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Rosetta 3.5
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Rosetta 3.5
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This is the complete list of members for protocols::hybridization::TMalign, including all inherited members.
| a_opt | protocols::hybridization::TMalign | private |
| 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) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| alignment2strings(string &seqxA, string &seqyA, string &seqM) | protocols::hybridization::TMalign | inline |
| apply(core::pose::Pose const &pose1, core::pose::Pose const &pose2) | protocols::hybridization::TMalign | inline |
| apply(core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > residue_list1, std::list< core::Size > residue_list2) | protocols::hybridization::TMalign | inline |
| convert_matrix_to_xyz(vector< vector< core::Real > > const x, numeric::xyzMatrix< core::Real > &xx) | protocols::hybridization::TMalign | inline |
| convert_vector_to_xyz(vector< core::Real > const x, numeric::xyzVector< core::Real > &xx) | protocols::hybridization::TMalign | inline |
| convert_xyz_to_matrix(numeric::xyzMatrix< core::Real > const x, vector< vector< core::Real > > &xx) | protocols::hybridization::TMalign | inline |
| convert_xyz_to_vector(numeric::xyzVector< core::Real > const x, vector< core::Real > &xx) | protocols::hybridization::TMalign | inline |
| convert_xyz_v_to_vectors(vector< numeric::xyzVector< core::Real > > const x, vector< vector< double > > &xx) | protocols::hybridization::TMalign | inline |
| d0 | protocols::hybridization::TMalign | private |
| D0_MIN | protocols::hybridization::TMalign | private |
| d0_out_ | protocols::hybridization::TMalign | private |
| d0_scale | protocols::hybridization::TMalign | private |
| d0_search | protocols::hybridization::TMalign | private |
| d0A | protocols::hybridization::TMalign | private |
| d0a | protocols::hybridization::TMalign | private |
| d0B | protocols::hybridization::TMalign | private |
| d0u | protocols::hybridization::TMalign | private |
| d_opt | protocols::hybridization::TMalign | private |
| dcu0 | protocols::hybridization::TMalign | private |
| detailed_search(vector< numeric::xyzVector< core::Real > > const x, vector< numeric::xyzVector< core::Real > > const y, int const, int const y_len, vector< int > const invmap0, numeric::xyzVector< core::Real > &t, numeric::xyzMatrix< core::Real > &u, int simplify_step, int score_sum_method) | protocols::hybridization::TMalign | inline |
| dist(numeric::xyzVector< core::Real > x, numeric::xyzVector< core::Real > y) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| DP_iter(vector< numeric::xyzVector< core::Real > > const x, 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, vector< int > &invmap0, int const g1, int const g2, int const iteration_max) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| get_initial(vector< numeric::xyzVector< core::Real > > const x, vector< numeric::xyzVector< core::Real > > const y, int const x_len, int const y_len, vector< int > &y2x) | protocols::hybridization::TMalign | inline |
| 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, vector< int > const xresno, vector< int > const yresno, vector< int > &y2x) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| get_score_fast(vector< numeric::xyzVector< core::Real > > const x, vector< numeric::xyzVector< core::Real > > const y, int const , int const y_len, vector< int > const invmap) | protocols::hybridization::TMalign | inline |
| Kabsch(vector< numeric::xyzVector< core::Real > > const x, 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) | protocols::hybridization::TMalign | inline |
| Kabsch(vector< vector< double > > const x, vector< vector< double > > const y, int const n, int const mode, double *rms, vector< double > &t, vector< vector< double > > &u) | protocols::hybridization::TMalign | inline |
| Lnorm | protocols::hybridization::TMalign | private |
| Lnorm_ass | protocols::hybridization::TMalign | private |
| Lnorm_d0 | protocols::hybridization::TMalign | private |
| load_pose_allocate_memory(core::pose::Pose pose1, core::pose::Pose pose2, std::list< core::Size > residue_list1, std::list< core::Size > residue_list2) | protocols::hybridization::TMalign | inline |
