- j -

• j() : protocols::frag_picker::Contact
• jacobi() : protocols::evaluation::PCA , protocols::frag_picker::scores::RDCScore
• Jcomputed() : core::scoring::RDC
• JCoupling() : protocols::frag_picker::scores::JCoupling
• JCouplingIO() : protocols::frag_picker::JCouplingIO
• jd2_signal_handler() : protocols::jd2::JobDistributor
• JD2ResourceManager() : protocols::jd2::JD2ResourceManager
• JD2ResourceManagerJobInputter() : protocols::jd2::JD2ResourceManagerJobInputter
• Jdipolar() : core::scoring::RDC , core::scoring::RDC_Rohl
• JJH_Minimizer() : core::optimization::JJH_Minimizer
• Job() : protocols::jd2::Job
• job_failed() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor
• job_has_completed() : protocols::enzdes::EnzdesJobOutputter , protocols::features::DatabaseJobOutputter , protocols::jd2::AtomTreeDiffJobOutputter , protocols::jd2::FileJobOutputter , protocols::jd2::JobOutputter , protocols::jd2::NoOutputJobOutputter , protocols::jd2::PDBJobOutputter , protocols::jd2::ScoreOnlyJobOutputter , protocols::jd2::SilentFileJobOutputter
• job_inputter() : protocols::jd2::JobDistributor
• job_inputter_input_source() : protocols::jd2::JobDistributor
• job_inputter_input_source_to_string() : protocols::jd2::JobInputter
• job_outputter() : protocols::jd2::JobDistributor
• job_parameters() : protocols::swa::rna::StepWiseRNA_JobParameters_Setup , protocols::swa::StepWisePoseSetup
• job_succeeded() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• JobDataFeatures() : protocols::features::JobDataFeatures
• JobDataFeaturesCreator() : protocols::features::JobDataFeaturesCreator
• JobDistributor() : protocols::jd2::JobDistributor
• JobInputterCreator() : protocols::jd2::JobInputterCreator
• JobInputterFactory() : protocols::jd2::JobInputterFactory
• JobInputterRegistrator() : protocols::jd2::JobInputterRegistrator< T >
• JobOutputter() : protocols::jd2::JobOutputter
• JobOutputterCreator() : protocols::jd2::JobOutputterCreator
• JobOutputterFactory() : protocols::jd2::JobOutputterFactory
• JobOutputterRegistrator() : protocols::jd2::JobOutputterRegistrator< T >
• jobs_completed() : protocols::jd2::archive::ArchiveManager
• join() : protocols::pockets::PClusterSet
• JointScore() : protocols::sic_dock::JointScore
• JointSequenceOperation() : protocols::toolbox::task_operations::JointSequenceOperation
• JScoreEvaluator() : protocols::simple_filters::JScoreEvaluator
• JScoreEvaluatorCreator() : protocols::simple_filters::JScoreEvaluatorCreator
• Jump() : core::kinematics::Jump
• jump() : core::conformation::Conformation , core::io::silent::BinaryProteinSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RNA_SilentStruct , core::kinematics::AtomTree , core::kinematics::tree::Atom , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , protocols::simple_filters::DeltaFilter , core::pose::Pose , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::rna::RNA_PairingTemplate , protocols::scoring::Interface , protocols::simple_filters::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• jump_atom() : protocols::topology_broker::JumpClaim
• jump_atom_id() : core::conformation::Conformation
• jump_atoms() : protocols::jumping::JumpSample
• jump_backward() : protocols::rna::RNA_PairingTemplate
• jump_change_frequency() : protocols::rna::RNA_DeNovoProtocol
• jump_clones() : core::conformation::symmetry::SymmetryInfo
• jump_containing_helix() : protocols::nonlocal::HelixRotate
• jump_containing_sheet() : protocols::nonlocal::SheetTranslate
• jump_cycles() : protocols::abinitio::JumpingFoldConstraints
• jump_def() : protocols::topology_broker::JumpClaimer
• jump_direction() : core::conformation::symmetry::SymDof
• jump_edge() : core::kinematics::FoldTree
• jump_exists() : core::kinematics::FoldTree
• jump_follows() : core::conformation::symmetry::SymmetryInfo
• jump_forward() : protocols::rna::RNA_PairingTemplate
• jump_id() : protocols::simple_filters::ShapeComplementarityFilter , protocols::scoring::Interface , protocols::docking::DockingEnsemble
• jump_id_begin() : core::kinematics::MoveMap
• jump_id_end() : core::kinematics::MoveMap
• jump_is_independent() : core::conformation::symmetry::SymmetryInfo
• jump_mover() : protocols::abinitio::KinematicControl
• jump_nr() : core::kinematics::FoldTree
• Jump_point() : protocols::swa::rna::Jump_point
• jump_point() : core::kinematics::FoldTree
• jumpAtoms() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• jumpAtoms_defined() : protocols::jumping::ResiduePairJumpSingle , protocols::jumping::ResiduePairJump
• JumpCalculator() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• JumpClaim() : protocols::topology_broker::JumpClaim
• JumpClaimer() : protocols::topology_broker::JumpClaimer
• JumpDef() : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• JumpEvaluator() : protocols::simple_filters::JumpEvaluator
• JumpID() : core::id::JumpID
• JumpingFoldConstraints() : protocols::abinitio::JumpingFoldConstraints
• JumpingFoldConstraintsWrapper() : protocols::abinitio::JumpingFoldConstraintsWrapper
• JumpingFrame() : core::fragment::JumpingFrame
• JumpNrEvaluator() : protocols::simple_filters::JumpNrEvaluator
• JumpNrEvaluatorCreator() : protocols::simple_filters::JumpNrEvaluatorCreator
• JumpOutMover() : protocols::moves::JumpOutMover
• JumpRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• jumps() : protocols::jumping::JumpSample , protocols::simple_filters::InterfaceSasaFilter
• jumps2pairings() : protocols::jumping::JumpSample
• jumps_and_cuts_from_foldtree() : protocols::hybridization::HybridizeFoldtreeDynamic
• JumpSample() : protocols::jumping::JumpSample
• JumpSelector() : protocols::jumping::JumpSelector
• JumpSetup() : protocols::jumping::JumpSetup
• JumpsFromAllPairings() : protocols::jumping::JumpsFromAllPairings
• JumpWeightDef() : protocols::jumping::JumpSelector::JumpWeightDef
• just_smooth_cycles() : protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio