| ▼ src | |
| ► apps | |
| ► benchmark | |
| ► performance | |
| compare_times.py | |
| DatabaseIO.bench.hh | |
| Design.bench.hh | |
| Docking.bench.hh | Run a performance benchmark of docking |
| FastRelax.bench.hh | |
| init_util.hh | Initialization subroutines for Benchmark |
| InteractionGraph.bench.hh | |
| LigandDock.bench.hh | |
| LigandDockScript.bench.hh | |
| Minimizer.bench.hh | |
| OptionCollection.bench.hh | |
| pdb_io.bench.hh | |
| performance_benchmark.cc | |
| performance_benchmark.hh | Base class for mini rosetta benchmark system |
| ResidueType.bench.hh | |
| score.bench.hh | |
| ScoreAnalyticEtable.bench.hh | |
| ScoreEach.bench.hh | |
| ShearMover.bench.hh | |
| SmallMover.bench.hh | |
| xml_parsing.bench.hh | |
| ► scientific | |
| ddg_benchmark.cc | |
| design_contrast_and_statistic.cc | |
| rotamer_recovery.cc | |
| ► public | |
| ► analysis | |
| batch_distances.cc | |
| contactMap.cc | Simple application for creating a contact map from multiple models of the same protein |
| ensemble_analysis.cc | Analyse sets of structures |
| fast_clustering.cc | Analyse sets of structures |
| InterfaceAnalyzer.cc | Q&D protocol to run InterfaceAnalyzerMover as protocol |
| PeptideDeriver.cc | Application that reads in dimer (composed of two chains) and outputs the peptide which contibutes most to the interface |
| per_residue_energies.cc | Simple application for printing out energies from a Pose |
| residue_energy_breakdown.cc | |
| score.cc | |
| score_jd2.cc | Score a pose! |
| ► antibody | |
| antibody_CR_paratope.cc | Calculate metrics over antibody paratopes |
| antibody_graft.cc | |
| antibody_H3.cc | |
| antibody_legacy.cc | |
| snugdock.cc | |
| ► boinc | |
| boinc_mac_app_icon.hh | |
| minirosetta.cc | |
| minirosetta_graphics.cc | |
| ► comparative_modeling | |
| cluster_alns.cc | |
| fast_gap.cc | |
| fix_alignment_to_match_pdb.cc | |
| full_length_model.cc | |
| partial_thread.cc | |
| score_aln.cc | |
| score_aln2.cc | |
| super_aln.cc | |
| template_features.cc | |
| validate_silent.cc | |
| ► coupled_moves | |
| coupled_moves.cc | |
| ► cyclic_peptide | |
| simple_cycpep_predict.cc | Predicts structure of N-to-C cyclic peptides from amino acid sequence |
| ► darc | |
| DARC.cc | |
| make_ray_files.cc | |
| theta_ligand.cc | |
| ► ddg | |
| ddg_monomer.cc | |
| ensemble_generator_score12_sidechain_ver2.cc | |
| minimize_with_cst.cc | |
| ► design | |
| beta_peptide_modeling.cc | |
| fixbb.cc | Fixed backbone design. Can do side chain minimization after PackRotamers by using the flag -minimize_sidechains. This is SLOW |
| mpi_msd.cc | |
| pmut_scan_parallel.cc | Main function for running the point mutant scan protocol |
| rna_design.cc | |
| sequence_recovery.cc | A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper |
| supercharge.cc | |
| zinc1_homodimer_design.cc | Symmetric design of a zinc-mediated homodimer. One zinc at the interface. Gridsearch (or not) of perturbations to the metalsite geometry using rollmoves about axes that pass through zinc. Metalsite constraints are in place to allow backbone minimization of the designs |
| zinc1_homodimer_setup.cc | Grafts a 2-residue + zinc match onto the match's scaffold, duplicates the pose, then performs two discrete flips (rollmoves) to the second chain that generates a symmetric pose with a tetrahedral metal binding site |
| zinc2_homodimer_design.cc | Starts with an undesigned symmetric dimer with two interface zinc sites as created by zinc2_homodimer_design_setup, and designs the interface with sc, bb, and jump minimization |
| zinc2_homodimer_setup.cc | Stage 1 of designing a two-zinc metal seeded symmetric interface |
| zinc_heterodimer_design.cc | This is the application for a metal interface design project. In its initial conception, the idea was to design an interface between ankyrin and ubc12. First, RosettaMatch is used to design a histidine/cystine zinc binding site on ankyrin (3 residues). The fourth residue to coordinate a tetrahedral zinc then comes from ubc12 (present natively). This metal binding gets the interface going; the protocol searches rigid-body space to try to find a shape-complementary interaction and then designs the interface |
| ► docking | |
| docking_prepack_protocol.cc | |
| docking_protocol.cc | |
| ► electron_density | |
| denovo_density.cc | |
| density_tools.cc | |
| mr_protocols.cc | |
| ► enzdes | |
| CstfileToTheozymePDB.cc | |
| enzyme_design.cc | |
| ► farna | |
| cs_rosetta_rna.cc | |
| rna_cluster.cc | |
| rna_database.cc | |
| rna_denovo.cc | |
| rna_extract.cc | |
| rna_minimize.cc | |
| rna_score.cc | |
| ► fiber_diffraction | |
| FiberDiffractionFreeSet.cc | |
| ► flexpep_docking | |
| BuildPeptide.cc | |
| FlexPepDocking.cc | |
| ► interface_design | |
| ► anchored_design | |
| AnchoredDesign.cc | Anchored Design protocol |
| AnchoredPDBCreator.cc | Anchored Design pre-protocol to make its inputs |
| AnchorFinder.cc | This code is intended to sift through the entire Protein Data Bank and find PDBs that fit certain criteria; in this case having loops with large numbers of cross-interface neighbors |
| ► internal | |
| validate_database.cc | |
| ► ligand_docking | |
| arls.py | |
| arls_impl.py | |
| assign_charges.py | |
| best_ifaceE.py | |
| extract_atomtree_diffs.cc | |
| get_scores.py | |
| ligand_dock.cc | |
| ligand_rpkmin.cc | Repack and minimize sidechains. For preparing structures prior to ligand docking |
| pdb_to_molfile.py | |
| prune_atdiff_top5pct.py | |
| select_best_unique_ligand_poses.cc | |
| ► loop_modeling | |
| loopmodel.cc | |
| ► magnesium | |
| mg_modeler.cc | |
| ► match | |
| gen_apo_grids.cc | Search pocket and generate grids |
| gen_lig_grids.cc | Generate matcher grids for a protein with a ligand |
| match.cc | |
| ► membrane | |
| mp_ddG.py | |
| mp_dock.cc | |
| mp_dock_setup.cc | |
| mp_mutate_relax.cc | Mutate a residue, then do quick relax for a membrane protein |
| mp_range_relax.cc | |
| mp_span_from_pdb.cc | |
| mp_symdock.cc | |
| mp_transform.cc | |
| mp_viewer.cc | |
| ► membrane_abinitio | |
| membrane_abinitio2.cc | |
| ► motif_tools | |
| extract_motifs.cc | Application to extract motifs from a set of pdb files |
| incorporate_motifs.cc | |
| ► ncaa_utilities | |
| make_rot_lib.cc | |
| MakeRotLib.cc | |
| UnfoldedStateEnergyCalculator.cc | |
| ► nmr | |
| r_noe_assign.cc | Read and write XEASY format peak-lists |
| ► noncanonical_backbones | |
| hbs_design.cc | |
| oop_design.cc | |
| peptoid_design.cc | |
| ► pepspec | |
| pepspec.cc | |
| pepspec_anchor_dock.cc | |
| ► pocket | |
| make_exemplar.cc | |
| pocket_measure.cc | |
| pocket_relax.cc | |
| pocket_suggest_target_residues_by_ddg.cc | |
| ► relax_w_allatom_cst | |
| amino_acids.py | |
| clean_pdb_keep_ligand.py | |
| sidechain_cst_3.py | |
| ► rna_util | |
| erraser_minimizer.cc | |
| nucleobase_sample_around.cc | |
| recces_turner.cc | |
| rna_features.cc | |
| rna_graft.cc | |
| rna_helix.cc | |
| rna_predict_chem_map.cc | |
| rna_suitename.cc | |
| rna_thread.cc | |
| ► rosetta_scripts | |
| revert_design_to_native.cc | |
| rosetta_scripts.cc | The application file for rosetta_scripts, aka jd2_scripting or the parser |
| ► rosettaDNA | |
| rosettaDNA.cc | Runs DockDesignParser via the JobDistributor v. 2, provides access to protein-DNA interface modeling code in protocols/dna, and uses a custom PDBJobOutputter to add protein-DNA specific information to output pdb files |
| ► scenarios | |
| ► beta_strand_homodimer_design | |
| exposed_strand_finder.cc | Finds exposed strands with option to check rmsd to another strand |
| homodimer_design.cc | Symmetric homodimer design |
| homodimer_maker.cc | Takes a found exposed beta strand and tries to make the starting file for a symmetric homodimer |
| ► chemically_conjugated_docking | |
| Gp_extra_bodies.hh | Helper quantification metrics for the original publication of the UBQ_Gp code |
| Gp_quantification_metrics.hh | Helper quantification metrics for the original publication of the UBQ_Gp code |
| UBQ_E2_thioester.cc | This application is a one-shot for modeling the thioester bond between UBQ and an E2 |
| UBQ_Gp_CYD-CYD.cc | This application is a one-shot for modeling a ubiquitinated G-protein; this version uses a disulfide linkage to match an experimentally-induced disulfide |
| UBQ_Gp_LYX-Cterm.cc | This application is a one-shot for modeling a ubiquitinated G-protein; this version uses a native lysine to ubiquitin linkage via LYX |
| ca_to_allatom.cc | An app which constructs an all atom model from a CA-only input trace. The inputs are the starting CA trace, a list of residue ranges corresponding to secondary structure elements (as best as can be inferred from the initial trace) and a set of backbone torsion fragments |
| doug_dock_design_min_mod2_cal_cal.cc | |
| FloppyTail.cc | This app was initially intended for modeling the binding of a long unstructured C-terminal tail to some other part of a protein. It now works for N-terminal, C-terminal, and internal flexible regions. It works best as a method for sampling space to see what is possible, preferably in conjunction with extensive experimental constraints. It is not meant to produce ab-initio style models of folded complexes |
| ► sewing | |
| sewing_hasher.cc | |
| ► stepwise | |
| ► legacy | |
| swa_protein_main.cc | |
| swa_rna_main.cc | |
| swa_rna_util.cc | |
| stepwise.cc | |
| ► surface_docking | |
| surface_docking.cc | |
| ► symmetry | |
| make_symmdef_file_denovo.py | |
| ► weight_optimization | |
| optE_parallel.cc | |
| AbinitioRelax.cc | |
| backrub.cc | Run backrub Monte Carlo |
| cluster.cc | |
| combine_silent.cc | Simple application for combining a number of silent-files into a single silent-file |
| extract_pdbs.cc | Simple application for extracting PDBs from a silent-file |
| fragment_picker.cc | |
| idealize_jd2.cc | |
| minimize.cc | |
| minimize_ppi.cc | |
| packstat.cc | |
| relax.cc | |
| remodel.cc | |
| sequence_tolerance.cc | App for predicting the sequence tolerance of a structure or set of structures |
