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Classes | Macros | Typedefs | Functions | Variables
CXdock.cc File Reference
#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::RealVec
 
typedef numeric::xyzMatrix< core::RealMat
 
typedef numeric::xyzTransform< core::RealXform
 

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< Vecalign_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
 

Macro Definition Documentation

◆ CONTACT_TH

#define CONTACT_TH   0

◆ MAX_CYS_RES

#define MAX_CYS_RES   3

◆ MIN_HELEX_RES

#define MIN_HELEX_RES   20

Typedef Documentation

◆ Mat

◆ Vec

◆ Xform

Function Documentation

◆ align_native_state()

utility::vector1<Vec> align_native_state ( core::pose::Pose pose,
int  nfold 
)

◆ cmprmsd()

bool cmprmsd ( Hit  i,
Hit  j 
)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by dock().

◆ cmpscore()

bool cmpscore ( Hit  i,
Hit  j 
)

References create_a3b_hbs::i, and create_a3b_hbs::j.

Referenced by dock().

◆ dock()

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>() 
)

◆ get_cx_xform()

Xform get_cx_xform ( Hit const &  h)
inline

References get_rot_center(), and h.

Referenced by make_dock_olig().

◆ get_rmsd()

Real get_rmsd ( utility::vector1< Vec > const &  native_ca,
utility::vector1< Vec > const &  init_ca,
Hit const &  h 
)
inline

◆ get_rmsd_debug()

Real get_rmsd_debug ( utility::vector1< Vec > const &  native_ca,
utility::vector1< Vec > const &  init_ca,
Hit const &  h,
Pose  pose 
)
inline

◆ get_rot_center() [1/2]

Vec get_rot_center ( Xform const &  x1,
Xform const &  x2,
int  sym 
)
inline

References get_rot_center().

◆ get_rot_center() [2/2]

Vec get_rot_center ( Xform const &  xsym,
int  sym 
)
inline

References create_a3b_hbs::i.

Referenced by get_cx_xform(), and get_rot_center().

◆ get_tasks_from_command_line()

void get_tasks_from_command_line ( utility::vector1< std::pair< string, int > > &  tasks)

◆ main()

int main ( int  argc,
char *  argv[] 
)

◆ make_dock_olig()

void make_dock_olig ( core::pose::Pose const &  pose,
core::pose::Pose olig,
Hit  h 
)

◆ make_native_olig()

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().

◆ num_threads()

int num_threads ( )

Referenced by TCDock::TCDock(), and test().

◆ read_sphere()

void read_sphere ( vector1< Vec > &  ssamp)

◆ register_options()

void register_options ( )

◆ thread_num()

int thread_num ( )

Referenced by TCDock::TCDock().

Variable Documentation

◆ sfd

core::io::silent::SilentFileData sfd
static

◆ TR

basic::Tracer TR("CXdock") ( "CXdock"  )
static