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TCDock Struct Reference

Public Member Functions

 TCDock (Pose const &pose1, Pose const &pose2, string cmp1pdb, string cmp2pdb, string cmp1type, string cmp2type)
 
virtual ~TCDock ()
 
int num_threads ()
 
int thread_num ()
 
Vecf swap_axis (vector1< Vecf > &pts, string type)
 
Matf swap_axis_rotation (string type)
 
void precompute_intra ()
 
void dump_onecomp ()
 
void get_cmp1 (Real acmp1, vector1< Vecf > &pts, vector1< Vecf > &cbs)
 
void get_cmp2 (Real acmp2, vector1< Vecf > &pts, vector1< Vecf > &cbs)
 
void make_dimer (core::pose::Pose &pose)
 
void make_trimer (core::pose::Pose &pose)
 
void make_tetramer (core::pose::Pose &pose)
 
void make_pentamer (core::pose::Pose &pose)
 
void get_best_sub1_contact_delta_rotations (Real icmp1, Real dcmp1, Real icmp2, Real dcmp2, Real &out_delta_ang1, Real &out_delta_ang2)
 
void dump_pdb (int icmp2, int icmp1, int iori, string fname, int idx, bool dumpsym=true, bool sepcomp=true, bool termini=true)
 
Real __dock_base__ (int icmp2, int icmp1, int iori, Real &dori, Real &dcmp2, Real &dcmp1, Real &icbc, Real &cmp2cbc, Real &cmp1cbc, bool cache=true)
 
void dock_no_score (int icmp2, int icmp1, int iori)
 
Real dock_score (int icmp2, int icmp1, int iori, Real &icbc, Real &cmp2cbc, Real &cmp1cbc)
 
Real dock_score (int icmp2, int icmp1, int iori)
 
Real dock_get_geom (int icmp2, int icmp1, int iori, Real &dori, Real &dcmp2, Real &dcmp1, Real &icbc, Real &cmp2cbc, Real &cmp1cbc)
 
Real min_termini_dis (Real d1, Real a1, Real d2, Real a2)
 
Real min_termini_proj (Real a1, Real a2, Vec sicaxis)
 
Real termini_score (Real d1, Real a1, Real d2, Real a2)
 
void justone (int icmp1, int icmp2, int iori)
 
void run ()
 
Arch const & arch () const
 
 TCDock (ArchCOP _arch, Pose const &_pose1, Pose const &_pose2, string _cmp1pdb, string _cmp2pdb)
 
void init (bool reverse)
 
virtual ~TCDock ()
 
int num_threads ()
 
int thread_num ()
 
void precompute_intra ()
 
void dump_onecomp ()
 
void get_cmp1 (Real acmp1, vector1< Vec > &pts, vector1< Vec > &cbs)
 
void get_cmp2 (Real acmp2, vector1< Vec > &pts, vector1< Vec > &cbs)
 
void get_best_sub1_contact_delta_rotations (Real icmp1, Real dcmp1, Real icmp2, Real dcmp2, Real &out_delta_ang1, Real &out_delta_ang2)
 
void get_contacts_by_component (Real const &ang1, Real const &ang2, Real const &dis1, Real const &dis2, int &nresiface, int &nresiface0, int &nresiface1, int &nresiface2, int &ncontacts, int &ncontacts0, int &ncontacts1, int &ncontacts2, Real &nweighted, Real &nweighted0, Real &nweighted1, Real &nweighted2)
 
void dump_pdb (int icmp2, int icmp1, int iori, string fname, bool reverse, bool dumpsym)
 
Real __dock_base__ (int icmp2, int icmp1, int iori, Real &dori, Real &dcmp2, Real &dcmp1, Real &rscore, Real &cmp2cbc, Real &cmp1cbc, bool cache=true)
 
void dock_no_score (int icmp2, int icmp1, int iori)
 
