.cc.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::SS_KILLHAIRPINS_INFO, and core::scoring::total_score.

Referenced by sspair().

void core::scoring::SecondaryStructurePotential::helix_end	(	int 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

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 1298 of file SecondaryStructurePotential.cc.

References core::scoring::BB_Pos::C(), core::scoring::BB_Pos::CA(), and core::scoring::BB_Pos::N().

Referenced by hspair().

void core::scoring::SecondaryStructurePotential::hs_dp_initializer ( FArray1D_real & hs_dp)

staticprivate

Definition at line 1790 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::hspair	(	pose::Pose const &	pose,
		Real &	hs_score
	)		const

private

score hspair

Definition at line 177 of file SecondaryStructurePotential.cc.

References core::scoring::SS_Info::bb_pos(), core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), dist_pair(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), get_foldtree_seqsep(), core::graph::Edge::get_node(), core::scoring::SS_Info::helices(), helix_end(), core::pose::symmetry::is_symmetric(), pts_, core::scoring::retrieve_const_ss_info_from_pose(), spherical(), core::scoring::SS_Info::strands(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by score().

void core::scoring::SecondaryStructurePotential::identify_ss	(	pose::Pose const &	pose,
		Helices &	helices,
		Strands &	strands
	)		const

private

identifies secondary structure at the start of scoring and loads the Strands/Helices data

Definition at line 1183 of file SecondaryStructurePotential.cc.

References core::pack::dunbrack::c, core::pose::Pose::conformation(), core::conformation::Residue::has_variant_type(), core::scoring::Helices::HH_helix_end, core::scoring::Helices::HH_resnum, core::chemical::REPLONLY, core::pose::Pose::residue(), core::scoring::Strands::SS_dimer, core::scoring::Strands::SS_resnum, core::scoring::Strands::SS_strand, core::scoring::Strands::SS_strand_end, core::scoring::Helices::total_HH_dimer, core::pose::Pose::total_residue(), core::scoring::Strands::total_SS_dimer, and core::scoring::Strands::total_strands.

Referenced by setup_for_scoring().

void core::scoring::SecondaryStructurePotential::ids_initializer ( FArray1D_int & ids)

staticprivate

Definition at line 1752 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::idsn_initializer ( FArray1D_int & idsn)

staticprivate

Definition at line 1734 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::load_phi_theta_bins	(	std::string const &	hs_filename = `"scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth"`,
		std::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 1613 of file SecondaryStructurePotential.cc.

References ds_, ids_, idsn_, iptsn_, and pts_.

Referenced by SecondaryStructurePotential().

void core::scoring::SecondaryStructurePotential::m_term_initializer ( FArray1D_real & m_term)

staticprivate

Definition at line 2690 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::pair_dp	(	int const &	ss1,
		int const &	ss2,
		BB_Pos const &	bb_pos,
		Real &	dp,
		Vector const &	vdist,
		int &	sign1,
		int &	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

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 1337 of file SecondaryStructurePotential.cc.

References core::scoring::BB_Pos::C(), and core::scoring::BB_Pos::O().

Referenced by sspair().

void core::scoring::SecondaryStructurePotential::rsigma_dot_initializer ( FArray4D_real & rsigma_dot)

staticprivate

Definition at line 1809 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::score	(	pose::Pose const &	pose,
		SecondaryStructureWeights const &	weights,
		Real &	hs_score,
		Real &	ss_score,
		Real &	rsigma_score,
		Real &	sheet_score
	)		const

score secondary structure

Definition at line 153 of file SecondaryStructurePotential.cc.

References hspair(), sheets_from_dimers(), and sspair().

Referenced by core::scoring::methods::SecondaryStructureEnergy::finalize_total_energy().

void core::scoring::SecondaryStructurePotential::setup_for_scoring ( pose::Pose & pose) const

Definition at line 126 of file SecondaryStructurePotential.cc.

References core::scoring::SS_Info::bb_pos(), core::scoring::fill_bb_pos(), core::scoring::SS_Info::helices(), identify_ss(), core::scoring::SS_Info::resize(), core::scoring::retrieve_nonconst_ss_info_from_pose(), core::scoring::SS_Info::strands(), and core::pose::Pose::total_residue().

Referenced by core::scoring::methods::SecondaryStructureEnergy::setup_for_scoring().

