|
Rosetta
|
| ▼ src | |
| ► apps | |
| ► benchmark | |
| ► performance | |
| compare_times.py | |
| Design.bench.hh | |
| Docking.bench.hh | Run a performance benchmark of docking |
| FastRelax.bench.hh | |
| init_util.hh | Initialization subroutines for Benchmark |
| InstantiateModules.bench.hh | |
| InteractionGraph.bench.hh | |
| LigandDock.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 |
| 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 | |
| ► pilot | |
| ► aginsparg | |
| holes_identifier.cc | Aginsparg, ipatel, sthyme |
| ligand_discovery_search_protocol.cc | Aginsparg, ipatel, sthyme |
| space_fill_analysis.cc | Aginsparg, ipatel, sthyme |
| ► amelie | |
| design_tight_clusters.cc | |
| detect_tight_clusters.cc | |
| ► ameya | |
| mixedMC.cc | |
| ► andre | |
| SymmDataTest.cc | |
| ► andrew | |
| analyze_rtmin_failures.cc | |
| apl_msd.cc | Multistate design executable as written by apl |
| domain_assembly_jd2.cc | |
| find_buns.cc | Application that finds buried unsatisfied hydrogen bonding groups in proteins using the variable- distance to solvent logic. Outputs a kinemage that highlights the buried-unsatisfied polar groups and also displays all the exposed dots |
| fixbb_jd3.cc | |
| flex_regions_alc.cc | |
| interface_ddg_bind.cc | Interface ddG bind of mutation prediction protocol |
| kellogg_ddg_jd3.cc | |
| measure_catalytic_geometry.cc | |
| measure_lcaa_neighbor_radii.cc | |
| mmt_msd.cc | |
| mpi_msd.cc | |
| mpi_test.cc | |
| optest.cc | |
| relax_jd3.cc | Relax, using the jd3 JobDistributor |
| sweep_respair_energies.cc | |
| version_scorefunction.cc | |
| zn_match_symmdock.cc | |
| ► aroop | |
| model_e2c_ubiquitin.cc | |
| ► arubenstein | |
| sequence_tolerance_mf.cc | App for predicting the sequence tolerance of a structure or set of structures |
| spec_prof_compare.cc | |
| ► ashworth | |
| jd2_parser_DNAInt.cc | |
| MSA_design.cc | Test app for packer design that is biased toward a multiple sequence alignment/PSSM |
| multistate_design_ga.cc | |
| ► awatkins | |
| a3b_hbs_creator.cc | |
| a3b_hbs_dock_design.cc | |
| a3b_test.cc | |
| aggregate_coarse_rna_vdw.cc | |
| aramid_folding.cc | |
| b3a_distro_kinemage.cc | |
| best_beta_backbones.py | Scan through beta configurations, ruling out bump check violations |
| beta_314_vs_a3b.cc | |
| beta_nonlocal.py | Look for 'secondary structures' like sheets in beta AAs |
| beta_sc_scan.py | |
| build_a3b.cc | Miscellany with beta aas |
| cov_hbs.cc | Sidechain conjugation to acryl amides |
| cov_peptidomimetic_creator.cc | |
| cov_test.cc | |
| create_a3b_hbs.py | Scan the sidechain angles of a beta-AA |
| diversify_conotoxin.cc | |
| evaluate_beta_mutants.py | Aaa |
| get_dihedral_b3aa.cc | |
| hal_rna_denovo.cc | A first pass at running RNA fragment assembly in a HAL-aware fashion. Can only do single PDB input for now |
| hbs_creator.py | Creates an HBS from a peptide |
| hbs_dock_design.py | |
| indel.cc | |
| lactamize.py | Make any available lactam bridges in a PDB |
| macrocycle_sampling.cc | |
| make_a3b_bundle.cc | |
| make_ideal_a3b_fragment.cc | |
| mike_linker_test.cc | |