Real dock_score (int icmp2, int icmp1, int iori, Real &rscore, Real &cmp2cbc, Real &cmp1cbc)
 
Real dock_score (int icmp2, int icmp1, int iori)
 
Real dock_get_geom (int icmp2, int icmp1, int iori, Real &dori, Real &dcmp2, Real &dcmp1, Real &rscore, Real &cmp2cbc, Real &cmp1cbc)
 
Real min_termini_dis (Real d1, Real a1, Real d2, Real a2)
 
Real min_termini_proj (Real a1, Real a2, Vec sicaxis)
 
Real termini_score (Real d1, Real a1, Real d2, Real a2, Real &td)
 
void run ()
 
void get_moments (vector1< Vec > const &pts, Real &m1, Real &m2, Real &m3, Real &m4)
 
void gather_hits (vector1< LMAX > &local_maxima, bool const &reverse)
 
void dump_top_hits (vector1< LMAX > &local_maxima)
 

Public Attributes

vector1< Real > cmp2mnpos_
 
vector1< Real > cmp1mnpos_
 
vector1< Real > cmp2mnneg_
 
vector1< Real > cmp1mnneg_
 
vector1< Real > cmp2dspos_
 
vector1< Real > cmp1dspos_
 
vector1< Real > cmp2dsneg_
 
vector1< Real > cmp1dsneg_
 
ObjexxFCL::FArray2D< Real > cmp2cbpos_
 
ObjexxFCL::FArray2D< Real > cmp1cbpos_
 
ObjexxFCL::FArray2D< Real > cmp2cbneg_
 
ObjexxFCL::FArray2D< Real > cmp1cbneg_
 
ObjexxFCL::FArray3D< Real > gradii
 
ObjexxFCL::FArray3D< Real > gscore
 
Vecf cmp1axs_
 
Vecf cmp2axs_
 
Real alpha_
 
Real sin_alpha_
 
Real tan_alpha_
 
Real cmp1diapos_
 
Real cmp1dianeg_
 
Real cmp2diapos_
 
Real cmp2dianeg_
 
Real cmp1scale_
 
Real cmp2scale_
 
core::pose::Pose cmp1in_
 
core::pose::Pose cmp2in_
 
vector1< Vecf > cmp1pts_
 
vector1< Vecf > cmp1cbs_
 
vector1< Vecf > cmp2pts_
 
vector1< Vecf > cmp2cbs_
 
vector1< Real > cmp1wts_
 
vector1< Real > cmp2wts_
 
core::id::AtomID_Map< Real > cmp1wtmap_
 
core::id::AtomID_Map< Real > cmp2wtmap_
 
string cmp1name_
 
string cmp2name_
 
string cmp1type_
 
string cmp2type_
 
string symtype_
 
int cmp1nangle_
 
int cmp2nangle_
 
int cmp1nsub_
 
int cmp2nsub_
 
std::map< string, Vecf > axismap_
 
protocols::sic_dock::SICFast sic_
 
bool abort_
 
core::id::AtomID_Map< core::Real > clashmap1_
 
core::id::AtomID_Map< core::Real > clashmap2_
 
protocols::sic_dock::RigidScoreCOP rigid_sfxn_
 
protocols::sic_dock::LinkerScoreCOP lnscore_
 
Size conf_count_
 
Real start_time_
 
core::pose::Pose cmp1olig_
 
core::pose::Pose cmp2olig_
 
core::pose::Pose const & cmp1_
 
core::pose::Pose const cmp2_
 
vector1< Vec > cmp1pts_
 
vector1< Vec > cmp1cbs_
 
vector1< Vec > cmp2pts_
 
vector1< Vec > cmp2cbs_
 
protocols::sic_dock::RigidScoreCOP final_sfxn_
 
protocols::sic_dock::scores::MotifHashRigidScoreCOP mhscore_
 
utility::io::ozstream * xform_out_
 

Private Attributes

ArchCOP arch_
 

Constructor & Destructor Documentation

◆ TCDock() [1/2]

