crossmatch_3e.cc File Reference

#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>
#include <basic/options/keys/enzdes.OptionKeys.gen.hh>
#include <basic/options/keys/crossmatch.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/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/conformation/symmetry/SymmData.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.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/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/Stub.hh>
#include <core/pack/optimizeH.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.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/constraints/DihedralConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/packstat/compute_sasa.hh>
#include <core/scoring/packstat/sasa_dot_locations.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyz.io.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/symmetry/SymMinMover.hh>
#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>
#include <protocols/toolbox/SwitchResidueTypeSet.hh>
#include <sstream>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <utility/exit.hh>
#include <apps/pilot/will/will_util.ihh>

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

Functions
void	design_homodimer (Pose &pose, ScoreFunctionOP sf, vector1< Size > const &matchres, bool designall=false)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("crossmatch_3e")
static core::io::silent::SilentFileData	sfd

Typedef Documentation

Mat

typedef numeric::xyzMatrix<Real> Mat

Vec

typedef numeric::xyzVector<Real> Vec

Vecs

typedef utility::vector1<Vec> Vecs

Function Documentation

design_homodimer()

void design_homodimer	(	Pose &	pose,
		ScoreFunctionOP	sf,
		vector1< Size > const &	matchres,
		bool	designall = false
	)

References basic::options::OptionKeys::smhybrid::design_hydrophobic, basic::options::OptionKeys::willmatch::exclude_ala, detail::find(), create_a3b_hbs::i, interface, create_a3b_hbs::j, option, beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.

Referenced by main().

main()

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

References argv, test.T005_Bindings::base, clash(), design_homodimer(), numeric::distance_squared(), test.T009_Exceptions::e, ObjexxFCL::format::F(), test.T110_numeric::I, basic::init(), basic::options::OptionKeys::mh::filter::lig, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, basic::options::OptionKeys::willmatch::native1, basic::options::option, adapt_rotamers::ori, erraser_single_res_analysis::out, pyrosetta.distributed.io::pose_from_file, numeric::projection_matrix(), docking::R, basic::options::OptionKeys::in::file::residue_type_set, 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(), basic::options::TR, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

Variable Documentation

sfd

core::io::silent::SilentFileData sfd

static

Referenced by main().

TR

basic::Tracer TR("crossmatch_3e") ( "crossmatch_3e"  )

static