d3_bpy_linker.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/kinematics/Stub.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/designability_score.hh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Hit
class	SlideTask

Macros
#define	CONTACT_D2   20.25
#define	CONTACT_TH   30
#define	NSS   1812
#define	MIN_HELEX_RES   20
#define	MAX_CYS_RES   3
#define	MAX_NRES   200

Typedefs
typedef numeric::xyzVector< core::Real >	Vec
typedef numeric::xyzMatrix< core::Real >	Mat
typedef utility::pointer::owning_ptr< SlideTask >	SlideTaskOP
typedef utility::pointer::owning_ptr< SlideTask const >	SlideTaskCOP

Functions
void	register_options ()
int	num_threads ()
int	thread_num ()
bool	cmpHit (Hit i, Hit j)
void	make_nmer (SlideTaskOP stask)
void	dock (Pose const &init_pose, std::string const &fn, vector1< Vec > const &ssamp)
void	read_sphere (vector1< Vec > &ssamp)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("D3BPYDIG")
static core::io::silent::SilentFileData	sfd

Macro Definition Documentation

CONTACT_D2

#define CONTACT_D2   20.25

CONTACT_TH

#define CONTACT_TH   30

MAX_CYS_RES

#define MAX_CYS_RES   3

MAX_NRES

#define MAX_NRES   200

MIN_HELEX_RES

#define MIN_HELEX_RES   20

NSS

#define NSS   1812

Typedef Documentation

Mat

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

SlideTaskCOP

typedef utility::pointer::owning_ptr< SlideTask const > SlideTaskCOP

SlideTaskOP

typedef utility::pointer::owning_ptr< SlideTask > SlideTaskOP

Vec

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

Function Documentation

cmpHit()

bool cmpHit	(	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
	)

References cmpHit(), CONTACT_TH, utility::io::oc::cout, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, h, create_a3b_hbs::i, basic::init(), enumerate_junctions::int, test.T008_Serialization::iss, min(), NSS, local::nstruct, basic::options::OptionKeys::out::nstruct, num_threads(), basic::options::OptionKeys::out::file::o, basic::options::option, test.G203_Module_SQLPDB::outdir, numeric::constants::d::pi, docking::R, predPRE::R2, numeric::rotation_matrix_degrees(), create_a3b_hbs::score, ObjexxFCL::string_of(), predPRE::t, tag, tan, thread_num(), basic::options::TR, and xform_pose().

Referenced by main().

main()

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

References argv, dock(), basic::options::OptionKeys::in::file::dssp, test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::init(), NSS, basic::options::option, pyrosetta.distributed.io::pose_from_file, read_sphere(), register_options(), basic::options::OptionKeys::in::file::s, basic::options::TR, and trans_pose().

make_nmer()

void make_nmer

(

SlideTaskOP

stask

)

num_threads()

int num_threads

(

)

Referenced by dock().

read_sphere()

void read_sphere

(

vector1< Vec > &

ssamp

)

References utility::io::izstream::close(), create_a3b_hbs::i, NSS, basic::database::open(), str(), utility_exit_with_message, x, predPRE::y, and predPRE::z.

Referenced by main().

register_options()

void register_options

(

)

Referenced by main().

thread_num()

int thread_num

(

)

Referenced by dock().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

TR

basic::Tracer TR("D3BPYDIG") ( "D3BPYDIG"  )

static