HECT.hh File Reference

#include <core/pose/Pose.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/picking_old/vall/util.hh>
#include <core/fragment/picking_old/FragmentLibraryManager.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/task_operations/RestrictByCalculatorsOperation.hh>
#include <protocols/task_operations/RestrictToNeighborhoodOperation.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <protocols/pose_metric_calculators/InterGroupNeighborsCalculator.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/constraints/AmbiguousConstraint.hh>
#include <core/scoring/rms_util.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/minimization_packing/TaskAwareMinMover.hh>
#include <protocols/simple_moves/TorsionDOFMover.hh>
#include <protocols/moves/JumpOutMover.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <protocols/jd2/Job.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <numeric/xyz.functions.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <set>
#include <utility>

Classes
class	HECTMover
	HECT mover. More...

Namespaces
	basic
	Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or flagging as job as being a bad input.
	basic::options
	basic::options::OptionKeys

Functions
void	register_options ()
	utility function to register options More...

Variables
static basic::Tracer	TR ("apps.pilot.smlewis.HECT")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::e3_hinge_start_resnum ("e3_hinge_start_resnum")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::e3_hinge_stop_resnum ("e3_hinge_stop_resnum")
basic::options::StringOptionKey const	basic::options::OptionKeys::e3_hinge_chain ("e3_hinge_chain")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::e3_catalytic_resnum ("e3_catalytic_resnum")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::UBQ_tail_start_resnum ("UBQ_tail_start_resnum")
basic::options::StringOptionKey const	basic::options::OptionKeys::UBQ_tail_chain ("UBQ_tail_chain")
basic::options::StringOptionKey const	basic::options::OptionKeys::e2_chain ("e2_chain")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::e2_catalytic_resnum ("e2_catalytic_resnum")
basic::options::BooleanOptionKey const	basic::options::OptionKeys::debug_skip_fragment_generation ("debug_skip_fragment_generation")
basic::options::BooleanOptionKey const	basic::options::OptionKeys::debug ("debug")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::cycles ("cycles")
basic::options::IntegerOptionKey const	basic::options::OptionKeys::repack_cycles ("cycles")
basic::options::RealOptionKey const	basic::options::OptionKeys::catalytic_cst_sd ("catalytic_cst_sd")
basic::options::RealOptionKey const	basic::options::OptionKeys::ubq_cst_sd ("ubq_cst_sd")

Function Documentation

register_options()

void register_options

(

)

utility function to register options

References utility::options::OptionCollection::add(), basic::options::OptionKeys::catalytic_cst_sd, basic::options::OptionKeys::cycles, basic::options::OptionKeys::debug, basic::options::OptionKeys::debug_skip_fragment_generation, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::e2_catalytic_resnum, basic::options::OptionKeys::e2_chain, basic::options::OptionKeys::e3_catalytic_resnum, basic::options::OptionKeys::e3_hinge_chain, basic::options::OptionKeys::e3_hinge_start_resnum, basic::options::OptionKeys::e3_hinge_stop_resnum, basic::options::option, basic::options::OptionKeys::repack_cycles, basic::options::OptionKeys::ubq_cst_sd, basic::options::OptionKeys::UBQ_tail_chain, and basic::options::OptionKeys::UBQ_tail_start_resnum.

Variable Documentation

TR

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

static

Referenced by HECTMover::apply(), HECTMover::HECTMover(), HECTMover::make_frags(), HECTMover::parse_options(), and HECTMover::set_up_foldtree().