| struc_set_fragment_picker.cc | |
| SymDock.cc | |
| vip.cc | |
| ► tests | |
| test_C-terminal_conjugation.cc | This is an integration test app for testing reverse-fold-tree generation code |
| test_carbohydrate_scoring.cc | Application source code for testing carbohydrate scoring methods |
| test_CarbohydrateInfo.cc | Application source code for testing CarbohydrateInfo |
| test_CCD_loop_closure.cc | Integration test application for testing CCD loop closure |
| test_non-canonical_connectivities.cc | This is an integration test app for testing general non-canonical connectivities. |
| test_RingConformationMover.cc | Pilot application source code for testing RingConformationMover |
| ► basic | |
| ► database | |
| ► insert_statement_generator | |
| InsertGenerator.cc | Insert statement generator |
| InsertGenerator.fwd.hh | Insert statement generator |
| InsertGenerator.hh | Insert statement generator |
| RowData.cc | Column data object for the insert statement generator |
| RowData.fwd.hh | Column data object for the insert statement generator |
| RowData.hh | |
| ► schema_generator | |
| Column.cc | Column class for the schema generator framework |
| Column.fwd.hh | Forward hearder for the Column class in the schema generator framework |
| Column.hh | Column class for the schema generator framework |
| Constraint.cc | |
| Constraint.fwd.hh | Forwaard header for the constraints class in the schema generator framework |
| Constraint.hh | |
| DbDataType.cc | DbDataType class for the schema generator framework |
| DbDataType.fwd.hh | |
| DbDataType.hh | |
| ForeignKey.cc | ForeignKey class for the schema generator framework |
| ForeignKey.hh | ForeignKey class for the schema generator framework |
| Index.cc | Index class for the schema generator framework |
| Index.hh | Index class for the schema generator framework |
| PrimaryKey.cc | PrimaryKey class for the schema generator framework |
| PrimaryKey.hh | PrimaryKey class for the schema generator framework |
| Schema.cc | Construct a database backend independant schema |
| Schema.hh | Table definition for the schema generator framework |
| DatabaseSessionLoader.cc | Load the database session object |
| DatabaseSessionLoader.fwd.hh | Load the database session |
| DatabaseSessionLoader.hh | Load the utility database session |
| DatabaseSessionLoaderCreator.hh | Load the database session |
| DatabaseSessionOptions.cc | Load the database session |
| DatabaseSessionOptions.fwd.hh | Load the database session |
| DatabaseSessionOptions.hh | Load the database session |
| DatabaseSessionOptionsCreator.hh | Load the database session |
| open.cc | Functions for opening database files |
| open.hh | Functions for opening database files |
| sql_utils.cc | Database utility functions |
| sql_utils.hh | |
| ► datacache | |
| BasicDataCache.cc | A DataCache storing objects derived from basic::datacache::CacheableData |
| BasicDataCache.fwd.hh | Forward declaration for BasicDataCache |
| BasicDataCache.hh | A DataCache storing objects derived from basic::datacache::CacheableData |
| CacheableData.cc | |
| CacheableData.fwd.hh | |
| CacheableData.hh | |
| CacheableString.fwd.hh | |
| CacheableString.hh | |
| CacheableStringFloatMap.fwd.hh | |
| CacheableStringFloatMap.hh | |
| CacheableStringMap.fwd.hh | |
| CacheableStringMap.hh | |
| ConstDataMap.cc | |
| ConstDataMap.fwd.hh | |
| ConstDataMap.hh | Class for holding constant owning pointers to data so that it can be safely shared between threads without the need for deep-copy semantics |
| DataCache.cc | |
| DataCache.fwd.hh | Forward declaration for DataCache |
| DataCache.hh | |
| DataMap.cc | |
| DataMap.fwd.hh | |
| DataMap.hh | |
| DataMapObj.hh | |
| DiagnosticData.fwd.hh | |
| DiagnosticData.hh | |
| HierarchicalDataMap.cc | |
| HierarchicalDataMap.fwd.hh | |
| HierarchicalDataMap.hh | |
| WriteableCacheableData.fwd.hh | |
| WriteableCacheableData.hh | |
| WriteableCacheableDataCreator.cc | |
| WriteableCacheableDataCreator.hh | Base class for WriteableCacheableDataCreators for the WriteableCacheableData load-time factory registration scheme |
| WriteableCacheableDataFactory.cc | |
| WriteableCacheableDataFactory.fwd.hh | |
| WriteableCacheableDataFactory.hh | |
| WriteableCacheableMap.fwd.hh | |
| WriteableCacheableMap.hh | |
| ► gpu | |
| GPU.cc | OpenCL-based GPU scheduler class |
| GPU.hh | OpenCL-based GPU scheduler class |
| Timer.cc | High-resolution Timer (ns resolution) |
| Timer.hh | High-resolution Timer (ns resolution, but on *nix only) |
| ► mpi | |
| DbMoverMessageListener.cc | |
| DbMoverMessageListener.fwd.hh | |
| DbMoverMessageListener.hh | |
| MessageListener.fwd.hh | |
| MessageListener.hh | Base message listening class to be derived from for all message listeners |
| MessageListenerFactory.cc | A factory for lazily initializing message listeners. This should be used in conjunction the the MPIWorkPoolJobDistributor's message listening functionality |
| MessageListenerFactory.hh | |
| mpi_enums.hh | |
| util.cc | Utility functions for the message listening framework |
| util.hh | |
| ► options | |
| ► keys | |
| abinitio.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| abrelax.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| AnchoredDesign.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| antibody.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| archive.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| assembly.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| backrub.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| batch_relax.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| bbg.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| blivens.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| boinc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| broker.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| bunsat_calc2.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| canonical_sampling.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| carbohydrates.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| casp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| chemical.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| chemically_conjugated_docking.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| chunk.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cluster.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cm.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cmiles.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| constraints.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| contactMap.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| corrections.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| crossmatch.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cryst.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| csa.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cutoutdomain.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cyclic_peptide.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| cyclization.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| dc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| ddg.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| DenovoProteinDesign.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| dna.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| docking.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| DomainAssembly.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| dwkulp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| edensity.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| enzdes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| evaluation.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| evolution.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| fast_loops.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| filters.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| fingerprint.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| flexpack.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| flexPepDocking.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| FloppyTail.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| flxbb.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| fold_and_dock.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| fold_cst.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| fold_from_loops.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| frags.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| full_model.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| gen_pharmacophore.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| gpu.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| holes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| hotspot.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| in.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| indexed_structure_store.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| inout.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| intf.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| james.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| jd2.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| jumps.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| krassk.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| lh.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| loodo.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| loopfcst.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| LoopModel.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| loops.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| magnesium.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| make_rot_lib.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| match.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| matdes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| mc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| membrane.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| mh.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| mistakes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| MonteCarlo.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| motifs.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| mp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| ms.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| murphp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| nonlocal.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| optE.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| optimization.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| OptionKeys.cc.gen0.hh | |