| m1_ | protocols::hybridization::TMalign | private |
| m2_ | protocols::hybridization::TMalign | private |
| make_sec(std::vector< numeric::xyzVector< core::Real > > const x, int const len, vector< int > &sec) | protocols::hybridization::TMalign | inline |
| minlen | protocols::hybridization::TMalign | private |
| n_ali8_ | protocols::hybridization::TMalign | private |
| NWDP_TM(Size const len1, Size const len2, double const gap_open, vector< int > &j2i) | protocols::hybridization::TMalign | inline |
| 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, vector< int > &j2i) | protocols::hybridization::TMalign | inline |
| NWDP_TM(std::vector< int > const secx, std::vector< int > const secy, int const len1, int const len2, double gap_open, vector< int > &j2i) | protocols::hybridization::TMalign | inline |
| o_opt | protocols::hybridization::TMalign | private |
| parameter_set4final(double len) | protocols::hybridization::TMalign | inline |
| parameter_set4scale(int len, double d_s) | protocols::hybridization::TMalign | inline |
| parameter_set4search(int xlen, int ylen) | protocols::hybridization::TMalign | inline |
| path | protocols::hybridization::TMalign | private |
| PrintErrorAndQuit(string sErrorString) | protocols::hybridization::TMalign | inline |
| r1 | protocols::hybridization::TMalign | private |
| r2 | protocols::hybridization::TMalign | private |
| read_pose(core::pose::Pose const &pose, std::list< core::Size > const &residue_list, std::vector< numeric::xyzVector< core::Real > > &a, string &seq, std::vector< int > &resno) | protocols::hybridization::TMalign | inline |
| ResizeArray(A &array, int Narray1, int Narray2) | protocols::hybridization::TMalign | inline |
| score | protocols::hybridization::TMalign | private |
| score_d8 | protocols::hybridization::TMalign | private |
| score_fun8(vector< numeric::xyzVector< core::Real > > const xa, vector< numeric::xyzVector< core::Real > > const ya, int const n_ali, double const d, vector< int > &i_ali, double *score1, int score_sum_method) | protocols::hybridization::TMalign | inline |
| 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) | protocols::hybridization::TMalign | inline |
| score_matrix_rmsd_sec(vector< numeric::xyzVector< core::Real > > const x, vector< numeric::xyzVector< core::Real > > const y, int const x_len, int const y_len, vector< int > const y2x) | protocols::hybridization::TMalign | inline |
| sec_str(double dis13, double dis14, double dis15, double dis24, double dis25, double dis35) | protocols::hybridization::TMalign | inline |
| secx | protocols::hybridization::TMalign | private |
| secy | protocols::hybridization::TMalign | private |
| seqx | protocols::hybridization::TMalign | private |
| seqy | protocols::hybridization::TMalign | private |
| smooth(vector< int > &sec, int const len) | protocols::hybridization::TMalign | inline |
| t | protocols::hybridization::TMalign | private |
| TM3 | protocols::hybridization::TMalign | private |
| TM4 | protocols::hybridization::TMalign | private |
| TM5 | protocols::hybridization::TMalign | private |
| TMscore(Size length) | protocols::hybridization::TMalign | inline |
| TMscore8_search(vector< numeric::xyzVector< core::Real > > const xtm, 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) | protocols::hybridization::TMalign | inline |
| transform(numeric::xyzVector< core::Real > const t, numeric::xyzMatrix< core::Real > const u, numeric::xyzVector< core::Real > x, numeric::xyzVector< core::Real > &x1) | protocols::hybridization::TMalign | inline |
| u | protocols::hybridization::TMalign | private |
| u_opt | protocols::hybridization::TMalign | private |
| v_opt | protocols::hybridization::TMalign | private |
| val | protocols::hybridization::TMalign | private |
| version | protocols::hybridization::TMalign | private |
| xa | protocols::hybridization::TMalign | private |
| xlen | protocols::hybridization::TMalign | private |
| xresno | protocols::hybridization::TMalign | private |
| xt | protocols::hybridization::TMalign | private |
| xtm | protocols::hybridization::TMalign | private |
| ya | protocols::hybridization::TMalign | private |
| ylen | protocols::hybridization::TMalign | private |
| yresno | protocols::hybridization::TMalign | private |
| ytm | protocols::hybridization::TMalign | private |
1.8.4