TCDock::TCDock ( Pose const &  pose1,
Pose const &  pose2,
string  cmp1pdb,
string  cmp2pdb,
string  cmp1type,
string  cmp2type 
)
inline

References alignaxis(), angle_degrees(), basic::options::OptionKeys::sicdock::clash_dis, basic::options::OptionKeys::sicdock::contact_dis, utility::io::oc::cout, basic::options::OptionKeys::msd::debug, ObjexxFCL::FArray2D< T >::dimension(), ObjexxFCL::FArray3D< T >::dimension(), utility::file_basename(), create_a3b_hbs::i, create_a3b_hbs::j, max(), min(), neighbor_count(), numeric::xyzVector< T >::normalized(), num_threads(), basic::options::option, test.T008_Serialization::pose1, test.T008_Serialization::pose2, numeric::conversions::radians(), reverse(), rot_pose(), tan, thread_num(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, and orn_macrocycle::wt.

◆ ~TCDock() [1/2]

virtual TCDock::~TCDock ( )
inlinevirtual

◆ TCDock() [2/2]

TCDock::TCDock ( ArchCOP  _arch,
Pose const &  _pose1,
Pose const &  _pose2,
string  _cmp1pdb,
string  _cmp2pdb 
)
inline

References utility::io::oc::cout, utility::file_basename(), create_a3b_hbs::i, create_a3b_hbs::j, max(), num_threads(), out::file::o(), basic::options::option, option, ObjexxFCL::string_of(), thread_num(), basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

◆ ~TCDock() [2/2]

virtual TCDock::~TCDock ( )
inlinevirtual

Member Function Documentation

◆ __dock_base__() [1/2]

Real TCDock::__dock_base__ ( int  icmp2,
int  icmp1,
int  iori,
Real &  dori,
Real &  dcmp2,
Real &  dcmp1,
Real &  icbc,
Real &  cmp2cbc,
Real &  cmp1cbc,
bool  cache = true 
)
inline

References numeric::xyzVector< T >::cross(), loops::gamma, enumerate_junctions::int, min(), basic::options::option, numeric::conversions::radians(), numeric::rotation_matrix_degrees(), toXform(), utility_exit_with_message, w, x, predPRE::y, and predPRE::z.

◆ __dock_base__() [2/2]

Real TCDock::__dock_base__ ( int  icmp2,
int  icmp1,
int  iori,
Real &  dori,
Real &  dcmp2,
Real &  dcmp1,
Real &  rscore,
Real &  cmp2cbc,
Real &  cmp1cbc,
bool  cache = true 
)
inline

References docking::a1, docking::a2, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, min(), basic::options::option, option, numeric::xyzTransform< T >::R, numeric::rotation_matrix_degrees(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::scale, create_a3b_hbs::score, ObjexxFCL::string_of(), numeric::xyzTransform< T >::t, basic::options::OptionKeys::mp::transform::transform, and utility_exit_with_message.

◆ arch()

Arch const& TCDock::arch ( ) const
inline

◆ dock_get_geom() [1/2]

Real TCDock::dock_get_geom ( int  icmp2,
int  icmp1,
int  iori,
Real &  dori,
Real &  dcmp2,
Real &  dcmp1,
Real &  icbc,
Real &  cmp2cbc,
Real &  cmp1cbc 
)
inline

◆ dock_get_geom() [2/2]

Real TCDock::dock_get_geom ( int  icmp2,
int  icmp1,
int  iori,
Real &  dori,
Real &  dcmp2,
Real &  dcmp1,
Real &  rscore,
Real &  cmp2cbc,
Real &  cmp1cbc 
)
inline

◆ dock_no_score() [1/2]

void TCDock::dock_no_score ( int  icmp2,
int  icmp1,
int  iori 
)
inline

◆ dock_no_score() [2/2]

void TCDock::dock_no_score ( int  icmp2,
int  icmp1,
int  iori 
)
inline

◆ dock_score() [1/4]

Real TCDock::dock_score ( int  icmp2,
int  icmp1,
int  iori 
)
inline

◆ dock_score() [2/4]

Real TCDock::dock_score ( int  icmp2,
int  icmp1,
int  iori 
)
inline

◆ dock_score() [3/4]

Real TCDock::dock_score ( int  icmp2,
int  icmp1,
int  iori,
Real &  icbc,
Real &  cmp2cbc,
Real &  cmp1cbc 
)
inline

◆ dock_score() [4/4]

Real TCDock::dock_score ( int  icmp2,
int  icmp1,
int  iori,
Real &  rscore,
Real &  cmp2cbc,
Real &  cmp1cbc 
)
inline

◆ dump_onecomp() [1/2]

void TCDock::dump_onecomp ( )
inline

References utility::io::oc::cout, utility::file_basename(), create_a3b_hbs::i, out::file::o(), basic::options::option, erraser_single_res_analysis::out, and utility_exit_with_message.

◆ dump_onecomp() [2/2]

void TCDock::dump_onecomp ( )
inline

References utility::io::oc::cout, utility::file_basename(), create_a3b_hbs::i, out::file::o(), option, erraser_single_res_analysis::out, and utility_exit_with_message.

◆ dump_pdb() [1/2]

void TCDock::dump_pdb ( int  icmp2,
int  icmp1,
int  iori,
string  fname,
bool  reverse,
bool  dumpsym 
)
inline

References a, alignaxis(), compute_difference::b, basic::options::OptionKeys::matdes::dock::dump_pdb, dumpsym(), end, numeric::expand_xforms(), PREcst::fname, create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, out::file::o(), basic::options::option, option, erraser_single_res_analysis::out, p2, reverse(), rot_pose(), numeric::rotation_matrix_degrees(), ObjexxFCL::string_of(), symm, basic::options::OptionKeys::symmetry::symmetry, basic::options::OptionKeys::symmetry::symmetry_definition, predPRE::t, trans_pose(), x, and xform_pose().

◆ dump_pdb() [2/2]

void TCDock::dump_pdb ( int  icmp2,
int  icmp1,
int  iori,
string  fname,
int  idx,
bool  dumpsym = true,
bool  sepcomp = true,
bool  termini = true 
)
inline

References numeric::conversions::degrees(), basic::options::OptionKeys::matdes::dock::dump_pdb, dumpsym(), detail::find(), PREcst::fname, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::idx, numeric::xyzVector< T >::length(), max(), lactamize::nr, out::file::o(), basic::options::option, p2, test.T500_Packing::pr2, projperp(), rot_pose(), numeric::rotation_matrix_degrees(), ObjexxFCL::string_of(), symm, symmetry::symmetry_definition(), termini(), toXform(), trans_pose(), and xform_pose().

◆ dump_top_hits()

void TCDock::dump_top_hits ( vector1< LMAX > &  local_maxima)
inline

References count, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::ddg::dump_pdbs, ObjexxFCL::format::F(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::docking::ligand::grid::grid, h, create_a3b_hbs::i, test.T110_numeric::I, if(), enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, oop_conformations::length, ObjexxFCL::format::LJ(), max(), N, basic::options::option, option, ObjexxFCL::pad(), ObjexxFCL::pow(), add_xyz_to_pose::pts, numeric::conversions::radians(), numeric::rotation_matrix_degrees(), subloop_histogram::size, ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), sphere_coverage(), ObjexxFCL::string_of(), SYMICS, SYMOCT, SYMTET, TR, basic::options::OptionKeys::mp::transform::transform, w, x, predPRE::y, and predPRE::z.

