Rosetta 3.4
Variables
make_table_of_pilot_apps Namespace Reference

Variables

tuple parser = OptionParser()
string action = "store"
string help = "Name of pilot_apps.src.settings.all file from which to generate table of applications and demos"
tuple f = open( options.filename, "r")
tuple d = open( options.doxyfile, "w")
tuple begin = line.find('/*')
tuple end = line.find('*/')
tuple start_name = line.find('"') end_name = line.find('"', start_name +1 )
list line_info = line[begin+1:end-1]
list name = line[start_name+1:end_name]
tuple app_info = line_info.split(",")

Variable Documentation

tuple make_table_of_pilot_apps::app_info = line_info.split(",")
tuple make_table_of_pilot_apps::begin = line.find('/*')

Referenced by protocols::ligand_docking::Translate::add_excluded_chains(), protocols::ligand_docking::append_ligand_RMSD(), protocols::qsar::qsarMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::CompoundTranslate::apply(), protocols::fldsgn::filters::HelixKinkFilter::apply(), protocols::docking::DockingPrepackProtocol::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::simple_moves::FragmentMover::apply_at_all_positions(), core::kinematics::FoldTree::apply_sequence_mapping(), protocols::vip::base_name(), core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), protocols::genetic_algorithm::GeneticAlgorithm::best_entities(), protocols::match::downstream::SecondaryMatcherToUpstreamResidue::build(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::build_rotamers(), protocols::match::BumpGrid::BumpGrid(), core::scoring::CA_rmsd_symmetric(), protocols::fldsgn::topology::Sheet::calc_geometry(), protocols::fldsgn::topology::Sheet::calc_sasa_bothsides(), core::io::silent::ProteinSilentStruct_Template< T >::chain_endings_str(), core::io::silent::BinaryProteinSilentStruct::chain_endings_str(), protocols::loophash::MPI_LoopHashRefine_Master::check_library_expiry_dates(), protocols::scoring::ImplicitFastClashCheck::clash_count(), core::pack::scmin::SCMinMinimizerMap::clear_active_chi(), core::scoring::electron_density::ElectronDensity::clear_dCCdx_res_cache(), protocols::abinitio::IterativeBase::cluster(), protocols::abinitio::IterativeBase::compute_beta_topology(), protocols::abinitio::IterativeBase::compute_cores(), protocols::pack_daemon::DaemonSet::compute_energy_for_assignment(), protocols::simple_moves::GunnCost::compute_gunn(), protocols::frag_picker::scores::GunnCost::compute_gunn(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig(), protocols::pack_daemon::MPIMultistateFitnessFunction::compute_state_energies(), core::scoring::packstat::compute_surrounding_sasa(), core::pose::PDBInfo::copy(), core::pose::Pose::copy_segment(), protocols::match::MatchCounter::count_n_matches(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::jumping::ResiduePairJumpSetup::create_jump_sample(), core::scoring::interface::DDPlookup::DDPlookup(), protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized(), core::kinematics::FoldTree::delete_jump_and_intervening_cutpoint(), protocols::enzdes::SecondaryMatchProtocol::determine_found_residues_compatibility(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::determine_res_cb_deviation(), protocols::optimize_weights::WrapperOptEMultifunc::dfunc(), core::scoring::constraints::AmbiguousNMRConstraint::dist(), protocols::protein_interface_design::movers::DisulfideMover::disulfide_list(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::match::Matcher::downstream_algorithms(), protocols::simple_moves::ClassicFragmentMover::end_bias_check(), protocols::multistate_design::MultiStatePacker::evaluate(), protocols::genetic_algorithm::GeneticAlgorithm::evaluate_fitnesses(), core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2(), protocols::fldsgn::topology::DimerPairings::finalize(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), core::fragment::FrameList::flat_size(), protocols::rosetta_scripts::foreach_movemap_tag(), core::fragment::FrameList::fragID(), core::fragment::picking_old::vall::VallLibrarian::fragments(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::abinitio::IterativeBase::gen_start_structures(), protocols::jd2::archive::DebugArchive::generate_batch(), protocols::noesy_assign::StructureDependentPeakCalibrator::generate_constraints(), core::fragment::FragSet::generate_insert_map(), protocols::jumping::ResiduePairJumpSetup::generate_jump_frags(), core::pose::get_chain_residues(), protocols::features::get_DB_filter_ptr(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::kinematics::FoldTree::get_outgoing_edges(), core::kinematics::FoldTree::get_polymer_residue_direction(), core::kinematics::FoldTree::get_residue_edge(), protocols::ddg::ddGMover::get_scorefunction_header(), protocols::forge::methods::grow_right_r(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::match::output::PoseMatchOutputWriter::insert_match_into_pose(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfoList::inverse_rotamers_against_residue(), core::kinematics::FoldTree::is_simple_tree(), protocols::loophash::LoopHashMap::lookup(), protocols::loops::loops_around_residues(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), core::conformation::symmetry::SymmetryInfo::map_symmetric_res_pairs(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), protocols::forge::methods::merge(), MinimizeInterface(), protocols::forge::build::RelativeConnectRight::modify_impl(), protocols::forge::build::SegmentRebuild::movemap(), core::scoring::trie::CPDataCorrespondence::n_connpoints_for_entry(), core::fragment::FragSet::nr_frames(), core::pose::num_atoms(), core::pose::num_chi_angles(), core::pose::num_hbond_acceptors(), core::pose::num_hbond_donors(), core::pose::num_heavy_atoms(), core::pack::interaction_graph::OnTheFlyEdge::OnTheFlyEdge(), core::pack::dunbrack::SingleResidueDunbrackLibrary::packed_rotno_2_rotwell(), protocols::simple_moves::SequenceProfileMover::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::seeded_abinitio::CAcstGenerator::parse_my_tag(), protocols::protein_interface_design::movers::SetupHotspotConstraintsMover::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::seeded_abinitio::parse_seeds(), protocols::seeded_abinitio::parse_spans(), core::kinematics::FoldTree::partition_by_residue(), protocols::antibody::Antibody::populate_all_cdrs(), core::pose::Pose::Pose(), core::coarse::Rule::pretty_print(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator::print(), core::io::silent::ProteinSilentStruct_Template< T >::print_conformation(), core::io::silent::BinaryRNASilentStruct::print_conformation(), core::io::silent::BinaryProteinSilentStruct::print_conformation(), protocols::genetic_algorithm::GeneticAlgorithm::print_generation_statistics(), protocols::genetic_algorithm::GeneticAlgorithm::print_population(), protocols::loophash::MPI_LoopHashRefine_Master::process_inbound_wus(), protocols::loophash::MPI_LoopHashRefine_Master::process_outbound_wus(), core::scoring::packstat::prune_1pass(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::ligand_docking::rb_grid_rotamer_trials_atr_rep(), protocols::ligand_docking::rb_grid_score_atr_rep(), core::sequence::Sequence::read_data(), protocols::loophash::BackboneDB::read_db(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::forge::methods::replace(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), core::sequence::SequenceProfile::rescale(), protocols::jd2::archive::EvaluatedArchive::rescore(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), core::pack::task::ResfileContents::ResfileContents(), protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator::residue_decomposition_to_set_numbers(), protocols::rna::RNA_ChunkLibrary::RNA_ChunkLibrary(), protocols::fldsgn::potentials::sspot::SSPairPotential::score(), protocols::constraints_additional::AmbiguousMultiConstraint::score(), core::scoring::constraints::KofNConstraint::score(), core::scoring::constraints::AmbiguousNMRConstraint::score(), core::scoring::constraints::AmbiguousConstraint::score(), core::scoring::packstat::search_x(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), core::chemical::Selector_CMDFLAG::Selector_CMDFLAG(), protocols::docking::DockMinMover::set_default(), protocols::docking::DockingHighResLegacy::set_default(), protocols::abinitio::ClassicAbinitio::set_default_options(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), protocols::match::Matcher::set_original_scaffold_build_points_for_constraint(), core::kinematics::MoveMap::set_ranges_unmodifiable(), core::conformation::symmetry::SymmetricConformation::set_xyz(), core::chemical::setup_aa2name(), core::chemical::setup_aa2oneletter(), protocols::match::output::CloudPDBWriter::setup_hitset_iterators_for_group(), protocols::frag_picker::setup_type2name(), protocols::constraints_additional::AmbiguousMultiConstraint::show(), core::scoring::constraints::SiteConstraint::show(), core::scoring::constraints::KofNConstraint::show(), core::scoring::constraints::ConstraintSet::show(), core::scoring::constraints::AmbiguousConstraint::show(), core::kinematics::FoldTree::show(), core::scoring::constraints::MultiConstraint::show_def(), core::scoring::constraints::AmbiguousNMRConstraint::show_def(), core::scoring::constraints::ConstraintSet::show_definition(), core::scoring::constraints::ConstraintSet::show_numbers(), core::scoring::Energies::show_total_headers(), core::scoring::Energies::show_totals(), core::scoring::constraints::ConstraintSet::show_violations(), core::scoring::constraints::AmbiguousNMRConstraint::show_violations(), core::scoring::constraints::AmbiguousConstraint::show_violations(), protocols::multistate_design::MultiStatePacker::single_state_design(), core::fragment::FragSet::size(), core::kinematics::FoldTree::slide_jump(), core::pose::Pose::split_by_chain(), protocols::fldsgn::CircularPermutation::split_chains(), core::scoring::sym_rmsd_with_super_subset(), protocols::jd2::archive::ArchiveManager::unfinished_batches(), protocols::simple_moves::symmetry::SymmetrySlider::very_far_away(), protocols::forge::remodel::WorkingRemodelSet::workingSetGen(), protocols::optimize_weights::WrapperOptEMultifunc::WrapperOptEMultifunc(), and protocols::optimize_weights::PNatAAOptEPositionData::write_to_binary_file().

tuple make_table_of_pilot_apps::d = open( options.doxyfile, "w")

Referenced by protocols::loops::Loops::add_overlap_loop(), protocols::abinitio::MembraneAbinitio::add_spanning_region(), core::scoring::sc::ShapeComplementarityCalculator::AddDot(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::simple_filters::JumpEvaluator::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::toolbox::KClusterElement::assign_type_data(), protocols::protein_interface_design::best_cutpoint(), protocols::toolbox::CA_superimpose(), protocols::frag_picker::scores::FragmentCrmsdResDepth::cached_score(), protocols::frag_picker::scores::FragmentCrmsd::cached_score(), protocols::frag_picker::scores::AtomPairConstraintsScore::cached_score(), protocols::toolbox::calc_fit_R(), protocols::fldsgn::topology::HSSTriplet::calc_geometry(), core::scoring::packstat::cavity_distance_constraint(), protocols::toolbox::DecoySetEvaluation::compute_average_structure(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), core::pose::copy_dofs(), protocols::scoring::methods::saxs::PDDFEnergy::create_pddf(), protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::ddG_threshold(), protocols::protein_interface_design::movers::LoopLengthChange::delta(), protocols::protein_interface_design::filters::FilterScanFilter::delta(), protocols::protein_interface_design::filters::DesignableResiduesFilter::designable(), core::scoring::SmoothScoreTermCoeffs::dfunc(), protocols::frag_picker::DiversifyDihedralsSelector::dihedral_rmsd(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), protocols::simple_filters::AlaScan::dist(), protocols::protein_interface_design::AlaScan::dist(), protocols::toolbox::KClusterData::dist_square(), protocols::features::SaltBridgeFeatures::distance_cutoff(), protocols::protein_interface_design::filters::AverageDegreeFilter::distance_threshold(), protocols::frag_picker::scores::CSScore::do_caching(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), core::scoring::mm::MMBondLengthScore::dscore(), protocols::protein_interface_design::filters::FilterScanFilter::dump_pdb(), protocols::evaluation::PCA::eval(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::CartesianBondedEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::evaluate_core(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), protocols::toolbox::fill_CA_coords(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), core::scoring::dna::find_basepairs(), protocols::dna::find_basepairs(), protocols::toolbox::DecoySetEvaluation::find_closest_to_average(), protocols::toolbox::fit_centered_coords(), core::scoring::rna::fix_sugar_coords(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd(), protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd(), protocols::frag_picker::scores::FragmentCrmsdResDepth::FragmentCrmsdResDepth(), protocols::frag_picker::scores::FragmentDME::FragmentDME(), core::scoring::get_2way_orientation(), core::scoring::get_orientation(), core::scoring::packstat::old::get_orientation(), protocols::canonical_sampling::HamiltonianExchange::initialize_from_file(), protocols::optimize_weights::operator<<(), protocols::match::Bool3DGrid::or_by_sphere_liberal(), core::scoring::packstat::Circle::overlap(), core::scoring::packstat::overlap(), core::scoring::constraints::AngleConstraint::p1_deriv(), core::scoring::constraints::AngleConstraint::p2_deriv(), core::chemical::patch_operation_from_patch_file_line(), core::scoring::disulfides::FullatomDisulfidePotential::print_score_functions(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), protocols::jumping::read_disulf_pairing_list(), core::coarse::CoarseEtable::read_files(), core::scoring::dssp::read_pairing_list(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), core::chemical::read_topology_file(), protocols::toolbox::reset_x(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), protocols::frag_picker::scores::PhiPsiSquareWell::score(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::score(), core::scoring::mm::MMBondLengthScore::score(), core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide(), core::scoring::disulfides::FullatomDisulfidePotential::score_this_disulfide(), protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_angle_pot(), protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_distance_pot(), protocols::canonical_sampling::HamiltonianExchange::show(), protocols::topology_broker::CoordConstraintClaimer::superimpose(), protocols::protein_interface_design::filters::RelativePoseFilter::thread_seq(), and protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak().

tuple make_table_of_pilot_apps::end = line.find('*/')
tuple make_table_of_pilot_apps::f = open( options.filename, "r")

Referenced by protocols::abinitio::LoopJumpFoldCst::add_rigidity_jumps(), protocols::forge::methods::add_vertex(), protocols::antibody2::Ab_Info::all_cdr_fold_tree(), protocols::antibody::Antibody::all_cdr_fold_tree(), protocols::antibody2::Ab_ModelCDRH3::all_cdr_VL_VH_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::antibody::CDRH3Modeler::antibody_modeling_insert_ter(), protocols::simple_filters::RGFilter::apply(), protocols::simple_filters::COFilter::apply(), protocols::rna::RNA_HelixAssembler::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::LoopRefine::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loops::FoldTreeFromLoops::apply(), protocols::idealize::IdealizeMover::apply(), protocols::antibody2::Ab_CloseOneCDR_Mover::apply(), protocols::loops::apply_sequence_mapping(), protocols::loophash::BackboneSegment::apply_to_pose(), core::pack::interaction_graph::SurfaceNode< V, E, G >::assign_state_surface(), protocols::frag_picker::quota::QuotaCollector::attach_secondary_structure_pools(), protocols::idealize::basic_idealize(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::pack::interaction_graph::PDNode::calc_deltaEpd(), core::pack::interaction_graph::LinearMemNode::calc_deltaEpd(), core::pack::interaction_graph::LazyNode::calc_deltaEpd(), core::pack::interaction_graph::DoubleLazyNode::calc_deltaEpd(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcs::PCS_data_per_lanthanides::calculate_tensor_and_cost_with_svd(), protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd(), core::optimization::cartesian_collect_torsional_deriv(), protocols::loops::loop_closure::ccd::ccd_moves(), protocols::comparative_modeling::hybridize::InsertChunkMover::change_anchor(), protocols::frag_picker::scores::FragmentScoreMap::clone(), core::scoring::packstat::compute_cav_ball_volumes(), core::scoring::packstat::compute_sasa(), protocols::forge::remodel::RemodelLoopMover::create_fragment_movers(), protocols::topology_broker::AsymFoldandDockClaimer::docking_jump(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::scoring::MembranePotential::evaluate_env(), core::scoring::MembranePotential::evaluate_pair(), protocols::loophash::LoopHashLibrary::extract_data_from_pose(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), protocols::rna::figure_out_reasonable_rna_fold_tree(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::protein_interface_design::filters::BoltzmannFilter::fitness_threshold(), core::io::silent::ProteinSilentStruct_Template< T >::fold_tree(), core::io::silent::BinaryProteinSilentStruct::fold_tree(), core::fragment::FragmentRmsd::fragment(), protocols::sparta::ftoa(), protocols::sparta::ANN::ftoa(), core::scoring::constraints::SumFunc::func(), protocols::swa::protein::generate_beta_database_test(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), core::scoring::get_2way_orientation(), protocols::swa::protein::StepWiseBetaAntiParallelJumpSampleGenerator::get_antiparallel_beta_jumps(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::scoring::dna::get_base_pair_params_old(), core::scoring::dna::get_base_step_params(), core::pack::annealer::SimAnnealerBase::get_inneriterations(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), core::scoring::dna::get_stub_stub_params(), protocols::sparta::PDB::getOrbitalShift(), core::io::silent::RNA_SilentStruct::init_from_lines(), core::io::silent::ProteinSilentStruct_Template< T >::init_from_lines(), core::io::silent::BinaryRNASilentStruct::init_from_lines(), core::io::silent::BinaryProteinSilentStruct::init_from_lines(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::cluster::APCluster::load_binary(), core::scoring::saxs::FormFactorManager::load_ff(), core::scoring::saxs::FormFactorManager::load_ff_from_db(), protocols::rna::make_coarse_pose(), protocols::swa::make_cut_at_moving_suite(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_(), protocols::forge::methods::merge(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::forge::build::BuildManager::modify(), core::pack::interaction_graph::OnTheFlyEdge::OnTheFlyEdge(), core::optimization::DFPMinConvergedFractional::operator()(), core::scoring::constraints::AngleConstraint::p1_theta_deriv(), protocols::frag_picker::FragmentPicker::pick_candidates(), protocols::frag_picker::FragmentPicker::pick_chunk_candidates(), core::pack::interaction_graph::DoubleDensePDEdge::prepare_for_simulated_annealing(), core::pack::interaction_graph::DensePDEdge::prepare_for_simulated_annealing(), protocols::wum::MPI_WorkUnitManager::print_stats(), protocols::optimize_weights::PNatRotOptEPositionData::process_score(), core::scoring::ResidualDipolarCoupling::Q(), core::import_pose::read_additional_pdb_data(), core::io::serialization::read_binary(), protocols::antibody2::Ab_H3_cter_insert_mover::read_H3_cter_fragment(), protocols::antibody::read_H3_cter_fragment(), protocols::protein_interface_design::PatchdockReader::read_poses(), protocols::jumping::remove_cut(), protocols::rna::remove_cutpoint_closed(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::fibril::reorient_extended_fibril(), protocols::forge::remodel::RemodelLoopMover::repeat_generation(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer(), core::scoring::methods::SuckerEnergy::residue_pair_energy(), protocols::scoring::methods::pcs2::PcsDataLanthanide::retrieve_tensor_from_svd(), core::fragment::FragmentRmsd::rmsd(), core::pose::symmetry::rotate_anchor_to_x_axis(), protocols::flexpack::annealer::FlexbbSimAnnealer::run(), core::pack::annealer::MultiCoolAnnealer::run(), core::pack::annealer::DebuggingAnnealer::run(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::optimization::AtomTreeMinimizer::run(), protocols::cluster::APCluster::save_binary(), core::optimization::Particle::score(), core::pose::symmetry::sealed_symmetric_fold_tree(), core::pose::symmetry::set_asymm_unit_fold_tree(), core::conformation::symmetry::set_asymm_unit_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::abinitio::KinematicControl::set_final_fold_tree(), core::io::silent::RNA_SilentStruct::set_fold_tree(), core::io::silent::BinaryRNASilentStruct::set_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::genetic_algorithm::GeneticAlgorithm::set_frac_by_recomb(), protocols::genetic_algorithm::GeneticAlgorithm::set_func(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::abinitio::KinematicControl::set_sampling_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style(), protocols::frag_picker::FragmentPicker::set_up_ss_abego_quota(), protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(), protocols::jumping::MembraneJump::setup_fold_tree(), protocols::docking::setup_foldtree(), setup_pert_foldtree(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::antibody2::setup_simple_fold_tree(), protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(), protocols::antibody::AntibodyModeler::setup_simple_fold_tree(), core::conformation::symmetry::setup_symmetric_conformation(), core::scoring::constraints::Func::show_violations(), protocols::antibody2::simple_fold_tree(), protocols::antibody::simple_fold_tree(), protocols::antibody2::simple_one_loop_fold_tree(), protocols::antibody::simple_one_loop_fold_tree(), protocols::forge::methods::smallmer_from_largemer(), protocols::simple_moves::GreedyOptMutationMover::stopping_condition(), protocols::moves::GenericMonteCarloMover::stopping_condition(), core::pose::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::loophash::LoopHashLibrary::test_loop_sample(), core::scoring::trie::trie_vs_trie(), and protocols::moves::PyMolMover::update_energy().

string make_table_of_pilot_apps::help = "Name of pilot_apps.src.settings.all file from which to generate table of applications and demos"
list make_table_of_pilot_apps::name = line[start_name+1:end_name]

Referenced by core::scoring::ScoringManager::add_etable(), protocols::simple_filters::NativeEvaluatorCreator::add_evaluators(), protocols::simple_filters::ExtraScoreEvaluatorCreator::add_evaluators(), protocols::match::downstream::ClassicMatchAlgorithm::add_external_geom_sampler(), core::scoring::ScoringManager::add_memb_etable(), protocols::multistate_design::MultiStateFitnessFunction::add_metric_value_getter(), protocols::toolbox::task_operations::JointSequenceOperation::add_pose(), protocols::topology_broker::TopologyClaimerFactory::add_type(), protocols::relax::add_virtual_residue_to_cterm(), core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(), core::pose::Pose::annotated_sequence(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::simple_filters::BatchEvaluator::apply(), protocols::simple_filters::AbinitioBaseFilter::apply(), protocols::protein_interface_design::movers::DisulfideMover::apply(), protocols::moves::StructureRestrictor::apply(), protocols::moves::PyMolMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator::apply(), protocols::canonical_sampling::CanonicalSamplingMover::apply(), protocols::motifs::bpdefs2map(), core::coarse::CoarseEtable::check_atomset_compatibility(), protocols::qsar::ColorGradient::ColorGradient(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::io::pdb::convert_res_name(), protocols::relax::coordinate_constrain_selection(), core::pack::task::create_command_map(), protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median(), protocols::motifs::defs2allowedtypes(), protocols::motifs::defs2map(), core::conformation::Conformation::detect_disulfides(), protocols::jobdist::PlainPdbJobDistributor::dump_pose_and_map(), core::io::silent::SilentStruct::energies_from_pose(), protocols::enzdes::EnzdesJobOutputter::EnzdesJobOutputter(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::chemical::expand_icoor_atom_name(), core::pose::symmetry::find_symmetric_basejump_anchor(), protocols::features::FeaturesReporter::find_tag(), core::scoring::find_weights_file(), protocols::rosetta_scripts::foreach_movemap_tag(), protocols::frag_picker::scores::FragmentScoringMethod::FragmentScoringMethod(), core::chemical::AtomTypeDatabaseIO::get_all_atom_types_in_database(), core::chemical::ResidueDatabaseIO::get_all_residues_in_database(), protocols::motifs::get_filenames(), protocols::vip::VIP_Report::get_GOE_relaxed_report(), protocols::vip::VIP_Report::get_GOE_repack_report(), core::coarse::Translator::get_RotamerLibrary(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line(), protocols::match::Matcher::initialize_from_file(), protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), core::pack::task::TARGET::initialize_from_tokens(), core::pack::task::EX_CUTOFF::initialize_from_tokens(), core::pack::task::NC::initialize_from_tokens(), core::pack::task::EX::initialize_from_tokens(), core::pack::task::APOLA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::PIKRNA::initialize_from_tokens(), core::pack::task::PIKNA::initialize_from_tokens(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::ALLAA::initialize_from_tokens(), core::pack::task::FIX_HIS_TAUTOMER::initialize_from_tokens(), protocols::comparative_modeling::initialize_ss(), protocols::qsar::scoring_grid::GridManager::insert_grid(), protocols::noesy_assign::CrossPeakInfo::label_atom_name(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::ligand_docking::LigandAreaLoader::load_data(), protocols::ligand_docking::MoveMapBuilderLoader::load_data(), protocols::ligand_docking::InterfaceBuilderLoader::load_data(), protocols::jd2::parser::TaskOperationLoader::load_data(), protocols::jd2::parser::FragSetLoader::load_data(), protocols::jobdist::load_s_and_l(), core::pack::dunbrack::load_unboundrot(), protocols::loop_build::LoopBuild_main(), protocols::qsar::scoring_grid::GridManager::make_new_grid(), protocols::fibril::make_symmetric_fibril(), protocols::multistate_design::SingleStateEntityData::metric_value(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::topology_broker::TopologyClaimerFactory::newTopologyClaimer(), core::scoring::operator>>(), core::chemical::operator>>(), OPT_1GRP_KEY(), protocols::optimize_weights::OptEPositionDataFactory::optE_type_from_name(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::rosetta_scripts::parse_movemap(), protocols::rigid::RollMover::parse_my_tag(), protocols::ligand_docking::StartFrom::parse_my_tag(), protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(), protocols::ligand_docking::CompoundTranslate::parse_my_tag(), protocols::canonical_sampling::MetricRecorder::parse_my_tag(), protocols::rosetta_scripts::parse_task_operations(), protocols::jd2::AtomTreeDiffJobInputter::pose_from_job(), protocols::moves::StructureRestrictor::pose_name(), protocols::comparative_modeling::poses_from_cmd_line(), protocols::swa::rna::Print_torsion_info(), protocols::RBSegmentRelax_main(), core::grid::CartGrid< core::Real >::read(), core::scoring::constraints::ConstraintIO::read_cst_bindingsites(), core::sequence::Sequence::read_data(), protocols::constraints_additional::BindingSiteConstraint::read_def(), core::scoring::constraints::SiteConstraint::read_def(), protocols::jumping::ResiduePairJumpSetup::read_file(), core::chemical::ElementSet::read_file(), core::chemical::CSDAtomTypeSet::read_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::noesy_assign::PeakFileFormat::read_header(), core::pose::read_psipred_ss2_file(), core::scoring::ResidualDipolarCoupling_Rohl::read_RDC_file(), core::scoring::ResidualDipolarCoupling::read_RDC_file(), protocols::topology_broker::MetalloClaimer::read_tag(), protocols::comparative_modeling::hybridize::HybridizeProtocol::read_template_structures(), core::chemical::read_topology_file(), protocols::wum::MoverList::register_mover(), protocols::wum::WorkUnitList::register_work_unit(), core::scoring::hbonds::HBondDatabase::report_parameter_features(), core::pack::task::TARGET::residue_action(), core::pack::task::SCAN::residue_action(), core::pack::task::AUTO::residue_action(), core::sequence::SequenceAlignment::score(), protocols::enzdes::EnzdesJobOutputter::scorefile(), protocols::moves::PyMolMover::send_energy(), protocols::moves::PyMolMover::send_RAW_Energies(), protocols::dna::DnaInterfacePacker::set_filename_root(), core::grid::CartGrid< core::Real >::set_name(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_pose(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::set_pose(), protocols::noesy_assign::CrossPeakInfo::set_proton(), protocols::jd2::SilentFileJobOutputter::set_silent_file_name(), protocols::frag_picker::FragmentPicker::set_up_quota_nnmake_style(), core::pose::setPoseExtraScores(), protocols::motifs::setup_conformer_map(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), protocols::abinitio::AbrelaxApplication::setup_fold(), core::scoring::setup_matching_heavy_atoms(), core::scoring::hbonds::Polynomial_1d::show(), core::scoring::hbonds::Polynomial_1d::show_values(), protocols::sparta::GDB::showGDB(), protocols::id::AlignmentID::template_name(), protocols::abinitio::Templates::Templates(), core::pack::interaction_graph::write_sphere_list_farray(), and core::pack::interaction_graph::write_sphere_list_uv1().

tuple make_table_of_pilot_apps::parser = OptionParser()
tuple make_table_of_pilot_apps::start_name = line.find('"') end_name = line.find('"', start_name +1 )
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