UBQ_Gp_CYD-CYD.cc File Reference

this application is a one-shot for modeling a ubiquitinated G-protein; this version uses a disulfide linkage to match an experimentally-induced disulfide More...

#include <apps/public/scenarios/chemically_conjugated_docking/Gp_quantification_metrics.hh>
#include <apps/public/scenarios/chemically_conjugated_docking/Gp_extra_bodies.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/task_operations/RestrictByCalculatorsOperation.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <protocols/moves/OutputMovers.hh>
#include <protocols/simple_moves/TorsionDOFMover.hh>
#include <protocols/moves/JumpOutMover.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh>
#include <protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/simple_moves/sidechain_moves/SidechainMover.hh>
#include <basic/MetricValue.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/metrics/simple_calculators/InterfaceSasaDefinitionCalculator.hh>
#include <core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.hh>
#include <protocols/pose_metric_calculators/NeighborhoodByDistanceCalculator.hh>
#include <protocols/pose_metric_calculators/InterGroupNeighborsCalculator.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <numeric/conversions.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <utility/exit.hh>
#include <basic/prof.hh>
#include <utility/excn/Exceptions.hh>
#include <string>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/AnchoredDesign.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <utility/vector0.hh>
#include <core/kinematics/AtomTree.hh>

Classes
class	UBQ_GTPase_disulfide_Mover

Typedefs
using	UBQ_GTPase_disulfide_MoverOP = utility::pointer::shared_ptr< UBQ_GTPase_disulfide_Mover >

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

Variables
static basic::Tracer	TR ("apps.public.scenarios.chemically_conjugated_docking.UBQ_Gp_CYD-CYD")

Detailed Description

this application is a one-shot for modeling a ubiquitinated G-protein; this version uses a disulfide linkage to match an experimentally-induced disulfide

Author

Steven Lewis

Typedef Documentation

using UBQ_GTPase_disulfide_MoverOP = utility::pointer::shared_ptr<UBQ_GTPase_disulfide_Mover>

Function Documentation

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

References utility::excn::Exception::display(), test.T009_Exceptions::e, devel::init(), basic::options::OptionKeys::in::file::l, basic::options::option, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::silent, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

Variable Documentation

basic::Tracer TR("apps.public.scenarios.chemically_conjugated_docking.UBQ_Gp_CYD-CYD")

static

Referenced by UBQ_GTPase_disulfide_Mover::analyze_and_filter(), UBQ_GTPase_disulfide_Mover::apply(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), main(), and UBQ_GTPase_disulfide_Mover::UBQ_GTPase_disulfide_Mover().