◆ gather_hits()

void TCDock::gather_hits ( vector1< LMAX > &  local_maxima,
bool const &  reverse 
)
inline

References angle_degrees(), begin, utility::io::ozstream::close(), utility::io::oc::cout, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, max(), min(), basic::options::option, option, adapt_rotamers::ori, numeric::conversions::radians(), reverse(), create_a3b_hbs::score, ObjexxFCL::FArray< T >::size(), ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), make_templates::tasks, TR, and basic::options::OptionKeys::inout::dbms::user.

◆ get_best_sub1_contact_delta_rotations() [1/2]

void TCDock::get_best_sub1_contact_delta_rotations ( Real  icmp1,
Real  dcmp1,
Real  icmp2,
Real  dcmp2,
Real &  out_delta_ang1,
Real &  out_delta_ang2 
)
inline

References basic::options::OptionKeys::sicdock::contact_dis, numeric::xyzVector< T >::distance_squared(), basic::options::option, and numeric::rotation_matrix_degrees().

◆ get_best_sub1_contact_delta_rotations() [2/2]

void TCDock::get_best_sub1_contact_delta_rotations ( Real  icmp1,
Real  dcmp1,
Real  icmp2,
Real  dcmp2,
Real &  out_delta_ang1,
Real &  out_delta_ang2 
)
inline

References basic::options::OptionKeys::sicdock::contact_dis, numeric::xyzVector< T >::distance_squared(), basic::options::option, numeric::xyzTransform< T >::R, and numeric::rotation_matrix_degrees().

◆ get_cmp1() [1/2]

void TCDock::get_cmp1 ( Real  acmp1,
vector1< Vec > &  pts,
vector1< Vec > &  cbs 
)
inline

References add_xyz_to_pose::pts, and basic::options::OptionKeys::mp::transform::transform.

◆ get_cmp1() [2/2]

void TCDock::get_cmp1 ( Real  acmp1,
vector1< Vecf > &  pts,
vector1< Vecf > &  cbs 
)
inline

References create_a3b_hbs::i, add_xyz_to_pose::pts, docking::R, and numeric::rotation_matrix_degrees().

◆ get_cmp2() [1/2]

void TCDock::get_cmp2 ( Real  acmp2,
vector1< Vec > &  pts,
vector1< Vec > &  cbs 
)
inline

References add_xyz_to_pose::pts, and basic::options::OptionKeys::mp::transform::transform.

◆ get_cmp2() [2/2]

void TCDock::get_cmp2 ( Real  acmp2,
vector1< Vecf > &  pts,
vector1< Vecf > &  cbs 
)
inline

References create_a3b_hbs::i, add_xyz_to_pose::pts, docking::R, and numeric::rotation_matrix_degrees().

◆ get_contacts_by_component()

void TCDock::get_contacts_by_component ( Real const &  ang1,
Real const &  ang2,
Real const &  dis1,
Real const &  dis2,
int &  nresiface,
int &  nresiface0,
int &  nresiface1,
int &  nresiface2,
int &  ncontacts,
int &  ncontacts0,
int &  ncontacts1,
int &  ncontacts2,
Real &  nweighted,
Real &  nweighted0,
Real &  nweighted1,
Real &  nweighted2 
)
inline

References begin, basic::options::OptionKeys::sicdock::contact_dis, create_a3b_hbs::i, create_a3b_hbs::j, basic::options::option, docking::s, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, sqr(), and basic::options::OptionKeys::mp::transform::transform.

◆ get_moments()

void TCDock::get_moments ( vector1< Vec > const &  pts,
Real &  m1,
Real &  m2,
Real &  m3,
Real &  m4 
)
inline

References create_a3b_hbs::i, ObjexxFCL::pow(), add_xyz_to_pose::pts, and create_a3b_hbs::r.

◆ init()

void TCDock::init ( bool  reverse)
inline

References alignaxis(), basic::options::OptionKeys::sicdock::contact_dis, utility::io::oc::cout, basic::options::OptionKeys::msd::debug, ObjexxFCL::FArray2D< T >::dimension(), ObjexxFCL::FArray3D< T >::dimension(), create_a3b_hbs::i, create_a3b_hbs::j, min(), neighbor_count(), basic::options::option, option, reverse(), rot_pose(), TR, basic::options::OptionKeys::inout::dbms::user, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, basic::Tracer::Warning, and orn_macrocycle::wt.

◆ justone()

void TCDock::justone ( int  icmp1,
int  icmp2,
int  iori 
)
inline

References count, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, ObjexxFCL::format::F(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::docking::ligand::grid::grid, h, create_a3b_hbs::i, test.T110_numeric::I, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, oop_conformations::length, max(), min(), N, basic::options::OptionKeys::out::file::o, basic::options::option, ObjexxFCL::pow(), reverse(), ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), ObjexxFCL::string_of(), and w.

Referenced by main().

◆ make_dimer()

void TCDock::make_dimer ( core::pose::Pose &  pose)
inline

References create_a3b_hbs::i, beta_nonlocal::pose, and rot_pose().

◆ make_pentamer()

void TCDock::make_pentamer ( core::pose::Pose &  pose)
inline

References create_a3b_hbs::i, beta_nonlocal::pose, and rot_pose().

◆ make_tetramer()

void TCDock::make_tetramer ( core::pose::Pose &  pose)
inline

References create_a3b_hbs::i, beta_nonlocal::pose, and rot_pose().

◆ make_trimer()

void TCDock::make_trimer ( core::pose::Pose &  pose)
inline

References create_a3b_hbs::i, beta_nonlocal::pose, and rot_pose().

◆ min_termini_dis() [1/2]

Real TCDock::min_termini_dis ( Real  d1,
Real  a1,
Real  d2,
Real  a2 
)
inline

References docking::a1, docking::a2, numeric::xyzVector< T >::distance(), min(), basic::options::option, numeric::rotation_matrix_degrees(), and td.

◆ min_termini_dis() [2/2]

Real TCDock::min_termini_dis ( Real  d1,
Real  a1,
Real  d2,
Real  a2 
)
inline

References docking::a1, docking::a2, numeric::xyzVector< T >::distance(), min(), basic::options::option, option, numeric::rotation_matrix_degrees(), and td.

◆ min_termini_proj() [1/2]

Real TCDock::min_termini_proj ( Real  a1,
Real  a2,
Vec  sicaxis 
)
inline

References docking::a1, docking::a2, oop_conformations::length, min(), basic::options::option, projperp(), numeric::rotation_matrix_degrees(), and td.

◆ min_termini_proj() [2/2]

Real TCDock::min_termini_proj ( Real  a1,
Real  a2,
Vec  sicaxis 
)
inline

References docking::a1, docking::a2, oop_conformations::length, min(), basic::options::option, option, projperp(), numeric::rotation_matrix_degrees(), and td.

◆ num_threads() [1/2]

int TCDock::num_threads ( )
inline

◆ num_threads() [2/2]

int TCDock::num_threads ( )
inline

◆ precompute_intra() [1/2]

void TCDock::precompute_intra ( )
inline

References numeric::angle_radians(), basic::options::OptionKeys::sicdock::clash_dis, CONTACT_D2, basic::options::OptionKeys::sicdock::contact_dis, utility::io::oc::cout, create_a3b_hbs::i, basic::options::option, prune_cb_pairs(), numeric::rotation_matrix_degrees(), test.T120_core::sfxn, sigmoid(), sqr(), ObjexxFCL::string_of(), and utility_exit_with_message.

◆ precompute_intra() [2/2]

void TCDock::precompute_intra ( )
inline

References basic::options::OptionKeys::sicdock::clash_dis, CONTACT_D2, basic::options::OptionKeys::sicdock::contact_dis, utility::io::oc::cout, create_a3b_hbs::i, numeric::xyzMatrix< Real >::identity(), beta_nonlocal::jj, basic::options::option, prune_cb_pairs(), numeric::xyzTransform< T >::R, numeric::rotation_matrix_degrees(), test.T120_core::sfxn, sqr(), ObjexxFCL::string_of(), basic::options::OptionKeys::mp::transform::transform, and utility_exit_with_message.

