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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)
 
core::Real 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, core::Real 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, core::Real d02, core::Real 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, core::Real gap_open, std::vector< int > &j2i)
 
void convert_xyz_to_vector (numeric::xyzVector< core::Real > const &x, std::vector< core::Real > &xx)
 
void resize_for_xyz_matrix (std::vector< 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< core::Real > > &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, core::Real *rms, numeric::xyzVector< core::Real > &t, numeric::xyzMatrix< core::Real > &u)
 
bool Kabsch (std::vector< std::vector< core::Real > > const &x, std::vector< std::vector< core::Real > > const &y, int const n, int const mode, core::Real *rms, std::vector< core::Real > &t, std::vector< std::vector< core::Real > > &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, core::Real const d, std::vector< int > &i_ali, core::Real *score1, int score_sum_method)
 
core::Real 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, core::Real *Rcomm)
 
core::Real 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)
 
core::Real 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)
 
core::Real 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 (core::Real dis13, core::Real dis14, core::Real dis15, core::Real dis24, core::Real dis25, core::Real 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)
 
core::Real 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)
 
core::Real 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 (core::Real len)
 
void parameter_set4scale (int len, core::Real 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

core::Real D0_MIN_
 
core::Real Lnorm_
 
core::Real score_d8_
 
core::Real d0_
 
core::Real d0_search_
 
core::Real dcu0_
 
std::vector< std::vector
< core::Real > > 
score_
 
std::vector< std::vector< bool > > path_
 
std::vector< std::vector
< core::Real > > 
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::Realt_
 
numeric::xyzMatrix< core::Realu_
 
int n_ali8_
 
std::vector< int > m1_
 
std::vector< int > m2_
 
core::Real d0_out_
 
core::Real d0A_
 
core::Real d0B_
 

Constructor & Destructor Documentation

protocols::hybridization::TMalign::TMalign ( )
default

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 
)
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 
)
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 
)
void protocols::hybridization::TMalign::alignment2strings ( std::string &  seqxA,
std::string &  seqyA,
std::string &  seqM 
)
int protocols::hybridization::TMalign::apply ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
)
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 
)
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 
)
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< core::Real > > &  xx 
)

References convert_xyz_to_vector().

Referenced by Kabsch().

core::Real 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().

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

core::Real 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 
)
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 
)
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().

core::Real 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 
)
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,
core::Real rms,
numeric::xyzVector< core::Real > &  t,
numeric::xyzMatrix< core::Real > &  u 
)
bool protocols::hybridization::TMalign::Kabsch ( std::vector< std::vector< core::Real > > const &  x,
std::vector< std::vector< core::Real > > const &  y,
int const  n,
int const  mode,
core::Real rms,
std::vector< core::Real > &  t,
std::vector< std::vector< core::Real > > &  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 
)
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,
core::Real const  gap_open,
std::vector< int > &  j2i 
)
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,
core::Real  d02,
core::Real  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,
core::Real  gap_open,
std::vector< int > &  j2i 
)

References path_, and val_.

void protocols::hybridization::TMalign::parameter_set4final ( core::Real  len)

References d0_, D0_MIN_, d0_search_, and Lnorm_.

Referenced by apply(), and TMscore().

void protocols::hybridization::TMalign::parameter_set4scale ( int  len,
core::Real  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 
)
void protocols::hybridization::TMalign::resize_for_xyz_matrix ( std::vector< std::vector< core::Real > > &  xx)

Referenced by Kabsch().

template<class A >
void protocols::hybridization::TMalign::ResizeArray ( A array,
int  Narray1,
int  Narray2 
)
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,
core::Real const  d,
std::vector< int > &  i_ali,
core::Real score1,
int  score_sum_method 
)
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 
)
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 
)
int protocols::hybridization::TMalign::sec_str ( core::Real  dis13,
core::Real  dis14,
core::Real  dis15,
core::Real  dis24,
core::Real  dis25,
core::Real  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)
core::Real 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,
core::Real Rcomm 
)
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 
)

Member Data Documentation

core::Real protocols::hybridization::TMalign::d0_
private
core::Real protocols::hybridization::TMalign::D0_MIN_
private
core::Real protocols::hybridization::TMalign::d0_out_
private
core::Real protocols::hybridization::TMalign::d0_search_
private
core::Real protocols::hybridization::TMalign::d0A_
private

Referenced by apply(), and TMscore().

core::Real protocols::hybridization::TMalign::d0B_
private

Referenced by apply().

core::Real protocols::hybridization::TMalign::dcu0_
private
core::Real protocols::hybridization::TMalign::Lnorm_
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
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 < core::Real > > protocols::hybridization::TMalign::score_
private
core::Real 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
numeric::xyzMatrix<core::Real> protocols::hybridization::TMalign::u_
private
std::vector< std::vector < core::Real > > protocols::hybridization::TMalign::val_
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 files: