protocols::hybridization::TMalign Class Reference

#include <TMalign.hh>

Public Member Functions
	TMalign ()
void	PrintErrorAndQuit (std::string sErrorString)
template<class A >
void	ResizeArray (A &array, int Narray1, int Narray2)
int	read_pose (core::pose::Pose const &pose, std::list< core::Size > const &residue_list, std::vector< numeric::xyzVector< core::Real > > &a, std::string &seq, std::vector< int > &resno)
double	dist (numeric::xyzVector< core::Real > x, numeric::xyzVector< core::Real > y)
void	transform (numeric::xyzVector< core::Real > const &t, numeric::xyzMatrix< core::Real > const &u, numeric::xyzVector< core::Real > x, numeric::xyzVector< core::Real > &x1)
void	do_rotation (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > &x1, int len, numeric::xyzVector< core::Real > const &t, numeric::xyzMatrix< core::Real > const &u)
void	NWDP_TM (core::Size const len1, core::Size const len2, double const gap_open, std::vector< int > &j2i)
void	NWDP_TM (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const len1, int const len2, numeric::xyzVector< core::Real > const &t, numeric::xyzMatrix< core::Real > const &u, double d02, double gap_open, std::vector< int > &j2i)
void	NWDP_TM (std::vector< int > const &secx, std::vector< int > const &secy, int const len1, int const len2, double gap_open, std::vector< int > &j2i)
void	convert_xyz_to_vector (numeric::xyzVector< core::Real > const &x, std::vector< core::Real > &xx)
void	convert_xyz_to_matrix (numeric::xyzMatrix< core::Real > const &x, std::vector< std::vector< core::Real > > &xx)
void	convert_vector_to_xyz (std::vector< core::Real > const &x, numeric::xyzVector< core::Real > &xx)
void	convert_matrix_to_xyz (std::vector< std::vector< core::Real > > const &x, numeric::xyzMatrix< core::Real > &xx)
void	convert_xyz_v_to_vectors (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< std::vector< double > > &xx)
bool	Kabsch (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const n, int const mode, double *rms, numeric::xyzVector< core::Real > &t, numeric::xyzMatrix< core::Real > &u)
bool	Kabsch (std::vector< std::vector< double > > const &x, std::vector< std::vector< double > > const &y, int const n, int const mode, double *rms, std::vector< double > &t, std::vector< std::vector< double > > &u)
void	load_pose_allocate_memory (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > &residue_list1, std::list< core::Size > &residue_list2)
int	score_fun8 (std::vector< numeric::xyzVector< core::Real > > const &xa, std::vector< numeric::xyzVector< core::Real > > const &ya, int const n_ali, double const d, std::vector< int > &i_ali, double *score1, int score_sum_method)
double	TMscore8_search (std::vector< numeric::xyzVector< core::Real > > const &xtm, std::vector< numeric::xyzVector< core::Real > > const &ytm, int Lali, numeric::xyzVector< core::Real > &t0, numeric::xyzMatrix< core::Real > &u0, int const simplify_step, int const score_sum_method, double *Rcomm)
double	detailed_search (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const, int const y_len, std::vector< int > const &invmap0, numeric::xyzVector< core::Real > &t, numeric::xyzMatrix< core::Real > &u, int simplify_step, int score_sum_method)
double	get_score_fast (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const , int const y_len, std::vector< int > const &invmap)
double	get_initial (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > &y2x)
void	smooth (std::vector< int > &sec, int const len)
int	sec_str (double dis13, double dis14, double dis15, double dis24, double dis25, double dis35)
void	make_sec (std::vector< numeric::xyzVector< core::Real > > const &x, int const len, std::vector< int > &sec)
void	get_initial_ss (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > &y2x)
bool	get_initial_local (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > &y2x)
void	score_matrix_rmsd (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > const &y2x)
void	score_matrix_rmsd_sec (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > const &y2x)
void	get_initial_ssplus (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > &y2x0, std::vector< int > &y2x)
void	find_max_frag (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< int > const &resno, int const len, int *start_max, int *end_max)
double	get_initial_fgt (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, std::vector< int > const &xresno, std::vector< int > const &yresno, std::vector< int > &y2x)
double	DP_iter (std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< numeric::xyzVector< core::Real > > const &y, int const x_len, int const y_len, numeric::xyzVector< core::Real > t, numeric::xyzMatrix< core::Real > u, std::vector< int > &invmap0, int const g1, int const g2, int const iteration_max)
void	alignment2AtomMap (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::id::AtomID_Map< core::id::AtomID > &atom_map)
void	alignment2AtomMap (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size &n_mapped_residues, core::id::AtomID_Map< core::id::AtomID > &atom_map)
void	alignment2AtomMap (core::pose::Pose const &pose, core::pose::Pose const &ref_pose, std::list< core::Size > const &residue_list, std::list< core::Size > const &ref_residue_list, core::Size &n_mapped_residues, core::id::AtomID_Map< core::id::AtomID > &atom_map)
void	alignment2strings (std::string &seqxA, std::string &seqyA, std::string &seqM)
void	parameter_set4search (int xlen, int ylen)
void	parameter_set4final (double len)
void	parameter_set4scale (int len, double d_s)
core::Real	TMscore (core::Size length)
int	apply (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
int	apply (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > residue_list1, std::list< core::Size > residue_list2)
const numeric::xyzVector < core::Real > &	get_t () const
const numeric::xyzMatrix < core::Real > &	get_u () const

Private Attributes
double	D0_MIN_
double	Lnorm_
double	score_d8_
double	d0_
double	d0_search_
double	dcu0_
std::vector< std::vector < double > >	score_
std::vector< std::vector< bool > >	path_
std::vector< std::vector < double > >	val_
int	xlen_
int	ylen_
int	minlen_
std::vector < numeric::xyzVector < core::Real > >	xa_
std::vector < numeric::xyzVector < core::Real > >	ya_
std::vector< int >	xresno_
std::vector< int >	yresno_
std::vector < numeric::xyzVector < core::Real > >	xtm_
std::vector < numeric::xyzVector < core::Real > >	ytm_
std::vector < numeric::xyzVector < core::Real > >	xt_
std::string	seqx_
std::string	seqy_
std::vector< int >	secx_
std::vector< int >	secy_
std::vector < numeric::xyzVector < core::Real > >	r1_
std::vector < numeric::xyzVector < core::Real > >	r2_
numeric::xyzVector< core::Real >	t_
numeric::xyzMatrix< core::Real >	u_
int	n_ali8_
std::vector< int >	m1_
std::vector< int >	m2_
double	d0_out_
double	d0A_
double	d0B_

Constructor & Destructor Documentation

protocols::hybridization::TMalign::TMalign

(

)

Member Function Documentation

void protocols::hybridization::TMalign::alignment2AtomMap	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::id::AtomID_Map< core::id::AtomID > &	atom_map
	)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), alignment2AtomMap(), protocols::hybridization::DomainAssembly::run(), and protocols::hybridization::TMalign_poses().

void protocols::hybridization::TMalign::alignment2AtomMap	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size &	n_mapped_residues,
		core::id::AtomID_Map< core::id::AtomID > &	atom_map
	)

References alignment2AtomMap(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

void protocols::hybridization::TMalign::alignment2AtomMap	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	ref_pose,
		std::list< core::Size > const &	residue_list,
		std::list< core::Size > const &	ref_residue_list,
		core::Size &	n_mapped_residues,
		core::id::AtomID_Map< core::id::AtomID > &	atom_map
	)

References core::chemical::ResidueType::atom_index(), d0_out_, dist(), do_rotation(), m1_, m2_, n_ali8_, core::pose::Pose::residue_type(), t_, u_, xa_, xlen_, xt_, and ya_.

void protocols::hybridization::TMalign::alignment2strings	(	std::string &	seqxA,
		std::string &	seqyA,
		std::string &	seqM
	)

References d0_out_, dist(), do_rotation(), m1_, m2_, n_ali8_, seqx_, seqy_, t_, u_, xa_, xlen_, xt_, ya_, and ylen_.

