homodimer_maker.cc File Reference

Takes a found exposed beta strand and tries to make the starting file for a symmetric homodimer. More...

#include <devel/init.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <numeric/xyzVector.io.hh>
#include <numeric/xyzVector.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Atom.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/conformation/Conformation.hh>
#include <core/id/AtomID_Map.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/methods/EnergyMethod.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/etable/EtableEnergy.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/rigid/RollMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/moves/StructureRestrictor.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/jd2.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <sstream>
#include <iostream>
#include <string>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>

Classes
class	HDmakerMover

Functions
numeric::xyzVector< core::Real >	xyz_center_vector (numeric::xyzVector< core::Real > const &a, numeric::xyzVector< core::Real > const &b)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.public.beta_strand_homodimer_design.homodimer_maker")
IntegerOptionKey const	window_size ("window_size")
IntegerOptionKey const	sheet_start ("sheet_start")
IntegerOptionKey const	sheet_stop ("sheet_stop")
RealOptionKey const	E_cutoff ("E_cutoff")
StringOptionKey const	struct_file ("struct_file")

Detailed Description

Takes a found exposed beta strand and tries to make the starting file for a symmetric homodimer.

Author

Ben Stranges

Function Documentation

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

References utility::io::oc::cout, test.T009_Exceptions::e, E_cutoff, devel::init(), utility::excn::Exception::msg(), basic::options::OptionKeys::jd2::no_output, basic::options::option, option, sheet_start, sheet_stop, struct_file, TR, and window_size.

numeric::xyzVector< core::Real > xyz_center_vector	(	numeric::xyzVector< core::Real > const &	a,
		numeric::xyzVector< core::Real > const &	b
	)

References numeric::xyzVector< typename >::x(), numeric::xyzVector< typename >::y(), and numeric::xyzVector< typename >::z().

Referenced by HDmakerMover::apply().

Variable Documentation

RealOptionKey const E_cutoff("E_cutoff")

Referenced by HDmakerMover::HDmakerMover(), and main().

IntegerOptionKey const sheet_start("sheet_start")

Referenced by HDmakerMover::apply(), HDmakerMover::HDmakerMover(), and main().

IntegerOptionKey const sheet_stop("sheet_stop")

Referenced by HDmakerMover::HDmakerMover(), and main().

StringOptionKey const struct_file("struct_file")

Referenced by HDmakerMover::apply(), and main().

basic::Tracer TR("apps.public.beta_strand_homodimer_design.homodimer_maker")

static

Referenced by HDmakerMover::apply(), HDmakerMover::bb_score(), and main().

IntegerOptionKey const window_size("window_size")

Referenced by add_rosetta_options_3(), HDmakerMover::apply(), and main().