Real core::scoring::SecondaryStructurePotential::sheets_from_dimers ( pose::Pose const & pose) const

private

This function takes a set of dimer neighbors, and determines how many sheets there, and how many strands are in each sheet This information is then used to calculate the "poker hand" score, which reflects to probability of that distribution of strands and sheets.

apl This function reads the strand pairing information for all dimer apl neighbors to determine how many strands are in each sheet. It apl uses a fast conected-component detection data structure to do so. apl Once the number of strands for each sheet is known, a per-sheet "poker apl hand score" is computed and these scores summed. apl Old comments follow.

js This function takes a set of dimer neighbors, and determines how js many sheets there, and how many strands are in each sheet js This information is then used to calculate the "poker hand" score, js which reflects to probability of that distribution of strands and js sheets. js In current version, it seems to simply penalize sheets with fewer js strands compared to those with more strands.

js This function looks at a list of dimers, which contains up to js two neighbors for each dimer. In priniciple these neighbors would js be hydrogen bond partners in neighboring strands. This function js will take this list, however it is made.

js Currently, dimer neighbors are defined somewhat arbitrarily. js If I understand the code correctly, the first and last dimers in js sequence that follow the current dimer, and that are within 6.5 js angstroms, are the neighbors. There is no orientation dependence js on what counts as a strand neighbor.

js A sheet is then loosely defined by all the strands that are connected js by one of these neighbors. This amounts to "single-linkage clustering." js A sheet is determined by the set of strands that can be linked by js the dimer neighbors. Note that a one neighbor is enough to say that js two strands are in a sheet.

js The final score is put into sheet_score, and is determined by the js number of sheets of each size.

js Basic strategy: go through all dimers, finding neigboring strands js Because each dimer can only have two neighbors we can first search js all the way down one side, and then the other. This will give a set js of dimers that are connected. The strands in which these dimers reside js are then considered connected into sheets. By going through all js dimers with the proper bookkeeping, we can determine how many sheets js there are, and how many strands in each.

Definition at line 1040 of file SecondaryStructurePotential.cc.

References core::pose::Pose::conformation(), core::graph::DisjointSets::disjoint_set_sizes(), core::graph::DisjointSets::ds_union(), core::pose::symmetry::is_symmetric(), m_term_, core::graph::DisjointSets::nodes_in_set(), core::scoring::retrieve_const_ss_info_from_pose(), core::graph::DisjointSets::sets(), core::scoring::SS_Info::strands(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by score().

void core::scoring::SecondaryStructurePotential::sigma	(	Vector const &	a2,
		Vector const &	cen1,
		Vector const &	v21,
		Real &	sig
	)

staticprivate

find angle sigma between vectors cen1->a2 and v21

Parameters

[out] sig sigma

Definition at line 1585 of file SecondaryStructurePotential.cc.

Referenced by sspair().

void core::scoring::SecondaryStructurePotential::spherical	(	Vector const &	a2,
		Vector const &	a4,
		Real &	phi,
		Real &	theta,
		Vector const &	cen1,
		Vector const &	cen2,
		Vector const &	v21
	)

staticprivate

find the angle (theta) between two vectors v1 and v2 and the angle (phi) by which v2 is rotated out of the plane defined by v1 and v21 around v1 (ie v1 is the z-axis)

define a coordinate system with Z axis along cen1->a2 (v1), xz plane defined by cen1->a2 and v21. and origin at cen1. Find the spherical coordinates phi,and theta of point a4 if vector cen2->a4 was moved such that cen2=cen1

Parameters

[out] v21 vector connecting midpoints

Definition at line 1499 of file SecondaryStructurePotential.cc.

Referenced by hspair(), and sspair().

void core::scoring::SecondaryStructurePotential::ss_penalty_initializer ( FArray1D_real & SS_penalty)

staticprivate

Penalty for pairing strand dimers that are close in sequence.

Inferred from the log ratio of pairing probabilities of strands

in the PDB vs. in Rosetta decoys. Calculated as a function of

strand separation.

Definition at line 2705 of file SecondaryStructurePotential.cc.

Referenced by sspair().

void core::scoring::SecondaryStructurePotential::ssdist_initializer ( FArray2D_real & ssdist)

staticprivate

Definition at line 1767 of file SecondaryStructurePotential.cc.

void core::scoring::SecondaryStructurePotential::sspair	(	pose::Pose const &	pose,
		SecondaryStructureWeights const &	weights,
		Real &	ss_score,
		Real &	rsigma_score
	)		const