willmatch_d6_bpy.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/willmatch.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/packing/compute_holes_score.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <basic/database/open.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/dunbrack/RotamerLibrary.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/Pose.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/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 <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <platform/types.hh>
#include <core/pose/init_id_map.hh>
#include <apps/pilot/will/will_util.ihh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

Typedefs
typedef utility::vector1< core::Real >	Reals
typedef utility::vector1< core::Size >	Sizes
typedef numeric::xyzVector< Real >	Vec
typedef numeric::xyzMatrix< Real >	Mat

Functions
void	myoptH (Pose &pose, ScoreFunctionOP sf)
void	refine (Pose &pose, ScoreFunctionOP sf, Size r1, Size r2, Size r3, Size r4)
void	run ()
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("willmatch_d6_bpy")

Typedef Documentation

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

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, basic::init(), and run().

myoptH()

void myoptH	(	Pose &	pose,
		ScoreFunctionOP	sf
	)

References beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

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, and vancomycin::task.

Referenced by run().

run()

void run

(

)

References a, kmeans_adaptive_kernel_density_bb_dependent_rotlib::ang, angle_degrees(), numeric::angle_degrees(), compute_difference::b, CD, CHI1, basic::options::OptionKeys::willmatch::chi1_increment, CHI2, basic::options::OptionKeys::willmatch::chi2_increment, clash(), basic::options::OptionKeys::willmatch::clash_dis, clashcheck(), utility::io::izstream::close(), utility::io::ozstream::close(), count, numeric::xyzVector< T >::cross(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, numeric::conversions::degrees(), numeric::dihedral_degrees(), numeric::distance_squared(), numeric::xyzVector< T >::distance_squared(), numeric::xyzVector< T >::dot(), basic::options::OptionKeys::willmatch::fa_dun_thresh, utility::file_basename(), basic::database::full_name(), h, create_a3b_hbs::i, ObjexxFCL::format::I(), create_a3b_hbs::ii, basic::options::OptionKeys::in::in, create_a3b_hbs::j, create_a3b_hbs::k, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, max(), basic::options::OptionKeys::willmatch::max_ang_metal, basic::options::OptionKeys::willmatch::max_dis_metal, min(), surface_app::native, create_a3b_hbs::nres, basic::options::OptionKeys::out::file::o, basic::options::option, adapt_rotamers::ori, beta_nonlocal::pose, test.T010_LoadPDB::pose3, pyrosetta.distributed.io::pose_from_file, numeric::conversions::radians(), refine(), residue, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::willmatch::residues, loops_kic::rms, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::sf, sfd, basic::options::OptionKeys::out::file::silent, ObjexxFCL::string_of(), stub(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("willmatch_d6_bpy") ( "willmatch_d6_bpy"  )

static