Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::hybridization::TMalign Class Reference

#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< intxresno
 
std::vector< intyresno
 
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< intsecx
 
std::vector< intsecy
 
std::vector
< numeric::xyzVector
< core::Real > > 
r1
 
std::vector
< numeric::xyzVector
< core::Real > > 
r2
 
numeric::xyzVector< core::Realt
 
numeric::xyzMatrix< core::Realu
 
int n_ali8_
 
std::vector< intm1_
 
std::vector< intm2_
 
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
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
void protocols::hybridization::TMalign::alignment2strings ( std::string seqxA,
std::string seqyA,
std::string seqM 
)
inline
int protocols::hybridization::TMalign::apply ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)
inline
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
void protocols::hybridization::TMalign::convert_matrix_to_xyz ( std::vector< std::vector< core::Real > > const  x,
numeric::xyzMatrix< core::Real > &  xx 
)
inline

Referenced by Kabsch().

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

Referenced by Kabsch().

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

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 
)
inline

References d0, D0_MIN, get_score_fast(), getmin, 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
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
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
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
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(), 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 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
template<class A >
void protocols::hybridization::TMalign::ResizeArray ( A &  array,
int  Narray1,
int  Narray2 
)
inline
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(), 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(), 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

Referenced by make_sec().

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

Member Data Documentation

bool protocols::hybridization::TMalign::a_opt
private
double protocols::hybridization::TMalign::d0
private
double protocols::hybridization::TMalign::D0_MIN
private
double protocols::hybridization::TMalign::d0_out_
private
double protocols::hybridization::TMalign::d0_scale
private
double protocols::hybridization::TMalign::d0_search
private
double protocols::hybridization::TMalign::d0A
private

Referenced by apply(), and TMscore().

double protocols::hybridization::TMalign::d0a
private
double protocols::hybridization::TMalign::d0B
private

Referenced by apply().

double protocols::hybridization::TMalign::d0u
private
bool protocols::hybridization::TMalign::d_opt
private
double protocols::hybridization::TMalign::dcu0
private
double protocols::hybridization::TMalign::Lnorm
private
double protocols::hybridization::TMalign::Lnorm_ass
private
double protocols::hybridization::TMalign::Lnorm_d0
private
std::vector< int > protocols::hybridization::TMalign::m1_
private
std::vector< int > protocols::hybridization::TMalign::m2_
private
int protocols::hybridization::TMalign::minlen
private
int protocols::hybridization::TMalign::n_ali8_
private
bool protocols::hybridization::TMalign::o_opt
private
std::vector< std::vector < bool > > protocols::hybridization::TMalign::path
private
std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::r1
private
std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::r2
private
std::vector< std::vector < double > > protocols::hybridization::TMalign::score
private
double protocols::hybridization::TMalign::score_d8
private
std::vector< int > protocols::hybridization::TMalign::secx
private
std::vector< int > protocols::hybridization::TMalign::secy
private
std::string protocols::hybridization::TMalign::seqx
private
std::string protocols::hybridization::TMalign::seqy
private
numeric::xyzVector<core::Real> protocols::hybridization::TMalign::t
private
double protocols::hybridization::TMalign::TM3
private
double protocols::hybridization::TMalign::TM4
private
double protocols::hybridization::TMalign::TM5
private
numeric::xyzMatrix<core::Real> protocols::hybridization::TMalign::u
private
bool protocols::hybridization::TMalign::u_opt
private
bool protocols::hybridization::TMalign::v_opt
private
std::vector< std::vector < double > > protocols::hybridization::TMalign::val
private
char protocols::hybridization::TMalign::version[20]
private
std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::TMalign::xa
private
int protocols::hybridization::TMalign::xlen
private
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
std::vector< numeric::xyzVector <core::Real> > protocols::hybridization::TMalign::xtm
private
std::vector< numeric::xyzVector<core::Real> > protocols::hybridization::TMalign::ya
private
int protocols::hybridization::TMalign::ylen
private
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

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