| OptionKeys.cc.gen1.hh | |
| OptionKeys.cc.gen10.hh | |
| OptionKeys.cc.gen11.hh | |
| OptionKeys.cc.gen12.hh | |
| OptionKeys.cc.gen13.hh | |
| OptionKeys.cc.gen14.hh | |
| OptionKeys.cc.gen15.hh | |
| OptionKeys.cc.gen2.hh | |
| OptionKeys.cc.gen3.hh | |
| OptionKeys.cc.gen4.hh | |
| OptionKeys.cc.gen5.hh | |
| OptionKeys.cc.gen6.hh | |
| OptionKeys.cc.gen7.hh | |
| OptionKeys.cc.gen8.hh | |
| OptionKeys.cc.gen9.hh | |
| OptionKeys.hh | Basic::options::OptionKeys collection |
| OptionKeys0.cc | |
| OptionKeys1.cc | |
| OptionKeys10.cc | |
| OptionKeys11.cc | |
| OptionKeys12.cc | |
| OptionKeys13.cc | |
| OptionKeys14.cc | |
| OptionKeys15.cc | |
| OptionKeys2.cc | |
| OptionKeys3.cc | |
| OptionKeys4.cc | |
| OptionKeys5.cc | |
| OptionKeys6.cc | |
| OptionKeys7.cc | |
| OptionKeys8.cc | |
| OptionKeys9.cc | |
| orbitals.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| out.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| packing.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| packstat.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| parser.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| patterson.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| pb_potential.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| PCS.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| PCSTS1.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| PCSTS2.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| PCSTS3.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| PCSTS4.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| pepspec.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| peptide_deriver.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| pH.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| phil.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| pocket_grid.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| pose_metrics.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| ProQ.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| qsar.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rbe.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| RBSegmentRelax.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rdc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| relax.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| remodel.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| resample.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rescore.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rigid.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rings.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rna.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| robert.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rot_anl.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| rotamerdump.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| run.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| sample_around.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| sasa.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| score.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| sewing.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| sicdock.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| smhybrid.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| SSrbrelax.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| stepwise.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| strand_assembly.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| symmetry.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| TailSegment.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| task_operations.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| templates.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| threadsc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| ufv.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| unfolded_state.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| willmatch.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| wum.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| after_opts.cc | Option lookup functions emulating Rosetta++ equivalents for transitional use |
| after_opts.hh | Option lookup functions emulating Rosetta++ equivalents for transitional use |
| option.cc | Program options global and initialization function |
| option.cc.gen.hh | |
| option.cc.include.gen.hh | |
| option.hh | Program options global and initialization function |
| option_macros.hh | Macros to define options on a per-application basis at the top of app files (those with main) |
| options.py | Program options generation script that is run to generate the options |
| options_class.py | Program options generation script classes |
| options_rosetta.py | Program options generation script: Rosetta options encoding |
| PyRosettaFunctions.cc | |
| PyRosettaFunctions.hh | Additional functions to set/get Options from PyRosetta |
| util.cc | |
| util.hh | |
| ► resource_manager | |
| ► fallback_configuration | |
| NativeFallbackConfiguration.cc | |
| NativeFallbackConfiguration.fwd.hh | |
| NativeFallbackConfiguration.hh | |
| NativeFallbackConfigurationCreator.hh | |
| ► locator | |
| DatabaseResourceLocator.cc | |
| DatabaseResourceLocator.fwd.hh | Forward header for DatabaseResourceLocator |
| DatabaseResourceLocator.hh | |
| DatabaseResourceLocatorCreator.hh | Header for DatabaseResourceLocator Creator for the load-time factory registration scheme |
| FileListResourceLocator.cc | |
| FileListResourceLocator.fwd.hh | Forward header for FileListResourceLocator |
| FileListResourceLocator.hh | |
| FileListResourceLocatorCreator.hh | Header for FileSystemResourceLocator Creator for the load-time factory registration scheme |
| FileSystemResourceLocator.cc | |
| FileSystemResourceLocator.fwd.hh | Forward header for FileSystemResourceLocator |
| FileSystemResourceLocator.hh | |
| FileSystemResourceLocatorCreator.hh | Header for FileSystemResourceLocator Creator for the load-time factory registration scheme |
| NullResourceLocator.cc | |
| NullResourceLocator.fwd.hh | Forward header for NullResourceLocator |
| NullResourceLocator.hh | |
| NullResourceLocatorCreator.hh | Header for NullResourceLocator Creator for the load-time factory registration scheme |
| StringResourceStream.cc | A thin wrapper around an std::stringstream for use with the ResourceManager |
| StringResourceStream.fwd.hh | Forward header for StringResourceStream |
| StringResourceStream.hh | A thin wrapper around an std::stringstream for use with the ResourceManager |
| FallbackConfiguration.cc | |
| FallbackConfiguration.fwd.hh | Forward hearder for FallbackConfiguration class |
| FallbackConfiguration.hh | |
| FallbackConfigurationCreator.cc | |
| FallbackConfigurationCreator.fwd.hh | |
| FallbackConfigurationCreator.hh | Declaration of the FallbackConfigurationCreator class |
| FallbackConfigurationFactory.cc | |
| FallbackConfigurationFactory.fwd.hh | |
| FallbackConfigurationFactory.hh | |
| JobOptions.cc | |
| JobOptions.fwd.hh | Forward hearder for JobOptions class |
| JobOptions.hh | |
| LazyResourceManager.cc | |
| LazyResourceManager.fwd.hh | Forward Header for base class for LazyResourceManager |
| LazyResourceManager.hh | |
| ResourceLoader.cc | |
| ResourceLoader.fwd.hh | |
| ResourceLoader.hh | |
| ResourceLoaderCreator.cc | |
| ResourceLoaderCreator.fwd.hh | |
| ResourceLoaderCreator.hh | |
| ResourceLoaderFactory.cc | |
| ResourceLoaderFactory.hh | |
| ResourceLoaderRegistrator.hh | Declaration of class ResourceLoaderRegistrator |
| ResourceLocator.cc | |
| ResourceLocator.fwd.hh | Forward header for ResourceLocator |
| ResourceLocator.hh | |
| ResourceLocatorCreator.cc | |
| ResourceLocatorCreator.fwd.hh | |
| ResourceLocatorCreator.hh | |
| ResourceLocatorFactory.cc | |
| ResourceLocatorFactory.hh | |
| ResourceLocatorRegistrator.hh | |
| ResourceManager.cc | |
| ResourceManager.fwd.hh | |
| ResourceManager.hh | |
| ResourceManagerCreator.cc | |
| ResourceManagerCreator.fwd.hh | |
| ResourceManagerCreator.hh | |
| ResourceManagerFactory.cc | |
| ResourceManagerFactory.fwd.hh | |
| ResourceManagerFactory.hh | |
| ResourceOptions.cc | |
| ResourceOptions.fwd.hh | |
| ResourceOptions.hh | |
| ResourceOptionsCreator.cc | |
| ResourceOptionsCreator.fwd.hh | |
| ResourceOptionsCreator.hh | |
| ResourceOptionsFactory.cc | |
| ResourceOptionsFactory.hh | |
| ResourceOptionsRegistrator.hh | |
| types.hh | |
| util.hh | |
| ► sampling | |
| ► orientations | |
| QuaternionGrid.cc | Provide an evenly spaced set of rotations |
| QuaternionGrid.fwd.hh | Basic::sampling::orientations::QuaternionGrid forward declaration |
| QuaternionGrid.hh | |
| ► svd | |
| SVD_Solver.cc | SVD solver class ` |
| SVD_Solver.fwd.hh | SVD solver class |
| SVD_Solver.hh | SVD solver class |
| basic.cc | |
| basic.hh | |
| ComparingTracer.cc | |
| ComparingTracer.hh | Version of Tracer calss for to tracking down the source of an instability by compare output with file |
| Emitter.cc | Lightweight class to ease writting YAML documents |
| Emitter.hh | Lightweight class to ease writting YAML documents |
| execute.cc | |
| execute.hh | Various functions to run external executables |
| init.cc | Some statics/funtions helpers for Rosetta init functions |
| init.hh | |
| interpolate.cc | |
| interpolate.hh | |
| MemTracer.cc | |
| MemTracer.hh | |
| MetricValue.fwd.hh | |
