#include <TMalign.hh>

Public Member Functions
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 (Size const len1, 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 pose1, core::pose::Pose 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::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 (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)

Private Attributes
char	version [20]

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	Lnorm_ass

double	Lnorm_d0

double	d0_scale

double	d0A

double	d0B

double	d0u

double	d0a

bool	o_opt

bool	a_opt

bool	u_opt

bool	d_opt

bool	v_opt

double	TM3

double	TM4

double	TM5

Member Function Documentation

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
	)

inline

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

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

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
	)

inline

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
	)

inline

References d0_out_, dist(), do_rotation(), j, m1_, m2_, n_ali8_, seqx, seqy, t, u, xa, xlen, xt, ya, and ylen.

Referenced by protocols::hybridization::HybridizeSetup::align_by_domain(), 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
	)

inline

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

Referenced by protocols::hybridization::HybridizeSetup::align_by_domain(), 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
	)

inline

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(), j, 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
	)

inline

References j.

Referenced by Kabsch().

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

inline

References numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by Kabsch().

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

inline

References j.

Referenced by Kabsch().

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

inline

References numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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
	)

inline

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
	)

inline

References j, rmsd, TMscore8_search(), xtm, and ytm.

Referenced by apply().

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

inline

References numeric::xyzVector< class >::distance().

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
	)

inline

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
	)

inline

References d0, j, NWDP_TM(), rmsd, 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
	)

inline

References dcu0, dist(), j, 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
	)

inline

References get_score_fast(), getmin, and j.

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
	)

inline

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

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
	)

inline

References d0, D0_MIN, get_score_fast(), getmin, j, Kabsch(), NWDP_TM(), r1, r2, rmsd, t, and 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
	)

inline

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
	)

inline

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
	)

inline

References d0, d0_search, dist(), j, Kabsch(), PrintErrorAndQuit(), r1, r2, rms, t, transform(), u, xtm, and ytm.

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

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
	)

inline

References convert_matrix_to_xyz(), convert_vector_to_xyz(), convert_xyz_to_matrix(), convert_xyz_to_vector(), convert_xyz_v_to_vectors(), and protocols::loops::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
	)

inline

References protocols::match::upstream::b, epsilon, j, l, ss, and u.

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

inline

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
	)

inline

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

Referenced by get_initial_ss().

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

inline

References j, 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
	)

inline

References dist(), j, 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
	)

inline

References j, path, and val.

void protocols::hybridization::TMalign::parameter_set4final ( double len )

inline

References d0, D0_MIN, d0_search, and Lnorm.

Referenced by apply(), and TMscore().

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

inline

References d0, d0_search, and Lnorm.

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

inline

References d0, D0_MIN, d0_search, dcu0, getmin, Lnorm, and score_d8.

Referenced by apply().

void protocols::hybridization::TMalign::PrintErrorAndQuit ( std::string sErrorString )

inline

References exit.

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
	)

inline

References 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
	)

inline

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
	)

inline

References d0, dist(), Lnorm, score_d8, xa, and 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
	)

inline

References d0, D0_MIN, dist(), j, Kabsch(), r1, r2, rmsd, score, t, transform(), and 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
	)

inline

References d0, D0_MIN, dist(), j, Kabsch(), r1, r2, rmsd, score, secx, secy, t, transform(), and u.

Referenced by get_initial_ssplus().

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

inline

References s.

Referenced by make_sec().

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

inline

References j.

Referenced by make_sec().

core::Real protocols::hybridization::TMalign::TMscore ( Size length )

inline

References d0, d0_out_, d0A, n_ali8_, parameter_set4final(), rmsd, t, TMscore8_search(), u, xtm, and ytm.

Referenced by protocols::hybridization::HybridizeSetup::align_by_domain(), 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
	)

inline

References d0_search, do_rotation(), Kabsch(), r1, r2, rmsd, score, score_fun8(), t, u, xt, xtm, and 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
	)