gen_homo_hc.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymDof.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/optimizeH.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.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 <numeric/kinematic_closure/bridgeObjects.hh>
#include <protocols/scoring/ImplicitFastClashCheck.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <platform/types.hh>
#include <core/pose/init_id_map.hh>
#include <protocols/moves/MoverStatistics.hh>
#include <apps/pilot/will/mynamespaces.ihh>
#include <apps/pilot/will/will_util.ihh>

Classes
struct	Hit

Typedefs
typedef utility::vector1< core::Real >	Reals
typedef utility::vector1< core::Size >	Sizes
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat
typedef utility::vector1< Vec >	Vecs
typedef utility::pointer::owning_ptr< Hit >	HitOP

Functions
Real	sqr (Real const r)
Real	sigmoidish_neighbor (Real const &sqdist)
vector1< Size >	read_res_list (string fn)
vector1< Reals >	vecs2vv (Vecs const &v)
vector1< Vec >	vv2vecs (vector1< Reals > const &vv)
core::kinematics::Stub	res2stub (core::pose::Pose const &pose, Size rsd, core::kinematics::Stub ref=core::kinematics::Stub())
Real	ik_his_clamp (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, std::string fname)
void	run (std::string fname)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("gen_d2")

Typedef Documentation

HitOP

typedef utility::pointer::owning_ptr<Hit> HitOP

Mat

typedef numeric::xyzMatrix<Real> Mat

Reals

typedef utility::vector1<core::Real> Reals

Sizes

typedef utility::vector1<core::Size> Sizes

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

ik_his_clamp()

Real ik_his_clamp	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		std::string	fname
	)

References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), numeric::xyzVector< T >::cross(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::dihedral_degrees(), numeric::distance_squared(), utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, PREcst::fname, create_a3b_hbs::i, create_a3b_hbs::j, numeric::xyzVector< T >::normalized(), run_backbone::pivots, beta_nonlocal::pose, projperp(), docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, vecs2vv(), and vv2vecs().

Referenced by run().

main()

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

References argv, test.T009_Exceptions::e, basic::init(), basic::options::option, run(), and basic::options::OptionKeys::in::file::s.

read_res_list()

vector1<Size> read_res_list

(

string

fn

)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, basic::options::OptionKeys::in::in, extract_by_sidechain_sasa_score::l, create_a3b_hbs::r, and utility_exit_with_message.

res2stub()

core::kinematics::Stub res2stub	(	core::pose::Pose const &	pose,
		Size	rsd,
		core::kinematics::Stub	ref = core::kinematics::Stub()
	)

References p2, and beta_nonlocal::pose.

run()

void run

(

std::string

fname

)

References orn_macrocycle::ala, pyrosetta::create_score_function, basic::options::OptionKeys::in::file::dssp, detail::find(), PREcst::fname, create_a3b_hbs::i, ik_his_clamp(), enumerate_junctions::int, create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::TR.

Referenced by main().

sigmoidish_neighbor()

Real sigmoidish_neighbor ( Real const &  sqdist )

inline

References dist(), and sqr().

sqr()

Real sqr ( Real const  r )

inline

References create_a3b_hbs::r.

Referenced by sigmoidish_neighbor().

vecs2vv()

vector1<Reals> vecs2vv

(

Vecs const &

v

)

References create_a3b_hbs::i, create_a3b_hbs::r, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by ik_his_clamp().

vv2vecs()

vector1<Vec> vv2vecs

(

vector1< Reals > const &

vv

)

References create_a3b_hbs::i, and create_a3b_hbs::r.

Referenced by ik_his_clamp().

Variable Documentation

TR

basic::Tracer TR("gen_d2") ( "gen_d2"  )

static