ConstraintFragmentSampler.cc File Reference

ab-initio fragment assembly protocol for proteins More...

#include <protocols/abinitio/ConstraintFragmentSampler.hh>
#include <protocols/topology_broker/TopologyBroker.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <protocols/moves/TrialMover.hh>
#include <utility/exit.hh>
#include <utility/vector1.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <numeric/numeric.functions.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/fold_cst.OptionKeys.gen.hh>
#include <basic/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <cstdlib>
#include <string>
#include <core/kinematics/ShortestPathInFoldTree.hh>
#include <protocols/constraints_additional/MaxSeqSepConstraintSet.hh>
#include <utility/vector1.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::abinitio

Functions
static thread_local basic::Tracer	tr ("protocols.abinitio")
Size	seq_sep_stage (core::Size total_res, Real factor)

Detailed Description

ab-initio fragment assembly protocol for proteins

Contains currently: Classic Abinitio

Author

Oliver Lange

James Thompson

Mike Tyka

Christopher Miles (cmile.nosp@m.s@uw.nosp@m..edu)

Function Documentation

Size seq_sep_stage	(	core::Size	total_res,
		Real	factor
	)

call this: ConstraintFragmentSampler::register_options() before devel::init(). Derived classes that overload this function should also call Parent::register_options()

Referenced by protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), and protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn().

static thread_local basic::Tracer tr ( "protocols.abinitio"  )

static

Referenced by protocols::abinitio::ConstraintFragmentSampler::apply(), protocols::abinitio::ConstraintFragmentSampler::do_stage1_cycles(), protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage3(), protocols::abinitio::ConstraintFragmentSampler::prepare_loop_in_stage4(), protocols::abinitio::ConstraintFragmentSampler::prepare_stage2(), protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().