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::DomainAssembly::run(), and protocols::hybridization::TMalign_poses().

int protocols::hybridization::TMalign::apply	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

References core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::DomainAssembly::run(), and protocols::hybridization::TMalign_poses().

int protocols::hybridization::TMalign::apply	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< core::Size >	residue_list1,
		std::list< core::Size >	residue_list2
	)

References d0_, d0_out_, d0A_, d0B_, detailed_search(), dist(), do_rotation(), DP_iter(), get_initial(), get_initial_fgt(), get_initial_local(), get_initial_ss(), get_initial_ssplus(), Lnorm_, load_pose_allocate_memory(), m1_, m2_, n_ali8_, parameter_set4final(), parameter_set4search(), score_d8_, t_, u_, xa_, xlen_, xresno_, xt_, xtm_, ya_, ylen_, yresno_, and ytm_.

void protocols::hybridization::TMalign::convert_matrix_to_xyz	(	std::vector< std::vector< core::Real > > const &	x,
		numeric::xyzMatrix< core::Real > &	xx
	)

Referenced by Kabsch().

void protocols::hybridization::TMalign::convert_vector_to_xyz	(	std::vector< core::Real > const &	x,
		numeric::xyzVector< core::Real > &	xx
	)

Referenced by Kabsch().

void protocols::hybridization::TMalign::convert_xyz_to_matrix	(	numeric::xyzMatrix< core::Real > const &	x,
		std::vector< std::vector< core::Real > > &	xx
	)

Referenced by Kabsch().

void protocols::hybridization::TMalign::convert_xyz_to_vector	(	numeric::xyzVector< core::Real > const &	x,
		std::vector< core::Real > &	xx
	)

Referenced by convert_xyz_v_to_vectors(), and Kabsch().

void protocols::hybridization::TMalign::convert_xyz_v_to_vectors	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< std::vector< double > > &	xx
	)

References convert_xyz_to_vector().

Referenced by Kabsch().

double protocols::hybridization::TMalign::detailed_search	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	,
		int const	y_len,
		std::vector< int > const &	invmap0,
		numeric::xyzVector< core::Real > &	t,
		numeric::xyzMatrix< core::Real > &	u,
		int	simplify_step,
		int	score_sum_method
	)

References TMscore8_search(), xtm_, and ytm_.

Referenced by apply().

double protocols::hybridization::TMalign::dist	(	numeric::xyzVector< core::Real >	x,
		numeric::xyzVector< core::Real >	y
	)

Referenced by alignment2AtomMap(), alignment2strings(), apply(), find_max_frag(), get_score_fast(), make_sec(), NWDP_TM(), score_fun8(), score_matrix_rmsd(), and score_matrix_rmsd_sec().

void protocols::hybridization::TMalign::do_rotation	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > &	x1,
		int	len,
		numeric::xyzVector< core::Real > const &	t,
		numeric::xyzMatrix< core::Real > const &	u
	)

References transform().

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and TMscore8_search().

double protocols::hybridization::TMalign::DP_iter	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		numeric::xyzVector< core::Real >	t,
		numeric::xyzMatrix< core::Real >	u,
		std::vector< int > &	invmap0,
		int const	g1,
		int const	g2,
		int const	iteration_max
	)

References d0_, NWDP_TM(), TMscore8_search(), xtm_, and ytm_.

Referenced by apply().

void protocols::hybridization::TMalign::find_max_frag	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< int > const &	resno,
		int const	len,
		int *	start_max,
		int *	end_max
	)

References protocols::hybridization::dcu0, dcu0_, dist(), and protocols::loops::start.

Referenced by get_initial_fgt().

double protocols::hybridization::TMalign::get_initial	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > &	y2x
	)

References get_score_fast(), and getmin.

Referenced by apply().

double protocols::hybridization::TMalign::get_initial_fgt	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > const &	xresno,
		std::vector< int > const &	yresno,
		std::vector< int > &	y2x
	)

References find_max_frag(), get_score_fast(), and getmin.

Referenced by apply().

bool protocols::hybridization::TMalign::get_initial_local	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > &	y2x
	)

References d0_, D0_MIN_, get_score_fast(), getmin, Kabsch(), NWDP_TM(), r1_, r2_, protocols::hybridization::t, and protocols::hybridization::u.

Referenced by apply().

void protocols::hybridization::TMalign::get_initial_ss	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > &	y2x
	)

References make_sec(), NWDP_TM(), secx_, and secy_.

