UBQ_E2_thioester.cc File Reference

this application is a one-shot for modeling the thioester bond between UBQ and an E2 More...

#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/operation/TaskOperations.hh>
#include <protocols/toolbox/task_operations/RestrictByCalculatorsOperation.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/id/TorsionID.hh>
#include <core/id/types.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/AtomType.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/simple_moves/RotamerTrialsMover.hh>
#include <protocols/simple_moves/TaskAwareMinMover.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/simple_moves/PackRotamersMover.hh>
#include <protocols/rigid/RotateJumpAxisMover.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/toolbox/pose_metric_calculators/NeighborhoodByDistanceCalculator.hh>
#include <protocols/toolbox/pose_metric_calculators/NeighborsByDistanceCalculator.hh>
#include <protocols/toolbox/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/vector0.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 <basic/options/keys/chemically_conjugated_docking.OptionKeys.gen.hh>
#include <utility/excn/Exceptions.hh>

Classes
class	UBQ_E2Mover

Typedefs
typedef utility::pointer::shared_ptr < UBQ_E2Mover >	UBQ_E2MoverOP

Functions
static thread_local basic::Tracer	TR ("apps.public.scenarios.chemically_conjugated_docking.UBQ_E2_thioester")
int	main (int argc, char *argv[])

Detailed Description

this application is a one-shot for modeling the thioester bond between UBQ and an E2

Author

Steven Lewis

Typedef Documentation

typedef utility::pointer::shared_ptr< UBQ_E2Mover > UBQ_E2MoverOP

Function Documentation

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

References utility::io::oc::cout, devel::init(), basic::options::OptionKeys::in::file::l, utility::excn::EXCN_Base::msg(), 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.

static thread_local basic::Tracer TR ( "apps.public.scenarios.chemically_conjugated_docking.UBQ_E2_thioester"  )

static

Referenced by UBQ_E2Mover::analyze_and_filter(), UBQ_E2Mover::apply(), UBQ_E2Mover::init_on_new_input(), main(), and UBQ_E2Mover::UBQ_E2Mover().