| MetricValue.hh | |
| MetricValueIO.cc | |
| MetricValueIO.hh | |
| prof.cc | |
| prof.hh | |
| pymol_chains.cc | Method definitions for a couple PyMOL helper functions |
| pymol_chains.hh | |
| Tracer.cc | |
| Tracer.fwd.hh | |
| Tracer.hh | Tracer IO system |
| TracerToFile.cc | |
| TracerToFile.hh | Class for a tracer that writes all output to a file |
| ► devel | |
| init.cc | |
| init.hh | |
| init.release.cc | Initialization function to ensure all load-time factory registration occurs for classes that live in the devel library. devel::init() calls protocols::init::init(), which in turn calls core::init::init(). Devel library does not exist in release; so the release version of this file is nearly empty |
| init.release.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the devel library. devel::init() calls protocols::init::init(), which in turn calls core::init::init(). Devel library does not exist in release; so the release version of this file is nearly empty |
| svn_version.hh | |
| ► numeric | |
| ► alignment | |
| QCP_Kernel.hh | |
| ► coordinate_fitting | |
| CoordinateArray_RMSD_FlatLookup.hh | |
| FlatLookup.hh | |
| ► crick_equations | |
| BundleParams.cc | Functions implementing the Crick equations for a helical bundle (a helix of helices) |
| BundleParams.hh | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| HelixParams.cc | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| HelixParams.hh | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| ► deriv | |
| angle_deriv.hh | Inline function for computing f1/f2 derivatives for a function of a distance |
| dihedral_deriv.hh | Inline function for computing f1/f2 derivatives for a function of a dihedral |
| distance_deriv.hh | Inline function for computing f1/f2 derivatives for a function of an angle |
| ► expression_parser | |
| Arithmetic.cc | Parse tree for arithmetic operations |
| Arithmetic.fwd.hh | Parse tree for arithmetic operations class forward declarations |
| Arithmetic.hh | Parse tree for arithmetic operations |
| ► fourier | |
| FFT.cc | Wrapper class performing ffts on 1,2, and 3 dimensional farrays |
| FFT.hh | |
| kiss_fft.cc | |
| kiss_fft.hh | |
| kiss_fft_state.cc | |
| kiss_fft_state.hh | |
| SHT.cc | A few spherical harmonic transform function: very simple, with support for real, even BW only |
| SHT.hh | A few spherical harmonic transform functions |
| ► geometry | |
| ► hashing | |
| SixDHasher.cc | Implementation of 6D hasher classes |
| SixDHasher.fwd.hh | Forward declaration for classes in 6D hasher |
| SixDHasher.hh | |
| xyzStripeHash.cc | |
| xyzStripeHash.fwd.hh | |
| xyzStripeHash.hh | |
| xyzStripeHashWithMeta.fwd.hh | |
| xyzStripeHashWithMeta.hh | |
| BoundingBox.fwd.hh | Numeric::geometry::BoundingBox forward declaration |
| BoundingBox.hh | 3d axis aligned bounding box |
| BoundingBox.srlz.cc | |
| BoundingBox.srlz.hh | |
| ring_plane.functions.cc | |
| ring_plane.functions.hh | Function definitions for ring-plane geometry functions |
| ► histograms | |
| OneDHistogram.hh | |
| TwoDHistogram.hh | |
| ► internal | |
| ColPointers.hh | 3x3 matrix column pointers wrapper class |
| ColsPointer.hh | Contiguous column-ordered 3x3 matrix pointer wrapper class |
| ColVectors.hh | 3x3 matrix column vectors wrapper class |
| RowPointers.hh | 3x3 matrix row pointers wrapper class |
| RowsPointer.hh | Contiguous row-ordered 3x3 matrix pointer wrapper class |
| RowVectors.hh | 3x3 matrix row vectors wrapper class |
| ► interpolation | |
| ► periodic_range | |
| ► full | |
| interpolation.hh | Interpolation over periodic range points at full bin width multiples |
| ► half | |
| interpolation.hh | Interpolation over periodic range points at half bin width multiples |
| ► spline | |
| Bicubic_spline.cc | |
| Bicubic_spline.fwd.hh | |
| Bicubic_spline.hh | |
| CompoundInterpolator.cc | Interpolation with cubic splines |
| CompoundInterpolator.hh | Interpolation with cubic splines |
| Cubic_spline.cc | |
| Cubic_spline.fwd.hh | |
| Cubic_spline.hh | |
| Interpolator.cc | |
| Interpolator.hh | |
| PolycubicSpline.cc | |
| PolycubicSpline.fwd.hh | |
| PolycubicSpline.hh | |
| SimpleInterpolator.cc | Interpolation with cubic splines |
| SimpleInterpolator.hh | Interpolation with cubic splines |
| spline_functions.cc | |
| spline_functions.hh | |
| SplineGenerator.cc | Interpolation with cubic splines |
| SplineGenerator.hh | |
| TricubicSpline.cc | |
| TricubicSpline.fwd.hh | |
| TricubicSpline.hh | |
| Histogram.fwd.hh | |
| Histogram.hh | A class for storing histogram data |
| Histogram.srlz.cc | Functions for serializing numeric::interpolation::Histogram instances |
| Histogram.srlz.hh | Functions for serializing numeric::interpolation::Histogram instances |
| interpolation.hh | Interpolation functions |
| util.cc | |
| util.hh | |
| ► kdtree | |
| calc_distance.cc | |
| calc_distance.hh | |
| constants.hh | Constants used for kd-tree implementation |
| construct_kdtree.cc | |
| construct_kdtree.hh | |
| HyperRectangle.cc | |
| HyperRectangle.fwd.hh | |
| HyperRectangle.hh | |
| KDNode.cc | Implementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| KDNode.fwd.hh | Forward declaration for KDNode class |
| KDNode.hh | Implementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| KDPoint.cc | |
| KDPoint.fwd.hh | Forward declaration for KDPoint class |
| KDPoint.hh | Utility functions for kd-tree. See kdtree.hh for more information |
| KDPointList.cc | Definition for a class that keeps track of the best N KDPoint objects by distance |
| KDPointList.hh | Definition for a class that keeps track of the best N KDPoint objects by distance |
| KDTree.cc | |
| KDTree.fwd.hh | Forward declaration for KDTree class |
| KDTree.hh | Implementation of a tree in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| nearest_neighbors.cc | |
| nearest_neighbors.hh | Utility functions for kd-tree. See kdtree.hh for more information |
| util.cc | |
| util.hh | |
| WrappedPrimitive.hh | |
| WrappedReal.hh | Silly little class to wrap a numeric::Real in an OP |
| ► kinematic_closure | |
| bridgeObjects.cc | Solves the triaxial loop closure problem for a system of atoms |
| bridgeObjects.hh | Header file for bridgeObjects code for ALC |
| closure.cc | |
| closure.hh | |
| dixon.cc | Computes the dixon resultant |
| dixon.f90 | |
| dixon.hh | Header file for dixon code for ALC |
| kinematic_closure_helpers.cc | Helpers for functions associated with bridgeObjects.cc |
| kinematic_closure_helpers.hh | Header file for kinematic_closure_helpers.cc |
| qq.f90 | |
| sturm.cc | Implements sturm chain solver |
| sturm.hh | Implements sturm chain solver |
| types.hh | Define the numeric types that are commonly used in this namespace |
| vector.cc | |
| vector.hh | Implement the primitive vector operations (again) |
| ► linear_algebra | |
| GeneralizedEigenSolver.fwd.hh | Forward header for GeneralizedEigenSolver |
| GeneralizedEigenSolver.hh | Header file for GeneralizedEigenSolver |
| rgg.cc | |
| rgg.hh | Header file for the EISPACK rgg routine |
| singular_value_decomposition.cc | |
| singular_value_decomposition.hh | Implementation file for Singular Value Decomposition |
| ► model_quality | |
| maxsub.cc | Ab-initio fragment assembly protocol for proteins |
| maxsub.hh | |
| rms.cc | |
| rms.hh | RMS functions imported from rosetta++ |
| RmsData.cc | |
| RmsData.hh | |
| ► nls | |
| lmmin.cc | |
| lmmin.hh | |
| ► random | |
| DistributionSampler.hh | |
| mt19937.hh | Mersenne Twister 19937 random number generator |
| random.cc | Random number generator system |
| random.functions.hh | |
| random.fwd.hh | Random number generator system |
| random.hh | Random number generator system |
| random_permutation.hh | Reorder the elements in a vector using a RNG object |
| random_xyz.cc | |
| random_xyz.hh | Random vectors and stuff |
| reservoir_sample.hh | Randomly select the best N elements from a stream of elements using one pass over a dataset |
| uniform.fwd.hh | |
| uniform.hh | Uniform random number generator |
| WeightedReservoirSampler.hh | |
| WeightedSampler.cc | Class to generate random positive integers using a given set of weights |
| WeightedSampler.fwd.hh | Forward declarations for class WeightedSampler |
| WeightedSampler.hh | Class to generate random positive integers using a given set of weights |
| ► statistics | |
| functions.cc | |
| functions.hh | Collection of various functions to compute statistics. feel free to add your own |
| agglomerative_hierarchical_clustering.cc | |
| agglomerative_hierarchical_clustering.hh | Hierarchical clustering utilities |
| all.fwd.hh | Numeric package forward declarations |
| angle.functions.hh | Trigonometric functions |
| BodyPosition.fwd.hh | Numeric::BodyPosition forward declarations |
| BodyPosition.hh | Rigid body 3-D position/transform |
| BodyPosition.io.hh | BodyPosition input/output functions |
| Calculator.cc | |
| Calculator.fwd.hh | |
| Calculator.hh | String-input calculator |
| ClusteringTreeNode.cc | |
| ClusteringTreeNode.fwd.hh | |
| ClusteringTreeNode.hh | Node of a hierarchical clustering tree |
| color_util.cc | |
| color_util.hh | |
| constants.cc | Common numeric constants in varying precisions |
| constants.hh | Common numeric constants in varying precisions |
| conversions.hh | Conversions between degrees and radians |
| cyclic_coordinate_descent.cc | Compute the angle that minimizes the deviation between a set of atoms |
| cyclic_coordinate_descent.hh | Compute the angle that minimizes the deviation between a set of atoms |
| EulerAngles.fwd.hh | Numeric::EulerAngles forward declarations |
| EulerAngles.hh | EulerAngles container derived from xyzVector.hh |
| HomogeneousTransform.fwd.hh | Fast coordinate frame container |
| HomogeneousTransform.hh | Fast coordinate frame container |
| HomogeneousTransform.srlz.cc | Functions for serializing HomogeneousTransforms |
| HomogeneousTransform.srlz.hh | Functions for serializing xyzVector and xyzMatrix |
| interpolate.hh | |
| IntervalSet.fwd.hh | IntervalSet forward declarations |
