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protocols::hybridization::TMalign Member List

This is the complete list of members for protocols::hybridization::TMalign, including all inherited members.

alignment2AtomMap(core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::id::AtomID_Map< core::id::AtomID > &atom_map)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)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)protocols::hybridization::TMalign
alignment2strings(std::string &seqxA, std::string &seqyA, std::string &seqM)protocols::hybridization::TMalign
apply(core::pose::Pose const &pose1, core::pose::Pose const &pose2)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)protocols::hybridization::TMalign
convert_matrix_to_xyz(std::vector< std::vector< core::Real > > const &x, numeric::xyzMatrix< core::Real > &xx)protocols::hybridization::TMalign
convert_vector_to_xyz(std::vector< core::Real > const &x, numeric::xyzVector< core::Real > &xx)protocols::hybridization::TMalign
convert_xyz_to_matrix(numeric::xyzMatrix< core::Real > const &x, std::vector< std::vector< core::Real > > &xx)protocols::hybridization::TMalign
convert_xyz_to_vector(numeric::xyzVector< core::Real > const &x, std::vector< core::Real > &xx)protocols::hybridization::TMalign
convert_xyz_v_to_vectors(std::vector< numeric::xyzVector< core::Real > > const &x, std::vector< std::vector< core::Real > > &xx)protocols::hybridization::TMalign
d0_protocols::hybridization::TMalignprivate
D0_MIN_protocols::hybridization::TMalignprivate
d0_out_protocols::hybridization::TMalignprivate
d0_search_protocols::hybridization::TMalignprivate
d0A_protocols::hybridization::TMalignprivate
d0B_protocols::hybridization::TMalignprivate
dcu0_protocols::hybridization::TMalignprivate
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)protocols::hybridization::TMalign
dist(numeric::xyzVector< core::Real > x, numeric::xyzVector< core::Real > y)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)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)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)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)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)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)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)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)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)protocols::hybridization::TMalign
get_t() const protocols::hybridization::TMaligninline
get_u() const protocols::hybridization::TMaligninline
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)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)protocols::hybridization::TMalign
Lnorm_protocols::hybridization::TMalignprivate
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)protocols::hybridization::TMalign
m1_protocols::hybridization::TMalignprivate
m2_protocols::hybridization::TMalignprivate
make_sec(std::vector< numeric::xyzVector< core::Real > > const &x, int const len, std::vector< int > &sec)protocols::hybridization::TMalign
minlen_protocols::hybridization::TMalignprivate
n_ali8_protocols::hybridization::TMalignprivate
NWDP_TM(core::Size const len1, core::Size const len2, core::Real const gap_open, std::vector< int > &j2i)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)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)protocols::hybridization::TMalign
parameter_set4final(core::Real len)protocols::hybridization::TMalign
parameter_set4scale(int len, core::Real d_s)protocols::hybridization::TMalign
parameter_set4search(int xlen, int ylen)protocols::hybridization::TMalign
path_protocols::hybridization::TMalignprivate
PrintErrorAndQuit(std::string sErrorString)protocols::hybridization::TMalign
r1_protocols::hybridization::TMalignprivate
r2_protocols::hybridization::TMalignprivate
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)protocols::hybridization::TMalign
resize_for_xyz_matrix(std::vector< std::vector< core::Real > > &xx)protocols::hybridization::TMalign
ResizeArray(A &array, int Narray1, int Narray2)protocols::hybridization::TMalign
score_protocols::hybridization::TMalignprivate
score_d8_protocols::hybridization::TMalignprivate
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)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)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)protocols::hybridization::TMalign
sec_str(core::Real dis13, core::Real dis14, core::Real dis15, core::Real dis24, core::Real dis25, core::Real dis35)protocols::hybridization::TMalign
secx_protocols::hybridization::TMalignprivate
secy_protocols::hybridization::TMalignprivate
seqx_protocols::hybridization::TMalignprivate
seqy_protocols::hybridization::TMalignprivate
smooth(std::vector< int > &sec, int const len)protocols::hybridization::TMalign
t_protocols::hybridization::TMalignprivate
TMalign()protocols::hybridization::TMalign
TMscore(core::Size length)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)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)protocols::hybridization::TMalign
u_protocols::hybridization::TMalignprivate
val_protocols::hybridization::TMalignprivate
xa_protocols::hybridization::TMalignprivate
xlen_protocols::hybridization::TMalignprivate
xresno_protocols::hybridization::TMalignprivate
xt_protocols::hybridization::TMalignprivate
xtm_protocols::hybridization::TMalignprivate
ya_protocols::hybridization::TMalignprivate
ylen_protocols::hybridization::TMalignprivate
yresno_protocols::hybridization::TMalignprivate
ytm_protocols::hybridization::TMalignprivate
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