- j -

• j() : protocols::farna::BasePairStep , protocols::frag_picker::Contact
• j_next() : protocols::farna::BasePairStep
• jacobi() : protocols::evaluation::PCA
• 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
• Job() : protocols::jd2::Job
• job_failed() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MSDJobDistributor
• 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_id() : protocols::canonical_sampling::DbTrajectoryRecorder
• 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_succeeded() : protocols::jd2::BOINCJobDistributor , protocols::jd2::FileSystemJobDistributor , protocols::jd2::JobDistributor , protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::MPIWorkPoolJobDistributor
• job_succeeded_additional_output() : protocols::jd2::JobDistributor
• 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::CClusterSet , protocols::pockets::PClusterSet
• join_two_poses_by_jump() : protocols::motif_grafting::movers::MotifGraftMover
• JointScore() : protocols::sic_dock::JointScore
• JointSequenceOperation() : protocols::toolbox::task_operations::JointSequenceOperation
• JScoreEvaluator() : protocols::simple_filters::JScoreEvaluator
• JScoreEvaluatorCreator() : protocols::simple_filters::JScoreEvaluatorCreator
• JSON_RPC() : protocols::rpc::JSON_RPC
• judge_facing() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_dis_too_close() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_inter_dis() : protocols::features::strand_assembly::StrandBundleFeatures
• judge_sw_torsion() : protocols::features::strand_assembly::StrandBundleFeatures
• jump() : protocols::environment::claims::VirtResClaim , protocols::farna::RNA_PairingTemplate , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::scoring::Interface , protocols::simple_filters::AlaScan , protocols::simple_filters::DeltaFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• jump_atom() : protocols::topology_broker::claims::JumpClaim
• jump_atom1() : protocols::topology_broker::claims::JumpClaim
• jump_atom2() : protocols::topology_broker::claims::JumpClaim
• jump_atoms() : protocols::jumping::JumpSample
• jump_backward() : protocols::farna::RNA_PairingTemplate
• jump_change_frequency() : protocols::farna::RNA_DeNovoProtocol
• jump_containing_helix() : protocols::nonlocal::HelixRotate
• jump_containing_sheet() : protocols::nonlocal::SheetTranslate
• jump_def() : protocols::topology_broker::FragmentJumpClaimer
• jump_forward() : protocols::farna::RNA_PairingTemplate
• jump_id() : protocols::docking::DockingEnsemble , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::scoring::Interface , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter
• jump_mover() : protocols::abinitio::KinematicControl
• jump_num() : protocols::matdes::SymUnsatHbondFilter
• jump_number() : protocols::rigid::UniformRigidBodyMover
• Jump_point() : protocols::stepwise::modeler::rna::Jump_point
• jump_sample() : protocols::abinitio::abscript::JumpSampleData
• jump_set() : protocols::matdes::OligomericAverageDegreeFilter
• jumpAtoms() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• jumpAtoms_defined() : protocols::jumping::ResiduePairJump , protocols::jumping::ResiduePairJumpSingle
• JumpCalculator() : protocols::topology_broker::RigidChunkClaimer::JumpCalculator
• JumpClaim() : protocols::environment::claims::JumpClaim , protocols::topology_broker::claims::JumpClaim
• JumpDef() : protocols::jumping::JumpSetup::JumpDef , protocols::jumping::ResiduePairJumpSetup::JumpDef
• JumpElement() : protocols::environment::claims::JumpElement
• JumpEvaluator() : protocols::simple_filters::JumpEvaluator
• JumpingFoldConstraintsWrapper() : protocols::abinitio::JumpingFoldConstraintsWrapper
• 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
• JumpSampleData() : protocols::abinitio::abscript::JumpSampleData
• JumpSelector() : protocols::jumping::JumpSelector
• JumpSetup() : protocols::jumping::JumpSetup
• JumpsFromAllPairings() : protocols::jumping::JumpsFromAllPairings
• JumpStepWiseSampler() : protocols::stepwise::sampler::JumpStepWiseSampler
• JumpWeightDef() : protocols::jumping::JumpSelector::JumpWeightDef
• just_min_after_mutation_frequency() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• just_smooth_cycles() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio