JumpSpecificAbrelax.cc File Reference

#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/abinitio/AbrelaxApplication.hh>
#include "JumpSpecificAbrelax.hh"
#include "SpecificJumpSetup.cc"
#include "LibraryJumpSetup.cc"
#include <core/kinematics/util.hh>
#include <protocols/abinitio/ClassicAbinitio.hh>
#include <protocols/abinitio/FoldConstraints.hh>
#include <protocols/abinitio/JumpingFoldConstraints.hh>
#include <protocols/abinitio/KinematicTaskControl.hh>
#include <protocols/abinitio/LoopJumpFoldCst.hh>
#include <protocols/abinitio/DoubleLayerKinematicAbinitio.hh>
#include <protocols/abinitio/Templates.hh>
#include <protocols/abinitio/TemplateJumpSetup.hh>
#include <protocols/abinitio/PairingStatistics.hh>
#include <protocols/abinitio/StrandConstraints.hh>
#include <protocols/abinitio/FragmentMover.hh>
#include <protocols/Protocol.hh>
#include <protocols/relax_protocols.hh>
#include <protocols/jumping/SheetBuilder.hh>
#include <protocols/jumping/JumpSetup.hh>
#include <core/scoring/dssp/PairingsList.hh>
#include <protocols/jumping/ResiduePairJumpSetup.hh>
#include <protocols/jumping/SecondaryStructure.hh>
#include <protocols/jumping/StrandPairing.hh>
#include <protocols/jumping/util.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <basic/MetricValue.hh>
#include <basic/options/option.hh>
#include <basic/options/after_opts.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/util.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <protocols/pose_metric_calculators/ClashCountCalculator.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/sequence/util.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/evaluation/RmsdEvaluator.hh>
#include <protocols/evaluation/JumpEvaluator.hh>
#include <protocols/evaluation/TimeEvaluator.hh>
#include <protocols/evaluation/PCA.hh>
#include <protocols/evaluation/PoseMetricEvaluator.hh>
#include <protocols/evaluation/ConstraintEvaluator.hh>
#include <protocols/evaluation/util.hh>
#include <protocols/evaluation/EvaluationFactory.hh>
#include <protocols/loops/SlidingWindowLoopClosure.hh>
#include <protocols/loops/ShortLoopClosure.hh>
#include <protocols/loops/LoopClosure.hh>
#include <protocols/loops/LoopClass.hh>
#include <protocols/loops/LoopMover.hh>
#include <protocols/loops/util.hh>
#include <protocols/filters/Filter.hh>
#include <protocols/simple_filters/RGFilter.hh>
#include <protocols/simple_filters/COFilter.hh>
#include <protocols/simple_filters/SheetFilter.hh>
#include <numeric/random/random.hh>
#include <basic/options/option_macros.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <utility/io/util.hh>
#include <cstdlib>
#include <string>
#include <vector>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/filters.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Classes
class	protocols::abinitio::PcaEvaluator
class	protocols::abinitio::ShowViolation
class	protocols::abinitio::ComputeTotalDistCst
class	protocols::abinitio::Stage1Sampler

Namespaces
	protocols
	demo program for implementing loop relax + FA relax
	protocols::abinitio

Typedefs
typedef std::pair< core::pose::Pose, core::Real >	protocols::abinitio::PoseWithScore

Functions
bool	protocols::abinitio::sort_PoseWithScore (const PoseWithScore &left, const PoseWithScore &right)

Variables
static basic::Tracer	tr ("protocols.abinitio.JumpSpecificAbrelax")
	Application level code for relax-type protocols. More...

Variable Documentation

tr

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

static

Application level code for relax-type protocols.

use JumpSpecificAbrelax in the following way:

AbrelaxAppliaction::register_options(); devel::init AbrelaxAppliaction my_app; my_app.add_evaluation( new MySpecialEvaluator ); ... my_app.run();

---

control flow: the run method calls setup() and then either fold() or rerun() (depending on option -rerun )

each decoy is evaluated by process_decoy() and results are written to the score-file (if specified) or to the silent_output file ( if applicable ). the score file is a silent-file without structural data ( just SCORE lines )

rerun(): run thru structures in in:file:silent and call process_decoy for each fold(): produce structures with an Abinitio-type protocol and call process_decoy

options specific to JumpSpecificAbrelax can be found by using -help at the command-line. if you add new options please follow the scheme in the static method register options

the behaviour of JumpSpecificAbrelax is controlled by comman-line-options. Refer to -help (usage) and the code

information that is not always present is stored as xxxOP, and the NULL-pointer is interpreted that the respective behaviour is not present. (i.e., native_pose_ is either pointing to the native pose (-native) or to NULL. when you use such pointers ask if they are non-NULL.

Author

Oliver Lange