| IntervalSet.hh | Definition and implementation of IntervalSet class |
| io.hh | Numeric package i/o functions |
| IOTraits.hh | Numerics input/output type traits |
| MathMatrix.hh | |
| MathMatrix_operations.hh | |
| MathNTensor.hh | |
| MathTensor.hh | |
| MathVector.hh | |
| MathVector.srlz.cc | Serlialization routines for MathVectors |
| MathVector.srlz.hh | Serlialization routines for MathVector |
| MathVector_operations.hh | |
| MultiDimensionalHistogram.cc | Class for accumulating a histogram of one or more numeric variables |
| MultiDimensionalHistogram.fwd.hh | Forward declarations for class MultiDimensionalHistogram |
| MultiDimensionalHistogram.hh | Class for accumulating a histogram of one or more numeric variables |
| numeric.functions.hh | Numeric functions |
| NumericTraits.hh | Numeric type traits |
| PCA.hh | |
| polynomial.cc | Classes for polynomial evaluation functions |
| polynomial.fwd.hh | Forward header for Polynomial class |
| polynomial.hh | Polynomial evaluation class |
| prob_util.cc | |
| prob_util.hh | |
| Quaternion.fwd.hh | Numeric::Quaternion forward declarations |
| Quaternion.hh | Unit quaternion 3-D orientation representation |
| Quaternion.io.hh | Quaternion input/output functions |
| roc_curve.cc | |
| roc_curve.fwd.hh | |
| roc_curve.hh | |
| sphericalVector.fwd.hh | Numeric::sphericalVector forward declarations |
| sphericalVector.hh | Fast spherical-coordinate numeric vector |
| trig.functions.hh | Trigonometric functions |
| types.hh | Rosetta project type declarations. Should be kept updated with core/types.hh. This exists because numeric can't depend on files in core |
| UniformRotationSampler.fwd.hh | Numeric::UniformRotationSampler forward declarations |
| UniformRotationSampler.hh | |
| util.cc | Small bundle of utilities for dealing with numbers |
| util.hh | Small bundle of utilities for dealing with numbers |
| wrap_angles.hh | Functions to wrap angles in different ranges. author Kale Kundert (kale..nosp@m.kund.nosp@m.ert@u.nosp@m.csf..nosp@m.edu) |
| xyz.functions.fwd.hh | Numeric::xyzVector and numeric::xyzMatrix functions forward declarations |
| xyz.functions.hh | XyzVector and xyzMatrix functions |
| xyz.io.hh | XyzTriple, xyzVector, and xyzMatrix i/o functions |
| xyz.json.hh | |
| xyz.serialization.cc | Functions for serializing xyzVector and xyzMatrix |
| xyz.serialization.hh | Functions for serializing BoundingBox and xyzMatrix |
| xyzMatrix.fwd.hh | Numeric::xyzMatrix forward declarations |
| xyzMatrix.hh | Fast 3x3 matrix |
| xyzMatrix.io.hh | XyzMatrix input/output functions |
| xyzTransform.fwd.hh | Numeric::xyzTransform forward declarations |
| xyzTransform.hh | Fast rigid xform 3x3 matrix + vector |
| xyzTransform.io.hh | XyzTransform input/output functions |
| xyzTriple.fwd.hh | Numeric::xyzTriple forward declarations |
| xyzTriple.hh | Fast (x,y,z)-coordinate vector container |
| xyzTriple.io.hh | XyzTriple input/output functions |
| xyzVector.fwd.hh | Numeric::xyzVector forward declarations |
| xyzVector.hh | Fast (x,y,z)-coordinate numeric vector |
| xyzVector.io.hh | XyzVector input/output functions |
| xyzVector.string.hh | |
| ► ObjexxFCL | |
| array.iterator.hh | |
| byte.fwd.hh | |
| byte.hh | |
| CArray.fwd.hh | |
| CArray.hh | |
| CArray.io.hh | |
| CArrayP.fwd.hh | |
| CArrayP.hh | |
| CArrayP.io.hh | |
| char.functions.cc | |
| char.functions.hh | |
| Chunk.hh | |
| ChunkExponent.hh | |
| ChunkVector.fwd.hh | |
| ChunkVector.hh | |
| ChunkVector.io.hh | |
| Cstring.cc | |
| Cstring.fwd.hh | |
| Cstring.hh | |
| Dimension.cc | |
| Dimension.fwd.hh | |
| Dimension.hh | |
| DimensionExpression.cc | |
| DimensionExpression.hh | |
| DimensionExpressionCon.hh | |
| DimensionExpressionCube.hh | |
| DimensionExpressionDiv.hh | |
| DimensionExpressionMax.hh | |
| DimensionExpressionMin.hh | |
| DimensionExpressionMul.hh | |
| DimensionExpressionPow.hh | |
| DimensionExpressionRef.cc | |
| DimensionExpressionRef.hh | |
| DimensionExpressions.hh | |
| DimensionExpressionSquare.hh | |
| DimensionExpressionSub.hh | |
| DimensionExpressionSum.hh | |
| DynamicIndexRange.cc | |
| DynamicIndexRange.fwd.hh | |
| DynamicIndexRange.hh | |
| FArray.all.fwd.hh | |
| FArray.all.hh | |
| FArray.fwd.hh | |
| FArray.hh | |
| FArray.io.hh | |
| FArray1.all.fwd.hh | |
| FArray1.all.hh | |
| FArray1.fwd.hh | |
| FArray1.hh | |
| FArray1.io.hh | |
| FArray1A.fwd.hh | |
| FArray1A.hh | |
| FArray1D.fwd.hh | |
| FArray1D.hh | |
| FArray1P.fwd.hh | |
| FArray1P.hh | |
| FArray2.all.fwd.hh | |
| FArray2.all.hh | |
| FArray2.fwd.hh | |
| FArray2.hh | |
| FArray2.io.hh | |
| FArray2A.fwd.hh | |
| FArray2A.hh | |
| FArray2D.fwd.hh | |
| FArray2D.hh | |
| FArray2P.fwd.hh | |
| FArray2P.hh | |
| FArray3.all.fwd.hh | |
| FArray3.all.hh | |
| FArray3.fwd.hh | |
| FArray3.hh | |
| FArray3.io.hh | |
| FArray3A.fwd.hh | |
| FArray3A.hh | |
| FArray3D.fwd.hh | |
| FArray3D.hh | |
| FArray3P.fwd.hh | |
| FArray3P.hh | |
| FArray4.all.fwd.hh | |
| FArray4.all.hh | |
| FArray4.fwd.hh | |
| FArray4.hh | |
| FArray4.io.hh | |
| FArray4A.fwd.hh | |
| FArray4A.hh | |
| FArray4D.fwd.hh | |
| FArray4D.hh | |
| FArray4P.fwd.hh | |
| FArray4P.hh | |
| FArray5.all.fwd.hh | |
| FArray5.all.hh | |
| FArray5.fwd.hh | |
| FArray5.hh | |
| FArray5.io.hh | |
| FArray5A.fwd.hh | |
| FArray5A.hh | |
| FArray5D.fwd.hh | |
| FArray5D.hh | |
| FArray5P.fwd.hh | |
| FArray5P.hh | |
| FArray6.all.fwd.hh | |
| FArray6.all.hh | |
| FArray6.fwd.hh | |
| FArray6.hh | |
| FArray6.io.hh | |
| FArray6A.fwd.hh | |
| FArray6A.hh | |
| FArray6D.fwd.hh | |
| FArray6D.hh | |
| FArray6P.fwd.hh | |
| FArray6P.hh | |
| FArrayInitializer.fwd.hh | |
| FArrayInitializer.hh | |
| FArraySection.fwd.hh | |
| FArraySection.hh | |
| FArrayTraits.fwd.hh | |
| FArrayTraits.hh | |
| floops.hh | |
| Fmath.hh | |
| format.cc | |
| format.hh | |
| Fstring.cc | |
| Fstring.fwd.hh | |
| Fstring.hh | |
| IndexRange.cc | |
| IndexRange.fwd.hh | |
| IndexRange.hh | |
| InitializerSentinel.hh | |
| KeyFArray1D.fwd.hh | |
| KeyFArray1D.hh | |
| KeyFArray2D.fwd.hh | |
| KeyFArray2D.hh | |
| KeyFArray3D.fwd.hh | |
| KeyFArray3D.hh | |
| KeyFArray4D.fwd.hh | |
| KeyFArray4D.hh | |
| KeyFArray5D.fwd.hh | |
| KeyFArray5D.hh | |
| KeyFArray6D.fwd.hh | |
| KeyFArray6D.hh | |
| ObjexxFCL.2-3.py | |
| ObjexxFCL.fwd.hh | |
| ObjexxFCL.hh | |
| ObjexxFCL.Project.hh | |
| Observer.cc | |
| Observer.fwd.hh | |
| Observer.hh | |
| ObserverGraph.cc | |
| ObserverGraph.hh | |
| ObserverMediator.cc | |
| ObserverMediator.hh | |
| ObserverMulti.cc | |
| ObserverMulti.hh | |
| ObserverSingle.hh | |
| proxy_const_assert.hh | |
| ProxySentinel.hh | |
| rvalue_cast.hh | |
| sbyte.fwd.hh | |
| sbyte.hh | |
| SetWrapper.fwd.hh | |
| SetWrapper.hh | |
| Star.cc | |
| Star.fwd.hh | |
| Star.hh | |
| StaticIndexRange.fwd.hh | |
| StaticIndexRange.hh | |
| string.functions.cc | |
| string.functions.hh | |
| Time_Date.cc | |
| Time_Date.hh | |
| TypeTraits.hh | |
| ubyte.fwd.hh | |
| ubyte.hh | |
| ► platform | |
| ► cygwin | |
| ► platform | |
| types.hh | |
| ► linux | |
| ► GL | |
| freeglut.h | |
| freeglut_ext.h | |
| freeglut_std.h | |
| glut.h | |
| ► platform | |
| types.hh | Platform-specific types for Linux |
| ► macos | |
| ► platform | |
| types.hh | Platform-specific types for MacOS 10.4 on 32-bit PPC with GCC |
| ► windows | |
| ► 32 | |
| ► gcc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with GCC |
| ► icc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with Intel C++ |
| ► msvc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with MS VC++ |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows |
| ► 64 | |
| ► gcc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with GCC |
| ► icc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with Intel C++ |
| ► msvc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with MS VC++ |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows |
| ► PyRosetta | |
| ► platform | |
| types.hh | |
| ► python | |
| ► bindings | |
| ► app | |
| ► membrane | |
| predict_ddG.py | |
| ► pyrosetta_toolkit | |
| ► modules | |
| ► definitions | |
| __init__.py | |
| restype_definitions.py | |
| ► prettytable | |
| __init__.py | |
| prettytable.py | |
| prettytable_test.py | |
| setup.py | |
| ► protocols | |
| __init__.py | |
| AnalysisProtocols.py | |
| DesignProtocols.py | |
| DockingProtocols.py | |
| FloppyTailProtocol.py | |
| GraftingProtocols.py | |
| HighResLoopModelingProtocols.py | |
| LowResLoopModelingProtocols.py | |
| MinimizationProtocols.py | |
| ProtocolBaseClass.py | |
| ► tools | |
| __init__.py | |
| analysis.py | |
| general_tools.py | |
| input.py | |
| interfaces.py | |
| loops.py | |
| output.py | |
| protocols.py | |
| sequence.py | |
| __init__.py | |
| calibur.py | |
| DesignBreakdown.py | |
| help.py | |
| PythonPDB.py | |
| Region.py | |
| RegionalScoring.py | |
| ScoreAnalysis.py | |
| SQLPDB.py | |
| Structure.py | |
| ► tests | |
| __init__.py | |
| ► window_main | |
| ► frames | |
| __init__.py | |
| InputFrame.py | |
| OutputFrame.py | |
| QuickProtocolsFrame.py | |
| SimpleAnalysisFrame.py | |
| ► IO | |
| __init__.py | |
| GUIInput.py | |
| GUIOutput.py | |
| SessionIO.py | |
| __init__.py | |
| global_variables.py | |
| menu.py | |
| ► window_modules | |
| ► clean_pdb | |
| __init__.py | |
| FixPDBWindow.py | |
| ► design | |
| __init__.py | |
| ResfileDesignWindow.py | |
| ► full_control | |
| __init__.py | |
| FullControlWindow.py | |
| ► insert_bfactor | |
| __init__.py | |
| InsertBFactor.py | |
| ► interactive_terminal | |
| __init__.py | |
| interactive_terminal.py | |
| ► ligand_ncaa_ptm_manager | |
| __init__.py | |
| ligand_ncaa_ptm_manager.py | |
| ► options_system | |
| __init__.py | |
| OptionSystemManager.py | |
| ► protocol_builder | |
| __init__.py | |
| ProtocolBuilder.py | |
| ► pymol_integration | |
| __init__.py | |
| PyMOL.py | |
| ► scorefunction | |
| __init__.py | |
| ScoreFxnControl.py | |
| ► scripting | |
| rosetta_scripts.py | |
| ► vicinity_options | |
| __init__.py | |
| vicinity_window.py | |
| __init__.py | |
| __init__.py | |
| pyrosetta_toolkit.py | |
| ► surface_docking | |
| ► post_processing | |
| ► pdb_objects | |
| calccontacts.py | |
| contacts.py | |
| coordlib.py | |
| loadPDB.py | |
| .pymolSurfaceMode.py | |
| ContactMap.py | |
| Equations.py | |
| extract_scores_and_constraints.py | |
| IO.py | |
| make_amb_constr.py | |
| PDBInfo.py | |
| PhiPsi.py | |
| PlotSurfaceContactMap.py | |
| __init__.py | |
| append_data.py | |
| constraints.py | |
| movers.py | |
| surf_param.py | |
| surface_docking.py | |
| __init__.py | |
| delta_score_per_mutation.py | |
| ► demo | |
| ► untested | |
| docking.py | |
| loops.py | |
| loops_kic.py | |
| PyMOL_demo.py | |
| __init__.py | |
| D010_Pose_structure.py | |
| D020_Pose_scoring.py | |
| D030_Fold_tree.py | |
| D040_Movemap.py | |
| D050_Packer_task.py | |
| D060_Folding.py | |
| D070_Refinement.py | |
| D080_Loop_modeling.py | |
| D090_Ala_scan.py | |
| D100_Docking.py | |
| D110_DNA_interface.py | |
| D120_Ligand_interface.py | |
| ► src | |
| ► basic | |
| _basic__by_hand_beginning.cc | |
| ► core | |
| ► chemical | |
| ► orbitals | |
| _orbitals__by_hand_beginning.cc | |
| ► fragment | |
| ► picking_old | |
| ► vall | |
| __init__.py | |
| __init__.py | |
| _fragment__by_hand_beginning.cc | |
| ► import_pose | |
| _import_pose__by_hand_beginning.cc | |
| ► io | |
| ► silent | |
| __init__.py | |
| __init__.py | |
| _io__by_hand_ending.cc | |
| ► pose | |
| __init__.py | |
| _pose__by_hand_beginning.cc | |
| ► scoring | |
| ► constraints | |
| __init__.py | |
| _constraints__by_hand_beginning.cc | |
| __init__.py | |
| _scoring__by_hand_beginning.cc | |
| _core__by_hand_beginning.cc | |
| _core__by_hand_ending.cc | |
| ► numeric | |
| __init__.py | |
| _numeric__by_hand_ending.cc | |
| ► protocols | |
| ► abinitio | |
| _abinitio__by_hand_beginning.cc | |
| ► antibody | |
| __init__.py | |
| ► canonical_sampling | |
| __init__.py | |
| ► environment | |
| __init__.py | |
| ► jd2 | |
| __init__.py | |
| ► jobdist | |
| _jobdist__by_hand_beginning.cc | |
| ► loops | |
| __init__.py | |
| ► moves | |
| _moves__by_hand_beginning.cc | |
| ► rigid | |
| __init__.py | |
| ► rosetta_scripts | |
| __init__.py | |
| ► simple_filters | |
| __init__.py | |
| ► toolbox | |
| ► task_operations | |
| __init__.py | |
| __init__.py | |
| _protocols__by_hand_beginning.cc | |
| ► utility | |
| __init__.py | |
| _utility__by_hand_beginning.cc | |
| _utility__by_hand_ending.cc | |
| __init__.py | |
| logging_support.py | |
| PyMolLink.py | |
| ► test | |
| __init__.py | |
| G000_Main_GUI.py | |
| G100_Functions_Input.py | |
| G101_Functions_Output.py | |
| G102_Functions_General.py | |
| G103_Functions_Analysis.py | |
| G104_Functions_Sequence.py | |
| G200_Module_Region.py | |
| G201_Module_Structure.py | |
| G202_Module_PythonPDB.py | |
| G203_Module_SQLPDB.py | |
| G204_Module_ScoreAnalysis.py | |
| G205_Module_RegionalScoring.py | |
| T000_Imports.py | |
| T005_Bindings.py | |
| T007_TracerIO.py | |
| T010_LoadPDB.py | |
| T100_Basic.py | |
| T150_PyMOL_Integration.py | |
| T200_Scoring.py | |
| T220_AtomAtomPairEnergies.py | |
| T250_Constraints.py | |
| T400_Refinement.py | |
| T500_Packing.py | |
| T600_Docking.py | |
| T650_LoopsKIC.py | |
| T660_LoopBuilding.py | |
| T700_FoldTree.py | |
| T800_ClassicRelax.py | |
| T850_SubClassing.py | |
| T860_SubClassing_EnergyMethods.py | |
| T870_SubClassing_EnergyMethods2.py | |
| T880_Other.py | |
| Workshop2test.py | |
| Workshop3test.py | |
| Workshop4test.py | |
| Workshop5test.py | |
| Workshop6test.py | |
| Workshop7test.py | |
| Workshop8test.py | |
| Workshop9_my_shapes.py | |
| Workshop9test.py | |
| ► toolbox | |
| __init__.py | |
| adjust_library_path.py | Adjust shared library pasth in namespace .so files and set path it absolute value (required in El Capitan) |
| cleaning.py | |
| extract_coords_pose.py | |
| generate_resfile.py | |
| load_ligand.py | |
| make_rna_rosetta_ready.py | |
| mutants.py | |
| rcsb.py | |
| structural_alignment.py | |
| ► tools | |
| __init__.py | |
| CppParser.py | |
| dox_extract.py | |
| doxygen.py | |
| DoxygenExtractorPyPP.py | |
| BuildBindings.py | |
| exclude.py | |
| PyMOLPyRosettaServer.py | |
| TestBindings.py | Run bindings test and demo scrips |
| ► packaged_bindings | |
| ► src | |
| ► basic | |
| __init__.py | |
| ► core | |
| ► chemical | |
| ► orbitals | |
| _orbitals__by_hand_beginning.cc | |
| ► fragment | |
| ► picking_old | |
| ► vall | |
| __init__.py | |
| __init__.py | |
| _fragment__by_hand_beginning.cc | |
| ► io | |
| __init__.py | |
| ► pack | |
| ► task | |
| __init__.py | |
| ► pose | |
| ► datacache | |
| _datacache__by_hand_beginning.cc | |
| __init__.py | |
| _pose__by_hand_beginning.cc | |
| ► scoring | |
| _scoring__by_hand_beginning.cc | |
| __init__.py | |
| _core__by_hand_beginning.cc | |
| ► numeric | |
| __init__.py | |
| _numeric__by_hand_ending.cc | |
| ► protocols | |
| ► abinitio | |
| _abinitio__by_hand_beginning.cc | |
| ► jd2 | |
| __init__.py | |
| ► jobdist | |
| _jobdist__by_hand_beginning.cc | |
| ► loops | |
| __init__.py | |
| ► rosetta_scripts | |
| __init__.py | |
| ► simple_filters | |
| __init__.py | |
| ► toolbox | |
| ► task_operations | |
| __init__.py | |
| __init__.py | |
| ► utility | |
| __init__.py | |
| _utility__by_hand_beginning.cc | |
| _utility__by_hand_ending.cc | |
| __init__.py | |
| initialization.py | |
| logging_support.py | |
| PyMolLink.py | |
| ► static | |
| ► rosetta | |
| ► tests | |
| __init__.py | |
| test_basic.py | |
| setup.py | |
| ► tools | |
| __init__.py | |
| CppParser.py | |
| dox_extract.py | |
| doxygen.py | |
| DoxygenExtractorPyPP.py | |
| BuildPackagedBindings.py | |
| exclude.py | |
| ► utility | |
| ► boinc | |
| boinc_util.cc | |
| boinc_util.hh | Wrappers to make BOINC work |
| ► excn | |
| Exceptions.cc | |
| Exceptions.fwd.hh | Declarations for many of the common exception subclasses |
| Exceptions.hh | Common derived classes for thrown exceptions |
| EXCN_Base.fwd.hh | Declaration for the base class for Exception system |
| EXCN_Base.hh | Base class for Exception system |
| ► factory | |
| Factory.fwd.hh | Utility::factory::Factory forward declarations |
| Factory.hh | Pluggable factory |
| Registrant.fwd.hh | Utility::factory::Registrant forward declarations |
| Registrant.hh | Factory registrant |
| WidgetFactory.fwd.hh | WidgetFactory forward declaration |
| WidgetFactory.hh | WidgetFactory base class for load-time registration of WidgetCreators to the WidgetFactory |
| WidgetRegistrator.hh | WidgetRegistrator class which registers WidgetCreator classes at load time |
| ► file | |
| file_sys_util.cc | Platform independent operations on files (except I/O) |
| file_sys_util.hh | Platform independent operations on files (except I/O) |
| FileName.cc | |
| FileName.fwd.hh | Utility::file::FileName forward declarations |
| FileName.hh | File name class supporting Windows and UN*X/Linux format names |
| gzip_util.cc | Gzip utility functions |
| gzip_util.hh | Gzip utility functions |
| PathName.cc | |
| PathName.fwd.hh | Utility::file::PathName forward declarations |
| PathName.hh | Path name class supporting Windows and UN*X/Linux format names |
| ► graph | |
| BFS_prune.hh | A breadth first search with pruning for boost graphs |
| DFS_sort.hh | A depth first search with sorting for edge visitation |
| ring_detection.hh | Algorithms for working with rings in boost graphs |
| RingDetection.hh | |
| ► io | |
| all.fwd.hh | Utility::io package forward declarations |
| FileContentsMap.cc | Implementation of the FileContentsMap class, which loads and then maintains the contents of files as strings in memory |
| FileContentsMap.fwd.hh | Forward declaration of a class that maintains file contents in memory as strings |
| FileContentsMap.hh | Declaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed |
| icstream.cc | Input channel stream wrapper base class, |
| icstream.fwd.hh | Utility::io::icstream forward declarations |
| icstream.hh | Input channel stream wrapper class |
| irstream.fwd.hh | Utility::io::irstream forward declarations |
| irstream.hh | Input stream wrapper abstract base class |
| izstream.cc | Input file stream wrapper for uncompressed and compressed files |
| izstream.fwd.hh | Utility::io::izstream forward declarations |
| izstream.hh | Input file stream wrapper for uncompressed and compressed files |
| mpistream.hh | |
| mpistream.ipp | |
| ocstream.cc | Output channel stream wrapper base class, |
| ocstream.fwd.hh | Utility::io::ocstream forward declarations |
| ocstream.hh | Output channel stream wrapper class |
| orstream.fwd.hh | Utility::io::orstream forward declarations |
| orstream.hh | Output stream wrapper abstract base class |
| ozstream.cc | Output file stream wrapper for uncompressed and compressed files |
| ozstream.fwd.hh | Utility::io::ozstream forward declarations |
| ozstream.hh | Output file stream wrapper for uncompressed and compressed files |
| util.cc | General database input/output utility function definitions |
| util.hh | General database input/output utility functions |
| zipstream.hpp | Altered zipstream library header |
| zipstream.ipp | Altered zipstream library implementation |
| ► json_spirit | |
| json_spirit.h | |
| json_spirit_error_position.h | |
| json_spirit_reader.cc | |
| json_spirit_reader.h | |
| json_spirit_reader_template.h | |
| json_spirit_stream_reader.h | |
| json_spirit_tools.cc | Extra utilitiy functions not provided by json spirit library |
| json_spirit_tools.hh | Extra utilitiy functions not provided by json spirit library |
| json_spirit_utils.h | |
| json_spirit_value.cc | |
| json_spirit_value.h | |
| json_spirit_writer.cc | |
| json_spirit_writer.h | |
| json_spirit_writer_options.h | |
| json_spirit_writer_template.h | |
| ► keys | |
| AutoKey.fwd.hh | Utility::keys::AutoKey forward declarations |
| AutoKey.hh | Automatic hidden index key abstract base class |
| ClassKeyMap.fwd.hh | Utility::keys::ClassKeyMap forward declarations |