Referenced by apply().

void protocols::hybridization::TMalign::get_initial_ssplus	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > &	y2x0,
		std::vector< int > &	y2x
	)

References NWDP_TM(), and score_matrix_rmsd_sec().

Referenced by apply().

double protocols::hybridization::TMalign::get_score_fast	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	,
		int const	y_len,
		std::vector< int > const &	invmap
	)

References d0_, d0_search_, dist(), Kabsch(), PrintErrorAndQuit(), r1_, r2_, core::scoring::rms, t_, transform(), u_, xtm_, and ytm_.

Referenced by get_initial(), get_initial_fgt(), and get_initial_local().

const numeric::xyzVector<core::Real>& protocols::hybridization::TMalign::get_t ( ) const

inline

References t_.

const numeric::xyzMatrix<core::Real>& protocols::hybridization::TMalign::get_u ( ) const

inline

References u_.

bool protocols::hybridization::TMalign::Kabsch	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	n,
		int const	mode,
		double *	rms,
		numeric::xyzVector< core::Real > &	t,
		numeric::xyzMatrix< core::Real > &	u
	)

References convert_matrix_to_xyz(), convert_vector_to_xyz(), convert_xyz_to_matrix(), convert_xyz_to_vector(), convert_xyz_v_to_vectors(), and core::pack::tt().

Referenced by get_initial_local(), get_score_fast(), score_matrix_rmsd(), score_matrix_rmsd_sec(), and TMscore8_search().

bool protocols::hybridization::TMalign::Kabsch	(	std::vector< std::vector< double > > const &	x,
		std::vector< std::vector< double > > const &	y,
		int const	n,
		int const	mode,
		double *	rms,
		std::vector< double > &	t,
		std::vector< std::vector< double > > &	u
	)

References core::pose::motif::a(), protocols::match::upstream::b, and protocols::hybridization::u.

void protocols::hybridization::TMalign::load_pose_allocate_memory	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::list< core::Size > &	residue_list1,
		std::list< core::Size > &	residue_list2
	)

References minlen_, path_, r1_, r2_, read_pose(), ResizeArray(), score_, secx_, secy_, seqx_, seqy_, val_, xa_, xlen_, xresno_, xt_, xtm_, ya_, ylen_, yresno_, and ytm_.

Referenced by apply().

void protocols::hybridization::TMalign::make_sec	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		int const	len,
		std::vector< int > &	sec
	)

References dist(), sec_str(), and smooth().

Referenced by get_initial_ss().

void protocols::hybridization::TMalign::NWDP_TM	(	core::Size const	len1,
		core::Size const	len2,
		double const	gap_open,
		std::vector< int > &	j2i
	)

References path_, score_, and val_.

Referenced by DP_iter(), get_initial_local(), get_initial_ss(), and get_initial_ssplus().

void protocols::hybridization::TMalign::NWDP_TM	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	len1,
		int const	len2,
		numeric::xyzVector< core::Real > const &	t,
		numeric::xyzMatrix< core::Real > const &	u,
		double	d02,
		double	gap_open,
		std::vector< int > &	j2i
	)

References dist(), path_, transform(), and val_.

void protocols::hybridization::TMalign::NWDP_TM	(	std::vector< int > const &	secx,
		std::vector< int > const &	secy,
		int const	len1,
		int const	len2,
		double	gap_open,
		std::vector< int > &	j2i
	)

References path_, and val_.

void protocols::hybridization::TMalign::parameter_set4final

(

double

len

)

References d0_, D0_MIN_, d0_search_, and Lnorm_.

Referenced by apply(), and TMscore().

void protocols::hybridization::TMalign::parameter_set4scale	(	int	len,
		double	d_s
	)

References d0_, d0_search_, and Lnorm_.

void protocols::hybridization::TMalign::parameter_set4search	(	int	xlen,
		int	ylen
	)

References d0_, D0_MIN_, d0_search_, dcu0_, getmin, Lnorm_, and score_d8_.

Referenced by apply().

void protocols::hybridization::TMalign::PrintErrorAndQuit

(

std::string

sErrorString

)

Referenced by get_score_fast().

int protocols::hybridization::TMalign::read_pose	(	core::pose::Pose const &	pose,
		std::list< core::Size > const &	residue_list,
		std::vector< numeric::xyzVector< core::Real > > &	a,
		std::string &	seq,
		std::vector< int > &	resno
	)

References core::pose::motif::a(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::name1(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::conformation::Residue::xyz().

Referenced by load_pose_allocate_memory().

template<class A >

void protocols::hybridization::TMalign::ResizeArray	(	A &	array,
		int	Narray1,
		int	Narray2
	)

Referenced by load_pose_allocate_memory().

int protocols::hybridization::TMalign::score_fun8	(	std::vector< numeric::xyzVector< core::Real > > const &	xa,
		std::vector< numeric::xyzVector< core::Real > > const &	ya,
		int const	n_ali,
		double const	d,
		std::vector< int > &	i_ali,
		double *	score1,
		int	score_sum_method
	)

References d0_, dist(), Lnorm_, score_d8_, protocols::hybridization::xa, and protocols::hybridization::ya.

Referenced by TMscore8_search().

void protocols::hybridization::TMalign::score_matrix_rmsd	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > const &	y2x
	)

References d0_, D0_MIN_, dist(), Kabsch(), r1_, r2_, score_, protocols::hybridization::t, transform(), and protocols::hybridization::u.

void protocols::hybridization::TMalign::score_matrix_rmsd_sec	(	std::vector< numeric::xyzVector< core::Real > > const &	x,
		std::vector< numeric::xyzVector< core::Real > > const &	y,
		int const	x_len,
		int const	y_len,
		std::vector< int > const &	y2x
	)

References d0_, D0_MIN_, dist(), Kabsch(), r1_, r2_, score_, secx_, secy_, protocols::hybridization::t, transform(), and protocols::hybridization::u.

Referenced by get_initial_ssplus().

int protocols::hybridization::TMalign::sec_str	(	double	dis13,
		double	dis14,
		double	dis15,
		double	dis24,
		double	dis25,
		double	dis35
	)

Referenced by make_sec().

void protocols::hybridization::TMalign::smooth	(	std::vector< int > &	sec,
		int const	len
	)

Referenced by make_sec().

core::Real protocols::hybridization::TMalign::TMscore

(

core::Size

length

)

References d0_, d0_out_, d0A_, n_ali8_, parameter_set4final(), t_, TMscore8_search(), u_, xtm_, and ytm_.

Referenced by protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::hybridization::DomainAssembly::run(), and protocols::hybridization::TMalign_poses().

double protocols::hybridization::TMalign::TMscore8_search	(	std::vector< numeric::xyzVector< core::Real > > const &	xtm,
		std::vector< numeric::xyzVector< core::Real > > const &	ytm,
		int	Lali,
		numeric::xyzVector< core::Real > &	t0,
		numeric::xyzMatrix< core::Real > &	u0,
		int const	simplify_step,
		int const	score_sum_method,
		double *	Rcomm
	)

References d0_search_, do_rotation(), Kabsch(), r1_, r2_, protocols::hybridization::score, score_fun8(), protocols::hybridization::t, protocols::hybridization::u, xt_, protocols::hybridization::xtm, and protocols::hybridization::ytm.

Referenced by detailed_search(), DP_iter(), and TMscore().

void protocols::hybridization::TMalign::transform	(	numeric::xyzVector< core::Real > const &	t,
		numeric::xyzMatrix< core::Real > const &	u,
		numeric::xyzVector< core::Real >	x,
		numeric::xyzVector< core::Real > &	x1
	)

Referenced by do_rotation(), get_score_fast(), NWDP_TM(), score_matrix_rmsd(), and score_matrix_rmsd_sec().

