UBQ_UBQ_E2.cc File Reference

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

#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/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/util.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/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Loop.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/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/pose_metric_calculators/NeighborhoodByDistanceCalculator.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 <numeric/xyz.io.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>

Classes
class	UBQ_E2Mover

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

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

Variables
basic::options::FileOptionKey const	UBQpdb ("UBQpdb")
basic::options::FileOptionKey const	E2pdb ("E2pdb")
basic::options::IntegerOptionKey const	E2_residue ("E2_residue")
basic::options::RealOptionKey const	SASAfilter ("SASAfilter")
basic::options::RealOptionKey const	scorefilter ("scorefilter")
static basic::Tracer	TR ("apps.pilot.smlewis.UBQ_UBQ_E2")

Detailed Description

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

Author

Steven Lewis

Typedef Documentation

UBQ_E2MoverOP

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

Function Documentation

main()

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

References argv, test.T009_Exceptions::e, E2_residue, E2pdb, basic::init(), basic::options::OptionKeys::in::file::l, basic::options::option, option, basic::prof_reset(), basic::prof_show(), basic::options::OptionKeys::in::file::s, SASAfilter, scorefilter, basic::options::OptionKeys::in::file::silent, TR, UBQpdb, and utility_exit_with_message.

Variable Documentation

E2_residue

basic::options::IntegerOptionKey const E2_residue("E2_residue")

(

"E2_residue"

)

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

E2pdb

basic::options::FileOptionKey const E2pdb("E2pdb")

(

"E2pdb"

)

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

SASAfilter

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

(

"SASAfilter"

)

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

scorefilter

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

(

"scorefilter"

)

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

TR

basic::Tracer TR("apps.pilot.smlewis.UBQ_UBQ_E2") ( "apps.pilot.smlewis.UBQ_UBQ_E2"  )

static

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

UBQpdb

basic::options::FileOptionKey const UBQpdb("UBQpdb")

(

"UBQpdb"

)

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