| ClassKeyMap.hh | Keyed-access map with key subset map for each client class |
| ClassKeyVector.fwd.hh | Utility::keys::ClassKeyVector forward declarations |
| ClassKeyVector.hh | Keyed-access vector with key subset map for each client class |
| Key.fwd.hh | Utility::keys::Key forward declarations |
| Key.hh | Hidden index key interface class |
| Key2Tuple.fwd.hh | Utility::keys::Key2Tuple forward declarations |
| Key2Tuple.hh | 2-tuple meta-key |
| Key2Tuple.srlz.cc | |
| Key2Tuple.srlz.hh | Serlialization routines for Key2Tuples |
| Key2Vector.fwd.hh | Utility::keys::Key2Vector forward declarations |
| Key2Vector.hh | 2-key meta-key |
| Key3Tuple.fwd.hh | Utility::keys::Key3Tuple forward declarations |
| Key3Tuple.hh | 3-tuple meta-key |
| Key3Tuple.srlz.cc | Serlialization routines for Key3Tuples |
| Key3Tuple.srlz.hh | Serlialization routines for Key3Tuples |
| Key3Vector.fwd.hh | Utility::keys::Key3Vector forward declarations |
| Key3Vector.hh | 3-key meta-key |
| Key4Tuple.fwd.hh | Utility::keys::Key4Tuple forward declarations |
| Key4Tuple.hh | 4-tuple meta-key |
| Key4Vector.fwd.hh | Utility::keys::Key4Vector forward declarations |
| Key4Vector.hh | 4-key meta-key |
| KeyCount.fwd.hh | Utility::keys::KeyCount forward declarations |
| KeyCount.hh | Key counter functor |
| KeyLess.fwd.hh | Utility::keys::KeyLess forward declarations |
| KeyLess.hh | Key comparison functor template |
| KeyLookup.functors.hh | Utility::keys::KeyLookup functor declarations |
| KeyLookup.functors.ii | Utility::keys::KeyLookup functor declarations |
| KeyLookup.fwd.hh | Utility::keys::KeyLookup forward declarations |
| KeyLookup.hh | Key lookup map and collection and functors |
| KeyMapTraits.hh | KeyMap traits class |
| KeySetTraits.hh | KeySet traits class |
| KeyVector.fwd.hh | Utility::keys::KeyVector forward declarations |
| KeyVector.hh | Keyed-access vector |
| KeyVectorTraits.hh | KeyVector traits class |
| NoClient.fwd.hh | Utility::keys::NoClient forward declarations |
| NoClient.hh | Default key policy class when no client is needed to distinguish key type |
| SmallKeyMap.fwd.hh | Utility::keys::SmallKeyMap forward declarations |
| SmallKeyMap.hh | Keyed-access map with key subset map |
| SmallKeyVector.fwd.hh | Utility::keys::SmallKeyVector forward declarations |
| SmallKeyVector.hh | Keyed-access vector with key subset map |
| UserKey.fwd.hh | Utility::keys::UserKey forward declarations |
| UserKey.hh | User-created hidden index key abstract base class |
| VariantKey.fwd.hh | Utility::keys::VariantKey forward declarations |
| VariantKey.hh | Variant key class |
| ► libsvm | |
| Svm.cc | |
| Svm.hh | |
| Svm_rosetta.cc | A class to wrap libsvm for rosetta |
| Svm_rosetta.fwd.hh | Owning pointer for libsvm |
| Svm_rosetta.hh | |
| ► options | |
| ► keys | |
| all.fwd.hh | Utility::options package keys forward declarations |
| all.hh | Utility::options package keys declarations |
| AnyOptionKey.fwd.hh | Utility::options::AnyOptionKey forward declarations |
| AnyOptionKey.hh | Automatic hidden index key for any scalar-valued options |
| AnyVectorOptionKey.fwd.hh | Utility::options::AnyVectorOptionKey forward declarations |
| AnyVectorOptionKey.hh | Automatic hidden index key for any vector-valued options |
| BooleanOptionKey.fwd.hh | Utility::options::BooleanOptionKey forward declarations |
| BooleanOptionKey.hh | Automatic hidden index key for boolean options |
| BooleanVectorOptionKey.fwd.hh | Utility::options::BooleanVectorOptionKey forward declarations |
| BooleanVectorOptionKey.hh | Automatic hidden index key for boolean options |
| FileOptionKey.fwd.hh | Utility::options::FileOptionKey forward declarations |
| FileOptionKey.hh | Automatic hidden index key for file options |
| FileVectorOptionKey.fwd.hh | Utility::options::FileVectorOptionKey forward declarations |
| FileVectorOptionKey.hh | Automatic hidden index key for file options |
| IntegerOptionKey.fwd.hh | Utility::options::IntegerOptionKey forward declarations |
| IntegerOptionKey.hh | Automatic hidden index key for integer options |
| IntegerVectorOptionKey.fwd.hh | Utility::options::IntegerVectorOptionKey forward declarations |
| IntegerVectorOptionKey.hh | Automatic hidden index key for integer options |
| OptionKey.fwd.hh | Utility::options::OptionKey forward declarations |
| OptionKey.hh | Abstract automatic hidden index key for options |
| OptionKeys.cc | Utility::options::OptionKeys collection |
| OptionKeys.hh | Utility::options::OptionKeys collection |
| PathOptionKey.fwd.hh | Utility::options::PathOptionKey forward declarations |
| PathOptionKey.hh | Automatic hidden index key for path options |
| PathVectorOptionKey.fwd.hh | Utility::options::PathVectorOptionKey forward declarations |
| PathVectorOptionKey.hh | Automatic hidden index key for path options |
| RealOptionKey.fwd.hh | Utility::options::RealOptionKey forward declarations |
| RealOptionKey.hh | Automatic hidden index key for real options |
| RealVectorOptionKey.fwd.hh | Utility::options::RealVectorOptionKey forward declarations |
| RealVectorOptionKey.hh | Automatic hidden index key for real options |
| ResidueChainVectorOptionKey.fwd.hh | Utility::options::ResidueChainVectorOptionKey forward declarations |
| ResidueChainVectorOptionKey.hh | Automatic hidden index key for integer options |
| ScalarOptionKey.fwd.hh | Utility::options::ScalarOptionKey forward declarations |
| ScalarOptionKey.hh | Abstract automatic hidden index key for scalar-valued options |
| StringOptionKey.fwd.hh | Utility::options::StringOptionKey forward declarations |
| StringOptionKey.hh | Automatic hidden index key for string options |
| StringVectorOptionKey.fwd.hh | Utility::options::StringVectorOptionKey forward declarations |
| StringVectorOptionKey.hh | Automatic hidden index key for string options |
| VectorOptionKey.fwd.hh | Utility::options::VectorOptionKey forward declarations |
| VectorOptionKey.hh | Abstract automatic hidden index key for vector-valued options |
| AnyOption.fwd.hh | Utility::options::AnyOption forward declarations |
| AnyOption.hh | Program any scalar-valued option abstract base class |
| AnyVectorOption.fwd.hh | Utility::options::AnyVectorOption forward declarations |
| AnyVectorOption.hh | Program any vector-valued option abstract base class |
| BooleanOption.fwd.hh | Utility::options::BooleanOption forward declarations |
| BooleanOption.hh | Program boolean option class |
| BooleanVectorOption.fwd.hh | Utility::options::BooleanVectorOption forward declarations |
| BooleanVectorOption.hh | Program boolean vector option class |
| FileOption.fwd.hh | Utility::options::FileOption forward declarations |
| FileOption.hh | Program file option class |
| FileVectorOption.fwd.hh | Utility::options::FileVectorOption forward declarations |
| FileVectorOption.hh | Program file vector option class |
| IntegerOption.fwd.hh | Utility::options::IntegerOption forward declarations |
| IntegerOption.hh | Program integer option class |
| IntegerVectorOption.fwd.hh | Utility::options::IntegerVectorOption forward declarations |
| IntegerVectorOption.hh | Program integer vector option class |
| mpi_stderr.cc | |
| mpi_stderr.hh | |
| Option.fwd.hh | Utility::options::Option forward declarations |
| Option.hh | Program option interface class |
| OptionCollection.cc | Program options collection |
| OptionCollection.fwd.hh | Utility::options::OptionCollection forward declarations |
| OptionCollection.hh | Program options collection |
| PathOption.fwd.hh | Utility::options::PathOption forward declarations |
| PathOption.hh | Program path option class |
| PathVectorOption.fwd.hh | Utility::options::PathVectorOption forward declarations |
| PathVectorOption.hh | Program path vector option class |
| RealOption.fwd.hh | Utility::options::RealOption forward declarations |
| RealOption.hh | Program real option class |
| RealVectorOption.fwd.hh | Utility::options::RealVectorOption forward declarations |
| RealVectorOption.hh | Program real vector option class |
| ResidueChainVectorOption.cc | |
| ResidueChainVectorOption.fwd.hh | Utility::options::ResidueChainVectorOption forward declarations |
| ResidueChainVectorOption.hh | Program integer vector option class |
| ScalarOption.fwd.hh | Utility::options::ScalarOption forward declarations |
| ScalarOption.hh | Program scalar-valued option interface class |
| ScalarOption_T_.fwd.hh | Utility::options::ScalarOption_T_ forward declarations |
| ScalarOption_T_.hh | Program scalar-valued option abstract base class |
| StringOption.fwd.hh | Utility::options::StringOption forward declarations |
| StringOption.hh | Program string option class |
| StringVectorOption.fwd.hh | Utility::options::StringVectorOption forward declarations |
| StringVectorOption.hh | Program string vector option class |
| VariantOption.fwd.hh | Utility::options::VariantOption forward declarations |
| VariantOption.hh | Variant option class |
| VectorOption.fwd.hh | Utility::options::VectorOption forward declarations |
| VectorOption.hh | Program vector-valued option interface class |
| VectorOption_T_.fwd.hh | Utility::options::VectorOption_T_ forward declarations |
| VectorOption_T_.hh | Program vector-valued option abstract base class |
| ► pointer | |
| ► boost | |
| access_ptr.hh | Non-owning access smart pointer |
| owning_ptr.fwd.hh | |
| owning_ptr.hh | Owning smart pointer using C++11 |
| ReferenceCount.fwd.hh | |
| ReferenceCount.hh | Dummy base class |
| ► std | |
| access_ptr.hh | Non-owning access smart pointer |
| owning_ptr.fwd.hh | Owning smart pointer using C++11 |
| owning_ptr.hh | Owning smart pointer using C++11 |
| ReferenceCount.fwd.hh | |
| ReferenceCount.hh | Dummy base class |
| access_ptr.fwd.hh | Non-owning access smart pointer – dispatch class |
| access_ptr.hh | Non-owning access smart pointer – dispatch class |
| owning_ptr.functions.hh | |
| owning_ptr.fwd.hh | Non-owning owning smart pointer – dispatch class |
| owning_ptr.hh | Non-owning access smart pointer – dispatch class |
| ReferenceCount.fwd.hh | Utility::pointer::ReferenceCount forward declarations |