Member Data Documentation

double protocols::hybridization::TMalign::d0_

private

Referenced by apply(), DP_iter(), get_initial_local(), get_score_fast(), parameter_set4final(), parameter_set4scale(), parameter_set4search(), score_fun8(), score_matrix_rmsd(), score_matrix_rmsd_sec(), and TMscore().

double protocols::hybridization::TMalign::D0_MIN_

private

Referenced by get_initial_local(), parameter_set4final(), parameter_set4search(), score_matrix_rmsd(), and score_matrix_rmsd_sec().

double protocols::hybridization::TMalign::d0_out_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and TMscore().

double protocols::hybridization::TMalign::d0_search_

private

Referenced by get_score_fast(), parameter_set4final(), parameter_set4scale(), parameter_set4search(), and TMscore8_search().

double protocols::hybridization::TMalign::d0A_

private

Referenced by apply(), and TMscore().

double protocols::hybridization::TMalign::d0B_

private

Referenced by apply().

double protocols::hybridization::TMalign::dcu0_

private

Referenced by find_max_frag(), and parameter_set4search().

double protocols::hybridization::TMalign::Lnorm_

private

Referenced by apply(), parameter_set4final(), parameter_set4scale(), parameter_set4search(), and score_fun8().

std::vector< int > protocols::hybridization::TMalign::m1_

private

Referenced by alignment2AtomMap(), alignment2strings(), and apply().

std::vector< int > protocols::hybridization::TMalign::m2_

private

Referenced by alignment2AtomMap(), alignment2strings(), and apply().

int protocols::hybridization::TMalign::minlen_

private

Referenced by load_pose_allocate_memory().

int protocols::hybridization::TMalign::n_ali8_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and TMscore().

std::vector< std::vector < bool > > protocols::hybridization::TMalign::path_

private

Referenced by load_pose_allocate_memory(), and NWDP_TM().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::r1_

private

Referenced by get_initial_local(), get_score_fast(), load_pose_allocate_memory(), score_matrix_rmsd(), score_matrix_rmsd_sec(), and TMscore8_search().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::r2_

private

Referenced by get_initial_local(), get_score_fast(), load_pose_allocate_memory(), score_matrix_rmsd(), score_matrix_rmsd_sec(), and TMscore8_search().

std::vector< std::vector < double > > protocols::hybridization::TMalign::score_

private

Referenced by load_pose_allocate_memory(), NWDP_TM(), score_matrix_rmsd(), and score_matrix_rmsd_sec().

double protocols::hybridization::TMalign::score_d8_

private

Referenced by apply(), parameter_set4search(), and score_fun8().

std::vector< int > protocols::hybridization::TMalign::secx_

private

Referenced by get_initial_ss(), load_pose_allocate_memory(), and score_matrix_rmsd_sec().

std::vector< int > protocols::hybridization::TMalign::secy_

private

Referenced by get_initial_ss(), load_pose_allocate_memory(), and score_matrix_rmsd_sec().

std::string protocols::hybridization::TMalign::seqx_

private

Referenced by alignment2strings(), and load_pose_allocate_memory().

std::string protocols::hybridization::TMalign::seqy_

private

Referenced by alignment2strings(), and load_pose_allocate_memory().

numeric::xyzVector<core::Real> protocols::hybridization::TMalign::t_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), get_score_fast(), get_t(), and TMscore().

numeric::xyzMatrix<core::Real> protocols::hybridization::TMalign::u_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), get_score_fast(), get_u(), and TMscore().

std::vector< std::vector < double > > protocols::hybridization::TMalign::val_

private

Referenced by load_pose_allocate_memory(), and NWDP_TM().

std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::TMalign::xa_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and load_pose_allocate_memory().

int protocols::hybridization::TMalign::xlen_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and load_pose_allocate_memory().

std::vector< int > protocols::hybridization::TMalign::xresno_

private

Referenced by apply(), and load_pose_allocate_memory().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::xt_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), load_pose_allocate_memory(), and TMscore8_search().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::xtm_

private

Referenced by apply(), detailed_search(), DP_iter(), get_score_fast(), load_pose_allocate_memory(), and TMscore().

std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::TMalign::ya_

private

Referenced by alignment2AtomMap(), alignment2strings(), apply(), and load_pose_allocate_memory().

int protocols::hybridization::TMalign::ylen_

private

Referenced by alignment2strings(), apply(), and load_pose_allocate_memory().

std::vector< int > protocols::hybridization::TMalign::yresno_

private

Referenced by apply(), and load_pose_allocate_memory().

std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::ytm_

private

Referenced by apply(), detailed_search(), DP_iter(), get_score_fast(), load_pose_allocate_memory(), and TMscore().

---

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

• src/protocols/hybridization/TMalign.hh
• src/protocols/hybridization/TMalign.cc