zinc1_homodimer_design.cc File Reference

Symmetric design of a zinc-mediated homodimer. One zinc at the interface. Gridsearch (or not) of perturbations to the metalsite geometry using rollmoves about axes that pass through zinc. Metalsite constraints are in place to allow backbone minimization of the designs. 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/analysis/InterfaceAnalyzerMover.hh>
#include <protocols/rigid/RollMover.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.hh>
#include <protocols/toolbox/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/toolbox/task_operations/RestrictToInterfaceOperation.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <protocols/jobdist/Jobs.hh>
#include <core/conformation/Conformation.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <protocols/simple_moves/symmetry/SetupForSymmetryMover.hh>
#include <protocols/simple_moves/symmetry/SymPackRotamersMover.hh>
#include <protocols/simple_moves/symmetry/SymRotamerTrialsMover.hh>
#include <protocols/simple_moves/symmetry/SymMinMover.hh>
#include <core/scoring/symmetry/SymmetricScoreFunction.hh>
#include <core/conformation/symmetry/util.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ResidueTypeConstraint.hh>
#include <core/id/AtomID.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <numeric/xyz.io.hh>
#include <numeric/xyz.functions.hh>
#include <utility/file/FileName.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <string>
#include <sstream>

Go to the source code of this file.

Classes
class	zinc1_homodimer_design

Typedefs
typedef core::pose::Pose	Pose
typedef numeric::xyzVector < core::Real >	point
typedef point	axis
typedef utility::pointer::owning_ptr < zinc1_homodimer_design >	zinc1_homodimer_designOP

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.design.zinc1_homodimer_design")
int	main (int argc, char *argv[])

Variables
basic::options::IntegerOptionKey const	lowres_symmetric_design_cycles ("lowres_symmetric_design_cycles")
basic::options::IntegerOptionKey const	highres_symmetric_design_cycles ("highres_symmetric_design_cycles")
basic::options::BooleanOptionKey const	gridsearch_rollmove_angles ("gridsearch_rollmove_angles")
basic::options::RealOptionKey const	fav_nat_bonus ("fav_nat_bonus")
basic::options::IntegerOptionKey const	nstruct_iterations ("nstruct_iterations")

Detailed Description

Symmetric design of a zinc-mediated homodimer. One zinc at the interface. Gridsearch (or not) of perturbations to the metalsite geometry using rollmoves about axes that pass through zinc. Metalsite constraints are in place to allow backbone minimization of the designs.

Author

Bryan Der

Definition in file zinc1_homodimer_design.cc.

Typedef Documentation

typedef point axis

Definition at line 80 of file zinc1_homodimer_design.cc.

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

Definition at line 79 of file zinc1_homodimer_design.cc.

typedef core::pose::Pose Pose

Definition at line 78 of file zinc1_homodimer_design.cc.

typedef utility::pointer::owning_ptr< zinc1_homodimer_design > zinc1_homodimer_designOP

Definition at line 526 of file zinc1_homodimer_design.cc.

Function Documentation

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

Definition at line 530 of file zinc1_homodimer_design.cc.

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

static THREAD_LOCAL basic::Tracer TR ( "apps.public.design.zinc1_homodimer_design"  )

static

Referenced by zinc1_homodimer_design::apply(), zinc1_homodimer_design::design_symmetric_homodimer_interface(), zinc1_homodimer_design::gridsearch_rollmove_angles(), main(), zinc1_homodimer_design::setup_metalsite(), zinc1_homodimer_design::setup_metalsite_constraints(), zinc1_homodimer_design::setup_movemap_bb_chi(), zinc1_homodimer_design::setup_movers(), zinc1_homodimer_design::setup_scorefunctions(), and zinc1_homodimer_design::setup_taskfactory().

Variable Documentation

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

Referenced by main(), zinc1_homodimer_design::setup_metalsite_constraints(), and zinc1_homodimer_design::setup_scorefunctions().

basic::options::BooleanOptionKey const gridsearch_rollmove_angles("gridsearch_rollmove_angles")

Referenced by zinc1_homodimer_design::apply(), and main().

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

Referenced by main().

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

Referenced by main().

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

Referenced by zinc1_homodimer_design::apply(), and main().