◆ run() [1/2]

void TCDock::run ( )
inline

References angle_degrees(), begin, compareLMAX(), count, utility::io::oc::cout, basic::options::OptionKeys::matdes::dock::dump_pdb, ObjexxFCL::format::F(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::docking::ligand::grid::grid, h, create_a3b_hbs::i, test.T110_numeric::I, if(), enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, oop_conformations::length, ObjexxFCL::format::LJ(), max(), min(), N, basic::options::option, adapt_rotamers::ori, ObjexxFCL::pad(), ObjexxFCL::pow(), numeric::conversions::radians(), reverse(), numeric::rotation_matrix_degrees(), create_a3b_hbs::score, subloop_histogram::size, ObjexxFCL::FArray< T >::size(), ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), ObjexxFCL::string_of(), make_templates::tasks, toXform(), utility_exit_with_message, w, x, predPRE::y, and predPRE::z.

Referenced by main().

◆ run() [2/2]

void TCDock::run ( )
inline

References compareLMAX(), basic::init(), basic::options::option, option, and reverse().

◆ swap_axis()

Vecf TCDock::swap_axis ( vector1< Vecf > &  pts,
string  type 
)
inline

References create_a3b_hbs::i, numeric::xyzVector< T >::normalized(), add_xyz_to_pose::pts, create_a3b_hbs::r, and numeric::rotation_matrix_degrees().

◆ swap_axis_rotation()

Matf TCDock::swap_axis_rotation ( string  type)
inline

References numeric::xyzMatrix< Real >::identity(), and numeric::rotation_matrix_degrees().

◆ termini_score() [1/2]

Real TCDock::termini_score ( Real  d1,
Real  a1,
Real  d2,
Real  a2 
)
inline

References docking::a1, docking::a2, max(), basic::options::option, and td.

◆ termini_score() [2/2]

Real TCDock::termini_score ( Real  d1,
Real  a1,
Real  d2,
Real  a2,
Real &  td 
)
inline

References docking::a1, docking::a2, max(), basic::options::option, option, and td.

◆ thread_num() [1/2]

int TCDock::thread_num ( )
inline

◆ thread_num() [2/2]

int TCDock::thread_num ( )
inline

Member Data Documentation

◆ abort_

bool TCDock::abort_

◆ alpha_

Real TCDock::alpha_

◆ arch_

ArchCOP TCDock::arch_
private

◆ axismap_

std::map<string,Vecf> TCDock::axismap_

◆ clashmap1_

core::id::AtomID_Map< core::Real > TCDock::clashmap1_

◆ clashmap2_

core::id::AtomID_Map< core::Real > TCDock::clashmap2_

◆ cmp1_

core::pose::Pose const& TCDock::cmp1_

◆ cmp1axs_

Vecf TCDock::cmp1axs_

◆ cmp1cbneg_

ObjexxFCL::FArray2D< Real > TCDock::cmp1cbneg_

◆ cmp1cbpos_

ObjexxFCL::FArray2D< Real > TCDock::cmp1cbpos_

◆ cmp1cbs_ [1/2]

vector1<Vecf> TCDock::cmp1cbs_

◆ cmp1cbs_ [2/2]

vector1<Vec> TCDock::cmp1cbs_

◆ cmp1dianeg_

Real TCDock::cmp1dianeg_

◆ cmp1diapos_

Real TCDock::cmp1diapos_

◆ cmp1dsneg_

vector1<Real> TCDock::cmp1dsneg_

◆ cmp1dspos_

vector1<Real> TCDock::cmp1dspos_

◆ cmp1in_

core::pose::Pose TCDock::cmp1in_

◆ cmp1mnneg_

vector1< Real > TCDock::cmp1mnneg_

◆ cmp1mnpos_

vector1< Real > TCDock::cmp1mnpos_

◆ cmp1name_

string TCDock::cmp1name_

◆ cmp1nangle_

int TCDock::cmp1nangle_

◆ cmp1nsub_

int TCDock::cmp1nsub_

◆ cmp1olig_

core::pose::Pose TCDock::cmp1olig_

◆ cmp1pts_ [1/2]

