reportFragments.cc File Reference

#include <basic/options/util.hh>
#include <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/dwkulp.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/TaskOperations.fwd.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/CCDLoopClosureMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/loops/kinematic_closure/KinematicMover.hh>
#include <protocols/moves/kinematic_closure/KinematicPerturber.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <numeric/random/random.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/rms_util.hh>
#include <basic/MetricValue.hh>
#include <basic/Tracer.hh>
#include <core/fragment/FragData.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <protocols/frag_picker/FragmentPicker.hh>
#include <protocols/frag_picker/FragmentPicker.fwd.hh>
#include <protocols/frag_picker/VallProvider.hh>
#include <protocols/frag_picker/VallProvider.fwd.hh>
#include <protocols/frag_picker/VallChunk.hh>
#include <protocols/frag_picker/VallResidue.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/FragmentCandidate.fwd.hh>
#include <protocols/frag_picker/FragmentSelectingRule.hh>
#include <protocols/frag_picker/VallChunkFilter.hh>
#include <protocols/frag_picker/BoundedCollector.hh>
#include <protocols/frag_picker/BestTotalScoreSelector.hh>
#include <protocols/frag_picker/DiversifyCrmsdByClustering.hh>
#include <protocols/frag_picker/scores/FragmentScoringMethod.hh>
#include <protocols/simple_moves/FragmentMover.hh>
#include <protocols/loops/ccd_closure.hh>
#include <protocols/moves/Mover.hh>
#include <utility/excn/Exceptions.hh>
#include <core/import_pose/import_pose.hh>
#include <iostream>
#include <fstream>
#include <numeric>
#include <functional>

Typedefs
typedef utility::pointer::owning_ptr< AnnotatedFragData >	AnnotatedFragDataOP
typedef utility::pointer::owning_ptr< AnnotatedFragData const >	AnnotatedFragDataCOP

Functions
void	get_fragment_sets (core::pose::Pose &_pose, string _polyAminoAcidSequence, utility::vector1< core::fragment::ConstantLengthFragSetOP > &fragSets)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("reportFragments")

Typedef Documentation

AnnotatedFragDataCOP

typedef utility::pointer::owning_ptr< AnnotatedFragData const > AnnotatedFragDataCOP

AnnotatedFragDataOP

typedef utility::pointer::owning_ptr< AnnotatedFragData > AnnotatedFragDataOP

Function Documentation

get_fragment_sets()

void get_fragment_sets	(	core::pose::Pose &	_pose,
		string	_polyAminoAcidSequence,
		utility::vector1< core::fragment::ConstantLengthFragSetOP > &	fragSets
	)

References basic::options::OptionKeys::nonlocal::chunks, basic::options::OptionKeys::frags::scoring::config, utility::io::oc::cout, create_a3b_hbs::j, basic::options::option, secstruct(), basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::in::file::vall.

Referenced by main().

main()

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

References a, argv, utility::io::oc::cout, test.T009_Exceptions::e, create_a3b_hbs::f, basic::options::OptionKeys::dwkulp::forcePolyAAfragments, val2thr::fout, score_vs_rmsd::frames, get_fragment_sets(), create_a3b_hbs::i, basic::init(), basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::start_file(), and basic::options::OptionKeys::inout::dbms::user.

Variable Documentation

TR

basic::Tracer TR("reportFragments") ( "reportFragments"  )

static