hczndimer.cc File Reference

#include <basic/database/open.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <utility/graph/Graph.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.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 <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Hit

Macros
#define	sym_Clo   5
#define	sym_Chi   5
#define	CONTACT_D2   20.25
#define	CONTACT_TH   5
#define	MIN_HELEX_RES   20
#define	MAX_CYS_RES   3
#define	MAX_NRES   200
#define	MIN_NBR_COUNT   7
#define	MAX_ANG_METAL   15.0
#define	MAX_DIS_METAL   0.5
#define	MIN_DIS_METAL_SEP   10.0

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

Enumerations
enum	RTYPE {   CYS = 1 , HIS1 , HIS2 , ASP1 ,   ASP2 , ASP3 , NRTYPES = ASP3 }

Functions
vector1< pair< Real, Real > >	makerots (Pose const &p, Size ir, Pose const &rsd)
bool	clashcheck (Pose const &p, Vec v)
bool	clashcheckhalf (Pose const &p, Vec v)
std::ostream &	operator<< (std::ostream &o, Hit const &h)
std::istream &	operator>> (std::istream &i, Hit &h)
void	refine (Pose &pose, ScoreFunctionOP sf, Size r1, Size r2, Size r3, Size r4)
Pose	make_single_res_pose (string rt)
Real	sqr (Real x)
void	dock (Pose init, std::string const &fn)
int	main (int argc, char *argv[])

Variables
b typedef numeric::xyzVector< core::Real >	Vec
static basic::Tracer	tr ("hczndimer")
static core::io::silent::SilentFileData	sfd

Macro Definition Documentation

CONTACT_D2

#define CONTACT_D2   20.25

CONTACT_TH

#define CONTACT_TH   5

MAX_ANG_METAL

#define MAX_ANG_METAL   15.0

MAX_CYS_RES

#define MAX_CYS_RES   3

MAX_DIS_METAL

#define MAX_DIS_METAL   0.5

MAX_NRES

#define MAX_NRES   200

MIN_DIS_METAL_SEP

#define MIN_DIS_METAL_SEP   10.0

MIN_HELEX_RES

#define MIN_HELEX_RES   20

MIN_NBR_COUNT

#define MIN_NBR_COUNT   7

sym_Chi

#define sym_Chi   5

sym_Clo

#define sym_Clo   5

Typedef Documentation

Mat

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

Enumeration Type Documentation

RTYPE

enum RTYPE

Enumerator
CYS
HIS1
HIS2
ASP1
ASP2
ASP3
NRTYPES

Function Documentation

clashcheck()

bool clashcheck	(	Pose const &	p,
		Vec	v
	)

References numeric::distance_squared(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by dock(), run(), run_3bpy(), run_diiron_glu(), run_m8(), run_tyr_his(), and run_zn2his().

clashcheckhalf()

bool clashcheckhalf	(	Pose const &	p,
		Vec	v
	)

References numeric::distance_squared(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by dock().

dock()

void dock	(	Pose	init,
		std::string const &	fn
	)

References a, orn_macrocycle::ala, alignaxis(), angle_degrees(), ASP1, ASP2, ASP3, Hit::axs, Hit::cen, clash(), clashcheck(), clashcheckhalf(), basic::options::OptionKeys::constraints::constraints, utility::io::oc::cout, numeric::xyzVector< T >::cross(), CYS, numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), numeric::xyzVector< T >::dot(), test.T009_Exceptions::e, utility::file_basename(), create_a3b_hbs::first, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, h, HIS1, HIS2, create_a3b_hbs::i, Hit::ich1, Hit::ich2, basic::options::OptionKeys::in::in, basic::init(), Hit::ir, Hit::itype, Hit::jch1, Hit::jch2, Hit::jr, Hit::jtype, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, make_single_res_pose(), makerots(), MAX_ANG_METAL, MAX_DIS_METAL, MIN_DIS_METAL_SEP, MIN_NBR_COUNT, basic::options::OptionKeys::in::file::movemap, kmeans_adaptive_kernel_density_bb_dependent_rotlib::nd, NRTYPES, Hit::ori, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, p2, enumerate_junctions::q, res, residue, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::out::sf, sqr(), str(), tr, trans_pose(), utility_exit_with_message, Vec, and basic::options::OptionKeys::in::file::xyz.

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(), MAX_CYS_RES, MAX_NRES, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, subloop_histogram::size, and tr.

make_single_res_pose()

Pose make_single_res_pose

(

string

rt

)

Referenced by dock().

makerots()

vector1<pair<Real,Real> > makerots	(	Pose const &	p,
		Size	ir,
		Pose const &	rsd
	)

References create_a3b_hbs::i, subloop_histogram::iterator, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, and basic::options::OptionKeys::motifs::r2.

Referenced by dock().

operator<<()

std::ostream& operator<<	(	std::ostream &	o,
		Hit const &	h
	)

References h, and basic::options::OptionKeys::out::file::o.

operator>>()

std::istream& operator>>	(	std::istream &	i,
		Hit &	h
	)

References h, and create_a3b_hbs::i.

refine()

void refine	(	Pose &	pose,
		ScoreFunctionOP	sf,
		Size	r1,
		Size	r2,
		Size	r3,
		Size	r4
	)

References aj, test.T009_Exceptions::e, create_a3b_hbs::i, min(), basic::options::OptionKeys::in::file::movemap, N, beta_nonlocal::pose, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, vancomycin::task, and utility_exit_with_message.

sqr()

Real sqr

(

Real

x

)

References x.

Referenced by dock().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

tr

basic::Tracer tr("hczndimer") ( "hczndimer"  )

static

Referenced by dock(), and main().

Vec

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

Referenced by dock().