SimpleCycpepPredictApplication.cc File Reference

Application-level code for the simple_cycpep_predict app. More...

#include <protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.hh>
#include <protocols/cyclic_peptide_predict/HierarchicalHybridJD_JobResultsSummary.hh>
#include <protocols/cyclic_peptide_predict/util.hh>
#include <basic/options/option.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/util.hh>
#include <core/id/TorsionID.hh>
#include <core/id/AtomID.hh>
#include <core/id/NamedAtomID.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/OperateOnResidueSubset.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/palette/CustomBaseTypePackerPalette.hh>
#include <core/select/residue_selector/PhiSelector.hh>
#include <core/select/residue_selector/BinSelector.hh>
#include <core/select/residue_selector/NotResidueSelector.hh>
#include <core/select/residue_selector/ResidueIndexSelector.hh>
#include <utility/exit.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/Tracer.hh>
#include <core/pose/PDBInfo.hh>
#include <utility/io/ozstream.hh>
#include <utility/io/izstream.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/variant_util.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/Ramachandran.hh>
#include <core/scoring/RamaPrePro.hh>
#include <core/scoring/ScoringManager.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/filters/Filter.hh>
#include <protocols/rosetta_scripts/ParsedProtocol.hh>
#include <protocols/filters/BasicFilters.hh>
#include <protocols/aa_composition/AddCompositionConstraintMover.hh>
#include <protocols/aa_composition/ClearCompositionConstraintsMover.hh>
#include <protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.hh>
#include <protocols/cyclic_peptide/CycpepSymmetryFilter.hh>
#include <protocols/protein_interface_design/filters/HbondsToResidueFilter.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/denovo_design/movers/FastDesign.hh>
#include <protocols/cyclic_peptide/PeptideInternalHbondsFilter.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/scoring/Energies.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/string_util.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/func/CircularHarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/DihedralConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <protocols/cyclic_peptide/TryDisulfPermutations.hh>
#include <protocols/score_filters/ScoreTypeFilter.hh>
#include <protocols/simple_moves/ModifyVariantTypeMover.hh>
#include <protocols/cyclic_peptide/CrosslinkerMover.hh>
#include <protocols/cyclic_peptide/crosslinker/TBMB_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/TMA_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/1_4_BBMB_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/TrigonalPyramidalMetal_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/TrigonalPlanarMetal_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/SquarePyramidalMetal_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/SquarePlanarMetal_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/TetrahedralMetal_Helper.hh>
#include <protocols/cyclic_peptide/crosslinker/OctahedralMetal_Helper.hh>
#include <protocols/cyclic_peptide/PeptideStubMover.hh>
#include <protocols/cyclic_peptide/DeclareBond.hh>
#include <protocols/generalized_kinematic_closure/GeneralizedKIC.hh>
#include <basic/options/option_macros.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/cyclic_peptide.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <numeric/conversions.hh>
#include <numeric/random/random.hh>
#include <numeric/constants.hh>
#include <numeric/angle.functions.hh>
#include <cstdio>

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

Functions
static basic::Tracer	TR ("protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication")

Detailed Description

Application-level code for the simple_cycpep_predict app.

This application predicts structures of simple backbone-cyclized peptides made of alpha-, beta-, or gamma-amino acids (of any chirality) using generalized kinematic closure (GenKIC) for cyclization, and enforcing user-defined requiresments for numbers of mainchain hydrogen bonds. In April 2017, I also added support for cyclization through disulfide bonds.

Author

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

Function Documentation

static basic::Tracer TR ( "protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication"  )

static