Rosetta
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#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <basic/database/open.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/rms_util.hh>
#include <numeric/conversions.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <numeric/xyzVector.hh>
#include <protocols/sic_dock/SICFast.hh>
#include <protocols/sic_dock/RigidScore.hh>
#include <protocols/sic_dock/util.hh>
#include <apps/pilot/will/will_util.ihh>
#include <numeric/xyzTransform.hh>
Classes | |
struct | Hit |
Macros | |
#define | CONTACT_TH 0 |
#define | MIN_HELEX_RES 20 |
#define | MAX_CYS_RES 3 |
Typedefs | |
typedef numeric::xyzVector< core::Real > | Vec |
typedef numeric::xyzMatrix< core::Real > | Mat |
typedef numeric::xyzTransform< core::Real > | Xform |
Functions | |
void | register_options () |
int | num_threads () |
int | thread_num () |
bool | cmpscore (Hit i, Hit j) |
bool | cmprmsd (Hit i, Hit j) |
void | make_native_olig (core::pose::Pose const &pose, core::pose::Pose &olig, int nfold) |
Vec | get_rot_center (Xform const &xsym, int sym) |
Vec | get_rot_center (Xform const &x1, Xform const &x2, int sym) |
Xform | get_cx_xform (Hit const &h) |
void | make_dock_olig (core::pose::Pose const &pose, core::pose::Pose &olig, Hit h) |
Real | get_rmsd (utility::vector1< Vec > const &native_ca, utility::vector1< Vec > const &init_ca, Hit const &h) |
Real | get_rmsd_debug (utility::vector1< Vec > const &native_ca, utility::vector1< Vec > const &init_ca, Hit const &h, Pose pose) |
void | dock (Pose const &init_pose, std::string const &fn, vector1< Vec > const &ssamp, Pose const &, int native_nfold=1, vector1< Vec > const &native_ca=vector1< Vec >()) |
utility::vector1< Vec > | align_native_state (core::pose::Pose &pose, int nfold) |
void | read_sphere (vector1< Vec > &ssamp) |
void | get_tasks_from_command_line (utility::vector1< std::pair< string, int > > &tasks) |
int | main (int argc, char *argv[]) |
Variables | |
static basic::Tracer | TR ("CXdock") |
static core::io::silent::SilentFileData | sfd |
#define CONTACT_TH 0 |
#define MAX_CYS_RES 3 |
#define MIN_HELEX_RES 20 |
typedef numeric::xyzMatrix<core::Real> Mat |
typedef numeric::xyzVector<core::Real> Vec |
typedef numeric::xyzTransform<core::Real> Xform |
utility::vector1<Vec> align_native_state | ( | core::pose::Pose & | pose, |
int | nfold | ||
) |
References numeric::dihedral_degrees(), beta_nonlocal::pose, and rot_pose().
Referenced by main().
References create_a3b_hbs::i, and create_a3b_hbs::j.
Referenced by dock().
References create_a3b_hbs::i, and create_a3b_hbs::j.
Referenced by dock().
void dock | ( | Pose const & | init_pose, |
std::string const & | fn, | ||
vector1< Vec > const & | ssamp, | ||
Pose const & | , | ||
int | native_nfold = 1 , |
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vector1< Vec > const & | native_ca = vector1<Vec>() |
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) |
References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, begin, create_a3b_hbs::best_score, basic::options::OptionKeys::crossmatch::clash_dis, cmprmsd(), cmpscore(), basic::options::OptionKeys::sicdock::contact_dis, CONTACT_TH, utility::io::oc::cout, numeric::conversions::degrees(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::dis, end, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_rmsd(), h, create_a3b_hbs::i, enumerate_junctions::int, test.T008_Serialization::iss, create_a3b_hbs::j, numeric::xyzVector< T >::length(), make_dock_olig(), min(), local::nstruct, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::out::file::o, basic::options::option, test.G203_Module_SQLPDB::outdir, docking::R, numeric::xyzTransform< T >::R, average_rmsds::rmsd, numeric::rotation_axis(), numeric::rotation_matrix_degrees(), subloop_histogram::size, ObjexxFCL::string_of(), predPRE::t, numeric::xyzTransform< T >::t, tag, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.
Referenced by main().
References get_rot_center(), and h.
Referenced by make_dock_olig().
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inline |
References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::dihedral_degrees(), h, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, numeric::constants::d::pi, create_a3b_hbs::r, docking::R, average_rmsds::rmsd, tan, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, numeric::x_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().
Referenced by dock().
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inline |
References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, numeric::dihedral_degrees(), h, create_a3b_hbs::i, create_a3b_hbs::j, oop_conformations::length, numeric::constants::d::pi, beta_nonlocal::pose, create_a3b_hbs::r, docking::R, average_rmsds::rmsd, rot_pose(), tan, kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, numeric::x_rotation_matrix_degrees(), xform_pose(), and numeric::z_rotation_matrix_degrees().
References get_rot_center().
References create_a3b_hbs::i.
Referenced by get_cx_xform(), and get_rot_center().
void get_tasks_from_command_line | ( | utility::vector1< std::pair< string, int > > & | tasks | ) |
References basic::options::option, basic::options::OptionKeys::in::file::s, subloop_histogram::size, make_templates::tasks, and basic::options::OptionKeys::inout::dbms::user.
Referenced by main().
int main | ( | int | argc, |
char * | argv[] | ||
) |
References align_native_state(), argv, dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, get_tasks_from_command_line(), create_a3b_hbs::i, basic::init(), make_native_olig(), basic::options::OptionKeys::mh::harvest::max_res, basic::options::option, pyrosetta.distributed.io::pose_from_file, read_sphere(), register_options(), make_templates::tasks, basic::options::TR, trans_pose(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().
void make_dock_olig | ( | core::pose::Pose const & | pose, |
core::pose::Pose & | olig, | ||
Hit | h | ||
) |
References get_cx_xform(), h, beta_nonlocal::pose, numeric::rotation_matrix_degrees(), x, and xform_pose().
Referenced by dock().
void make_native_olig | ( | core::pose::Pose const & | pose, |
core::pose::Pose & | olig, | ||
int | nfold | ||
) |
References create_a3b_hbs::i, beta_nonlocal::pose, and rot_pose().
Referenced by main().
int num_threads | ( | ) |
Referenced by TCDock::TCDock(), and test().
void register_options | ( | ) |
int thread_num | ( | ) |
Referenced by TCDock::TCDock().
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