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/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.hh>
#include <protocols/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/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/FoldTree.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/symmetry/SetupForSymmetryMover.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.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>

Classes
class	zinc1_homodimer_design

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

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

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

Typedef Documentation

axis

typedef point axis

point

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

Pose

typedef core::pose::Pose Pose

zinc1_homodimer_designOP

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

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, fav_nat_bonus, gridsearch_rollmove_angles, highres_symmetric_design_cycles, basic::init(), lowres_symmetric_design_cycles, nstruct_iterations, basic::options::option, option, TR, and value.

Variable Documentation

fav_nat_bonus

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

(

"fav_nat_bonus"

)

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

gridsearch_rollmove_angles

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

(

"gridsearch_rollmove_angles"

)

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

highres_symmetric_design_cycles

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

(

"highres_symmetric_design_cycles"

)

Referenced by main().

lowres_symmetric_design_cycles

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

(

"lowres_symmetric_design_cycles"

)

Referenced by main().

nstruct_iterations

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

(

"nstruct_iterations"

)

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

TR

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