| ReferenceCount.hh | ReferenceCount base class – dispatch class |
| ReferenceCount.srlz.cc | |
| ReferenceCount.srlz.hh | Faux serialization routines for the ReferenceCount base class |
| ► py | |
| Inheritance.hh | |
| PyAssert.hh | |
| PyExitCallback.cc | |
| PyExitCallback.fwd.hh | |
| PyExitCallback.hh | |
| PyHelper.hh | |
| ► serialization | |
| ► ObjexxFCL | |
| DynamicIndexRange.srlz.cc | |
| DynamicIndexRange.srlz.hh | Serlialization routines for ObjexxFCL::DynamicIndexRanges; these functions have to live in namespace ObjexxFCL, even though they are being written and compiled in the utility library |
| FArray1D.srlz.cc | Serlialization routines for FArray1Ds |
| FArray1D.srlz.hh | Serlialization routines for ObjexxFCL::FArray1Ds; these functions have to live in namespace ObjexxFCL, even though they are being written and compiled in the utility library |
| FArray2D.srlz.cc | |
| FArray2D.srlz.hh | Serlialization routines for ObjexxFCL::FArray2Ds; these functions have to live in namespace ObjexxFCL, even though they are being written and compiled in the utility library |
| FArray3D.srlz.cc | |
| FArray3D.srlz.hh | Serlialization routines for ObjexxFCL::FArray3Ds; these functions have to live in namespace ObjexxFCL, even though they are being written and compiled in the utility library |
| ubyte.srlz.cc | |
| ubyte.srlz.hh | Serlialization routines for ObjexxFCL::ubytes; these functions have to live in namespace ObjexxFCL, even though they are being written and compiled in the utility library |
| serialization.cc | Common serlialization routines |
| serialization.hh | Commons serlialization routines |
| ► signals | |
| BufferedSignalHub.fwd.hh | Forward declaration for utility::signals::BufferedSignalHub |
| BufferedSignalHub.hh | SignalHub capable of buffering while blocking |
| Link.fwd.hh | Forward declaration for utility::signals::Link |
| Link.hh | Class storing the link between observers and subjects |
| LinkUnit.fwd.hh | Forward declaration for utility::signals::LinkUnit |
| LinkUnit.hh | Class specifying actual link data between observers and subjects |
| PausableSignalHub.fwd.hh | Forward declaration for utility::signals::PausableSignalHub |
| PausableSignalHub.hh | BufferedSignalHub capable of pausing and waiting for stdin |
| SignalHub.fwd.hh | Forward declaration for utility::signals::SignalHub |
| SignalHub.hh | Primary class for function based implementation of observer pattern |
| TokenHub.fwd.hh | Forward declaration for utility::signals::TokenHub |
| TokenHub.hh | BufferedSignalHub capable of passing observers |
| ► sql_database | |
| DatabaseSessionManager.cc | |
| DatabaseSessionManager.fwd.hh | |
| DatabaseSessionManager.hh | |
| types.cc | |
| types.hh | |
| util.hh | |
| ► tag | |
| Tag.cc | An object for reading/writing a simple xml-like language |
| Tag.fwd.hh | |
| Tag.hh | An object for reading/writing a simple xml-like language |
| XMLSchemaGeneration.cc | Definitions of the classes used to define an XML Schema |
| XMLSchemaGeneration.fwd.hh | Forward declaration of the classes used to define an XML Schema |
| XMLSchemaGeneration.hh | |
| ► thread | |
| backwards_thread_local.hh | File to provide backwards compatibility for the thread_local keyword |
| ReadWriteMutex.cc | Classes to manage data that can be read by multiple threads and written to by only one thread |
| ReadWriteMutex.hh | Classes to manage data that can be read by multiple threads and written to by only one thread |
| threadsafe_creation.fwd.hh | |
| threadsafe_creation.hh | |
| ► tools | |
| make_map.hh | Common function to build vector, vector0, vector1, map |
| make_templates.py | Program that generate make_vector.hh and make_map.hh files |
| make_vector.hh | Common function to build vector, vector0, vector1, map |
| make_vector1.hh | |
| assert.hh | |
| backtrace.hh | Programmatic backtrace whenever you want it |
| basic_sys_util.cc | All system functions in utility that have no other home |
| basic_sys_util.hh | All system functions in utility that have no other home |
| Binary_Util.cc | |
| Binary_Util.hh | |
| BitSet.fwd.hh | Utility::BitSet forward declarations |
| BitSet.hh | Simple bit set |
| BitVector.fwd.hh | Utility::BitVector forward declarations |
| BitVector.hh | Simple bit vector |
| Bound.fwd.hh | Utility::Bound forward declarations |
| Bound.hh | Bound value class |
| CSI_Sequence.cc | Terminal ASCII codes |
| CSI_Sequence.fwd.hh | Terminal ASCII codes |
| CSI_Sequence.hh | Terminal ASCII codes |
| curl.cc | Implements a OO interface to CURL wrapping and hiding the ugly C callbacks |
| curl.hh | Implements a OO interface to CURL wrapping and hiding the ugly C callbacks |
| DereferenceIterator.hh | Class for Iterating across a container of OPs if the function expects iterators of the dereferenced objects. example: if you have a loop that iterates on decoys via SilentFileData::begin()... SilentFileData::end() it uses the dereferenced objects: i.e., it->fill_pose() SilentFileData sfd; my_func( sfd.begin(), sfd.end() ); |
| down_cast.hh | Fast polymorphic down-casting functions |
| exit.cc | Program exit functions and macros |
| exit.hh | Program exit functions and macros |
| fix_boinc_read.hh | |
| fixedsizearray0.fwd.hh | Unresizable vector whose size is known at compile time, which may be allocated on the stack, and which indexes from 0 |
| fixedsizearray0.hh | |
| fixedsizearray0.srlz.hh | Serlialization routines for fixedsizearray0s |
| fixedsizearray1.fwd.hh | |
| fixedsizearray1.hh | |
| fixedsizearray1.srlz.hh | Serlialization routines for fixedsizearray1s |
| FixedSizeLexicographicalIterator.fwd.hh | |
| FixedSizeLexicographicalIterator.hh | Class for iterating across all words of a compile-time-known fixed-length, composed of letters from varying alphabets, where each alphabet is represented by its size. This iteration is performed in lexicographical order. All allocation of a FixedSizeLexicographicalIterator takes place on the stack, and is therefore much faster than a regular LexigographicalIterator |
| FixedSizeLexicographicalIterator.tmpl.hh | |
| heap.cc | Class definition for a heap object based on Charlie Strauss's heap code ported over from rosetta++ |
| heap.fwd.hh | Forward class definition of class heap |
| heap.hh | Class definition for a heap object based on Charlie Strauss's heap code ported over from rosetta++. Stores a sorted list of integers based on floating-point values |
| in_place_list.fwd.hh | |
| in_place_list.hh | Doubly linked list where elements are shuffled in place |
| inline_file_provider.cc | |
| inline_file_provider.hh | |
| integer_mapping.cc | A set of useful classes to map between two enumerations. So far, only a subset mapping is implemented |
| integer_mapping.fwd.hh | |
| integer_mapping.hh | A set of useful classes to map between two enumerations. So far, only a subset mapping is implemented |
| iter_util.hh | |
| LexicographicalIterator.cc | |
| LexicographicalIterator.fwd.hh | |
| LexicographicalIterator.hh | Class for iterating across all words of a fixed-length, composed of letters from varying alphabets, where each alphabet is represented by its size. This iteration is performed in lexicographical order |
| make_static_database.py | |
| map_util.cc | |
| map_util.hh | Utility functions for std::maps |
| minmax.hh | |
| mpi_util.cc | |
| mpi_util.hh | |
| numbers.hh | Brief utility classes for numeric usage |
| OrderedTuple.fwd.hh | Forward declaration of OrderedTuple class |
| OrderedTuple.hh | Class for compairing/sorting data where sort-precidence is in descending order from begin() to end() |
| recent_history_queue.cc | A queue for holding the history in which certain members of a set are promoted to the front of the queue before eventually falling off the end of the queue |
| recent_history_queue.hh | A queue for holding the history in which certain members of a set are promoted to the front of the queue before eventually falling off the end of the queue |
| Show.hh | Uniformed printing functionality for data types |
| SimulateMPI.cc | |
| SimulateMPI.fwd.hh | |
| SimulateMPI.hh | |
| SingletonBase.hh | A base class for all singltons using CRTP and managing the complexity of safely initializing singltons in a thread-safe way |
| sort_predicates.hh | |
| static_database.cc | |
| static_database.hh | |
| stream_util.hh | Implemention of ostream operator << for various common types |
| string_constants.hh | Commonly used string constants |
| string_util.cc | Some std::string helper functions |
| string_util.hh | Some std::string helper functions |
| utility.functions.hh | Numeric functions (to avoid dependency on numeric package) |
| vector0.fwd.hh | Utility::vector0 forward declarations |
| vector0.hh | Vector0: std::vector with assert-checked bounds |
| vector0.srlz.cc | Serlialization routines for vector0s |
| vector0.srlz.hh | Serlialization routines for vector0s |
| vector0_bool.hh | Vector0: std::vector with assert-checked bounds: bool specialization |
| vector1.functions.hh | Some useful functions for vector1 that I'm tired of rewriting |
| vector1.fwd.hh | Utility::vector1 forward declarations |
| vector1.hh | Vector1: std::vector with 1-based indexing |
| vector1.srlz.cc | Serlialization routines for vector1s |
| vector1.srlz.hh | Serlialization routines for vector1s |
| vector1_bool.hh | Vector1: std::vector with 1-based indexing: bool specialization |
| vectorL.fwd.hh | Utility::vectorL forward declarations |
| vectorL.hh | VectorL: std::vector with L-based indexing |
| vectorL_bool.hh | VectorL: std::vector with L-based indexing: bool specialization |
| vectorL_Selector.hh | VectorL lower index selectors |
| .ycm_extra_conf.py | |
| ▼ test | |
| ► yaml | |
| __init__.py | |
| composer.py | |
| constructor.py | |
| cyaml.py | |
| dumper.py | |
| emitter.py | |
| error.py | |
| events.py | |
| loader.py | |
| nodes.py | |
| parser.py | |
| reader.py | |
| representer.py | |
| resolver.py | |
| scanner.py | |
| serializer.py | |
| tokens.py | |
1.8.7
