test_ikrs2.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/match.OptionKeys.gen.hh>
#include <basic/options/keys/willmatch.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/util.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/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/MoveMap.hh>
#include <utility/graph/Graph.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibrary.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/PDBInfo.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.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/scoring/ImplicitFastClashCheck.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <numeric/kinematic_closure/bridgeObjects.hh>
#include <numeric/kinematic_closure/kinematic_closure_helpers.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <numeric/NumericTraits.hh>
#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
vector1< Reals >	vecs2vv (Vecs const &v)
vector1< Vec >	vv2vecs (vector1< Reals > const &vv)
Real	ik_arg_glu_frnt (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
Real	ik_arg_glu_side (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
Real	ik_arg_asp_frnt (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
Real	ik_arg_asp_side (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
void	ik_lys_ctp_asp (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
void	ik_lys_ctp_glu (Pose &pose, Size rsd1, Size rsd2, ImplicitFastClashCheck &ifc, vector1< HitOP > &hits, Pose ctp)
void	repack (Pose &arg)
int	main (int argc, char *argv[])

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

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_arg_asp_frnt()

Real ik_arg_asp_frnt	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().

Referenced by main().

ik_arg_asp_side()

Real ik_arg_asp_side	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().

Referenced by main().

ik_arg_glu_frnt()

Real ik_arg_glu_frnt	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), CA, numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().

Referenced by main().

ik_arg_glu_side()

Real ik_arg_glu_side	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References numeric::alignVectorSets(), numeric::angle_degrees(), atoms, numeric::kinematic_closure::bridgeObjects(), CA, numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::xyzVector< T >::cross(), numeric::distance_squared(), create_a3b_hbs::i, create_a3b_hbs::j, natoms(), numeric::xyzVector< T >::normalized(), adapt_rotamers::ori, run_backbone::pivots, beta_nonlocal::pose, docking::R, rot_pose(), numeric::rotation_matrix_degrees(), test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, predPRE::t, trans_pose(), numeric::xyzMatrix< T >::transposed(), vecs2vv(), and vv2vecs().

Referenced by main().

ik_lys_ctp_asp()

void ik_lys_ctp_asp	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::distance_squared(), h, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), run_backbone::pivots, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, vecs2vv(), and vv2vecs().

Referenced by main().

ik_lys_ctp_glu()

void ik_lys_ctp_glu	(	Pose &	pose,
		Size	rsd1,
		Size	rsd2,
		ImplicitFastClashCheck &	ifc,
		vector1< HitOP > &	hits,
		Pose	ctp
	)

References atoms, numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::chainXYZ(), clash(), count, numeric::distance_squared(), h, create_a3b_hbs::i, create_a3b_hbs::j, natoms(), run_backbone::pivots, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, vecs2vv(), and vv2vecs().

Referenced by main().

main()

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

References orn_macrocycle::ala, numeric::alignVectorSets(), numeric::angle_degrees(), Hit::apply(), arg(), argv, clash(), basic::options::OptionKeys::constraints::constraints, numeric::xyzVector< T >::distance_squared(), test.T009_Exceptions::e, utility::file_basename(), detail::find(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, Hit::frnt, create_a3b_hbs::i, ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), ik_lys_ctp_glu(), basic::options::OptionKeys::in::in, basic::init(), enumerate_junctions::int, max(), numeric::xyzVector< T >::max(), min(), basic::options::OptionKeys::in::file::movemap, natoms(), Hit::nego, basic::options::option, PI, numeric::NumericTraits< T >::pi(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, repack(), rot_pose(), Hit::rsd1, Hit::rsd2, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::match::scaffold_active_site_residues, basic::options::OptionKeys::out::sf, sfd, ObjexxFCL::FArray3< T >::size1(), ObjexxFCL::FArray3< T >::size2(), ObjexxFCL::FArray3D< T >::size3(), Hit::stub, basic::options::TR, trans_pose(), basic::options::OptionKeys::inout::dbms::user, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

repack()

void repack

(

Pose &

arg

)

References arg(), basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

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_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), and ik_lys_ctp_glu().

vv2vecs()

vector1<Vec> vv2vecs

(

vector1< Reals > const &

vv

)

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

Referenced by ik_arg_asp_frnt(), ik_arg_asp_side(), ik_arg_glu_frnt(), ik_arg_glu_side(), ik_lys_ctp_asp(), and ik_lys_ctp_glu().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

Referenced by main().

TR

basic::Tracer TR("test_ikrs") ( "test_ikrs"  )

static