ward_design.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/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/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/import_pose/import_pose.hh>
#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/symmetry/util.hh>
#include <core/pose/util.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.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/moves/MonteCarlo.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/symmetric_docking/SymDockingLowRes.hh>
#include <protocols/toolbox/SwitchResidueTypeSet.hh>
#include <sstream>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <apps/pilot/will/will_util.ihh>

Typedefs
typedef numeric::xyzVector< Real >	Vec
typedef utility::vector1< Vec >	Vecs
typedef numeric::xyzMatrix< Real >	Mat

Functions
vector1< Size >	interface_residues (core::pose::Pose const &pose, vector1< Size > primary_subs)
void	minimize (core::pose::Pose &pose, ScoreFunctionOP sf, vector1< Size > iface_res)
void	design (Pose &pose, ScoreFunctionOP sf, vector1< Size > iface_res)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("ward_design")
Size	INTERFACE_CONTACT_DIS = 9.0

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

design()

void design	(	Pose &	pose,
		ScoreFunctionOP	sf,
		vector1< Size >	iface_res
	)

References detail::find(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

interface_residues()

vector1<Size> interface_residues	(	core::pose::Pose const &	pose,
		vector1< Size >	primary_subs
	)

References detail::find(), create_a3b_hbs::i, INTERFACE_CONTACT_DIS, create_a3b_hbs::j, create_a3b_hbs::nres, and beta_nonlocal::pose.

Referenced by main().

main()

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

References argv, design(), test.T009_Exceptions::e, utility::file_basename(), create_a3b_hbs::i, basic::init(), interface_residues(), ObjexxFCL::lead_zero_string_of(), out::file::o(), basic::options::option, option, test.G203_Module_SQLPDB::outdir, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::s(), basic::options::OptionKeys::out::sf, subloop_histogram::size, TR, and numeric::random::uniform().

minimize()

void minimize	(	core::pose::Pose &	pose,
		ScoreFunctionOP	sf,
		vector1< Size >	iface_res
	)

References test.T009_Exceptions::e, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

Variable Documentation

INTERFACE_CONTACT_DIS

Size INTERFACE_CONTACT_DIS = 9.0

Referenced by interface_residues().

TR

basic::Tracer TR("ward_design") ( "ward_design"  )

static

Referenced by main().