FragmentSampler.cc File Reference

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

#include <core/types.hh>
#include <protocols/abinitio/FragmentSampler.hh>
#include <protocols/topology_broker/TopologyBroker.hh>
#include <core/pose/Pose.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/MembraneTopology.hh>
#include <protocols/canonical_sampling/mc_convergence_checks/util.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/jd2/util.hh>
#include <protocols/moves/TrialMover.hh>
#include <protocols/moves/RepeatMover.hh>
#include <protocols/moves/MonteCarloExceptionConverge.hh>
#include <protocols/moves/MoverStatus.hh>
#include <protocols/loophash/LoopHashLibrary.fwd.hh>
#include <protocols/loophash/LoopHashLibrary.hh>
#include <protocols/loophash/LoopHashMap.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/random/random.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/lh.OptionKeys.gen.hh>
#include <string>
#include <utility>
#include <iostream>
#include <protocols/moves/MonteCarlo.hh>
#include <core/kinematics/FoldTree.hh>

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

Functions
static basic::Tracer	tr ("protocols.abinitio")
bool	protocols::abinitio::contains_stageid (utility::vector1< abinitio::StageID > vec, abinitio::StageID query)

Detailed Description

ab-initio fragment assembly protocol for proteins

Contains currently: Classic Abinitio

Author

Oliver Lange

James Thompson

Mike Tyka

Contains currently: Classic Abinitio

Author

Oliver Lange

Contains currently: Classic Abinitio

Author

Oliver Lange

Note

Someone has clearly made some attempt at thread-safety, here, but unfortunately there exist "atomic" operations that are not truly atomic. If this protocol actually needs to be thread-safe, it will have to be refactored. – VKM, 15 Aug 2017.

Function Documentation

tr()

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

static

Referenced by protocols::abinitio::FragmentSampler::apply(), protocols::abinitio::FragmentSampler::check_loops(), protocols::abinitio::FragmentSampler::checkpointed_cycle_block(), protocols::abinitio::FragmentSampler::do_stage3_cycles(), protocols::abinitio::FragmentSampler::do_stage4_cycles(), protocols::abinitio::FragmentSampler::recover_low(), protocols::abinitio::FragmentSampler::set_default_scores(), and protocols::abinitio::FragmentSampler::set_score_weight().