zinc2_homodimer_design.cc File Reference

Starts with an undesigned symmetric dimer with two interface zinc sites as created by zinc2_homodimer_design_setup, and designs the interface with sc, bb, and jump minimization. More...

#include <devel/init.hh>
#include <protocols/metal_interface/MetalSiteResidue.hh>
#include <protocols/metal_interface/ZincSiteFinder.hh>
#include <protocols/metal_interface/AddZincSiteConstraints.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_moves/PackRotamersMover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/toolbox/task_operations/RestrictToInterfaceOperation.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>
#include <protocols/simple_moves/symmetry/SymPackRotamersMover.hh>
#include <protocols/simple_moves/symmetry/SymMinMover.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <sstream>
#include <core/conformation/Residue.hh>
#include <core/kinematics/Jump.hh>
#include <utility/vector0.hh>

Classes
class	zinc2_homodimer_design

Typedefs
typedef numeric::xyzVector < core::Real >	point
typedef point	axis
typedef core::pose::Pose	Pose
typedef utility::pointer::shared_ptr < zinc2_homodimer_design >	zinc2_homodimer_designOP

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.pilot.bder.zinc2_homodimer_design")
int	main (int argc, char *argv[])

Variables
basic::options::IntegerOptionKey const	repackmin_iterations ("repackmin_iterations")
basic::options::RealOptionKey const	fav_nat_bonus ("fav_nat_bonus")
basic::options::IntegerOptionKey const	nstruct_iterations ("nstruct_iterations")

Detailed Description

Starts with an undesigned symmetric dimer with two interface zinc sites as created by zinc2_homodimer_design_setup, and designs the interface with sc, bb, and jump minimization.

Prior to running this protocol, 'make_NCS.pl' must be applied to the symmetric zinc dimer to define the symmetry. The consequence is that the input PDB is actually the monomer generated by 'make_NCS.pl' along with the symmetry definition file. Reconstituting the dimer is the first step in this protocol. Next, the metal binding sites are located, an appropriate taskfactory, movemaps, and movers are setup, and finally the dimer is iteratively designed with packrotamers and minimization. Constraints are applied to the two metal sites, allowing minimization while respecting metal coordination geometry.

Author

Bryan Der

Typedef Documentation

typedef point axis

typedef numeric::xyzVector<core::Real> point

typedef core::pose::Pose Pose

typedef utility::pointer::shared_ptr< zinc2_homodimer_design > zinc2_homodimer_designOP

Function Documentation

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

References utility::io::oc::cout, fav_nat_bonus, devel::init(), utility::excn::EXCN_Base::msg(), nstruct_iterations, basic::options::option, option, repackmin_iterations, and TR().

static THREAD_LOCAL basic::Tracer TR ( "apps.pilot.bder.zinc2_homodimer_design"  )

static

Referenced by zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), main(), zinc2_homodimer_design::setup_metalsite(), zinc2_homodimer_design::setup_taskfactory_scorefunction_movers(), and zinc2_homodimer_design::zinc2_homodimer_design().

Variable Documentation

basic::options::RealOptionKey const fav_nat_bonus("fav_nat_bonus")

Referenced by add_rosetta_options_10(), main(), and zinc2_homodimer_design::setup_taskfactory_scorefunction_movers().

basic::options::IntegerOptionKey const nstruct_iterations("nstruct_iterations")

Referenced by zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), and main().

basic::options::IntegerOptionKey const repackmin_iterations("repackmin_iterations")

Referenced by zinc2_homodimer_design::design_symmetric_homodimer_metal_interface(), and main().