vector1<Vecf> TCDock::cmp1pts_

◆ cmp1pts_ [2/2]

vector1<Vec> TCDock::cmp1pts_

◆ cmp1scale_

Real TCDock::cmp1scale_

◆ cmp1type_

string TCDock::cmp1type_

◆ cmp1wtmap_

core::id::AtomID_Map< Real > TCDock::cmp1wtmap_

◆ cmp1wts_

vector1< Real > TCDock::cmp1wts_

◆ cmp2_

core::pose::Pose const TCDock::cmp2_

◆ cmp2axs_

Vecf TCDock::cmp2axs_

◆ cmp2cbneg_

ObjexxFCL::FArray2D< Real > TCDock::cmp2cbneg_

◆ cmp2cbpos_

ObjexxFCL::FArray2D< Real > TCDock::cmp2cbpos_

◆ cmp2cbs_ [1/2]

vector1<Vecf> TCDock::cmp2cbs_

◆ cmp2cbs_ [2/2]

vector1<Vec> TCDock::cmp2cbs_

◆ cmp2dianeg_

Real TCDock::cmp2dianeg_

◆ cmp2diapos_

Real TCDock::cmp2diapos_

◆ cmp2dsneg_

vector1<Real> TCDock::cmp2dsneg_

◆ cmp2dspos_

vector1<Real> TCDock::cmp2dspos_

◆ cmp2in_

core::pose::Pose TCDock::cmp2in_

◆ cmp2mnneg_

vector1< Real > TCDock::cmp2mnneg_

◆ cmp2mnpos_

vector1< Real > TCDock::cmp2mnpos_

◆ cmp2name_

string TCDock::cmp2name_

◆ cmp2nangle_

int TCDock::cmp2nangle_

◆ cmp2nsub_

int TCDock::cmp2nsub_

◆ cmp2olig_

core::pose::Pose TCDock::cmp2olig_

◆ cmp2pts_ [1/2]

vector1<Vecf> TCDock::cmp2pts_

◆ cmp2pts_ [2/2]

vector1<Vec> TCDock::cmp2pts_

◆ cmp2scale_

Real TCDock::cmp2scale_

◆ cmp2type_

string TCDock::cmp2type_

◆ cmp2wtmap_

core::id::AtomID_Map< Real > TCDock::cmp2wtmap_

◆ cmp2wts_

vector1< Real > TCDock::cmp2wts_

◆ conf_count_

Size TCDock::conf_count_

◆ final_sfxn_

protocols::sic_dock::RigidScoreCOP TCDock::final_sfxn_

◆ gradii

ObjexxFCL::FArray3D< Real > TCDock::gradii

◆ gscore

ObjexxFCL::FArray3D< Real > TCDock::gscore

◆ lnscore_

protocols::sic_dock::LinkerScoreCOP TCDock::lnscore_

◆ mhscore_

protocols::sic_dock::scores::MotifHashRigidScoreCOP TCDock::mhscore_

◆ rigid_sfxn_

protocols::sic_dock::RigidScoreCOP TCDock::rigid_sfxn_

◆ sic_

protocols::sic_dock::SICFast TCDock::sic_

◆ sin_alpha_

Real TCDock::sin_alpha_

◆ start_time_

Real TCDock::start_time_

◆ symtype_

string TCDock::symtype_

◆ tan_alpha_

Real TCDock::tan_alpha_

◆ xform_out_

utility::io::ozstream* TCDock::xform_out_
The documentation for this struct was generated from the following files:
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