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::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

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

typedef numeric::xyzMatrix<core::Real> Mat

Vec

typedef numeric::xyzVector<core::Real> Vec

Xform

typedef numeric::xyzTransform<core::Real> Xform

Function Documentation

align_native_state()

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().

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>()
	)

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().

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

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().

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

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().

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

)

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().

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().

make_dock_olig()

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().

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

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, utility::io::izstream::close(), create_a3b_hbs::i, max(), min(), basic::database::open(), basic::options::option, round(), str(), basic::options::TR, utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by main().

register_options()

void register_options

(

)

References basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::sicdock::contact_dis, basic::options::OptionKeys::mh::harvest::max_res, and NEW_OPT.

Referenced by main().

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