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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/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/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::owning_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

typedef core::pose::Pose Pose
typedef utility::pointer::owning_ptr< zinc1_homodimer_design > zinc1_homodimer_designOP

Function Documentation

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

Variable Documentation

basic::options::RealOptionKey const fav_nat_bonus("fav_nat_bonus")
basic::options::BooleanOptionKey const gridsearch_rollmove_angles("gridsearch_rollmove_angles")
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")
basic::Tracer TR("apps.public.design.zinc1_homodimer_design")
static