| oop_conformations.py | |
| oop_scan.py | Creates an OOP dimer and toys around with its dihedrals |
| orn_macrocycle.py | Create a macrocycle using ornithine residues |
| peptidomimetic_ensembles.cc | |
| peptoid_hbs.cc | |
| pna.py | Look for structure in peptide nucleic acids |
| polyaramid_test.cc | |
| pose_iteration.cc | |
| sec_struct_finder.cc | |
| test_d_l_readin.cc | |
| test_metapatch.cc | |
| test_mm_lj.py | ?? |
| test_nu_angles.py | Mmm |
| test_terpenes.py | Test terpene RTs |
| torsion_scoring.py | No clue |
| trial_rna_mutants.cc | Take a vector of name3s and positions. Do all combinations |
| triazolamer_creator.cc | |
| triazolamer_dock_design.cc | |
| trivial_alascan.py | An alascan that does no sampling |
| vancomycin.cc | |
| vancomycin.py | N/a |
| ► barak | |
| barak.score.cc | |
| barak_relax.cc | |
| BuildFloppyTail.cc | |
| compare_rms_byres.cc | |
| compare_structures.cc | |
| extend_range.cc | |
| overlay_bb_bondangles.cc | |
| overlay_sidechains.cc | |
| PeptideDeriver.cc | |
| phosphorylate_position.cc | |
| print_phipsi.cc | |
| test_frags.barak.cc | |
| thread_bb.cc | |
| thread_sidechains.cc | |
| ► barthp | |
| membrane_highres_score.cc | Rescore membrane protein test |
| membrane_relax.cc | |
| membrane_rescore.cc | Rescore membrane protein test |
| ► bazzoli | |
| bou-min-ubo-nrg-jump.cc | |
| cnl_env_lost_hbs.cc | |
| lig_low_sasa.cc | |
| lig_polar_sat.cc | |
| lig_polar_unsat.cc | |
| list_cnl_ngbs.cc | |
| nrg_res_set.cc | |
| sel_hbonds.cc | |
| tgtres_polar_sho_energies.cc | |
| ► bcorreia | |
| fold_from_loops.cc | |
| fold_from_loops.hh | |
| fold_from_loops_devel.cc | |
| fold_from_loops_devel.hh | |
| iterative_design.cc | |
| ► bder | |
| BuriedUnsatPolarsFinder.cc | |
| HbondZinc.cc | |
| HbondZinc_allpolar.cc | |
| HbondZinc_ser.cc | |
| HbondZincBackbone.cc | |
| HbondZincHHHO.cc | |
| xtal_water_bunsat.cc | |
| zinc_helix_cap.cc | |
| ZincMinimize.cc | |
| ZincSiteEvaluator.cc | |
| ► ben | |
| VIP_app.cc | |
| ► biokhar | |
| karen_compare_different_proteins.cc | |
| karen_compare_pocket_rmsd.cc | |
| karen_pocket_compare.cc | |
| karen_pocket_save.cc | |
| ► bjornw | |
| bus_error.cc | |
| jumpRT_test.cc | Rescore membrane protein test |
| ► blivens | |
| conserve_disulfides.cc | Confirms that disulfides are conserved across the cen<=>fa transition |
| convert.cc | Converts PDBs between residue type sets. Use -in:file:residue_type_set to specify type sets |
| create_disulf_file.cc | Given a pdb file, detect disulfides and output to a disulfide file |
| disulfide_filter.cc | Outputs a list of residue pairs which are likely candidates for disulfide bonds |
| disulfide_finder.cc | Gives some stats on disulfide bonds |
| disulfide_handoff.cc | Removes disulfides from a structure and tries to replace them |
| disulfide_scorer.cc | Looks through a PDB file and outputs disulfide formation scores |
| disulfides.hh | Some utility functions for dealing with disulfides |
| rotamerize_disulfides.cc | Reads in a pdb to rosetta |
| ► boon | |
| pilot.cc | |
| test.cc | This is simply a generic pilot app for testing changes |
| ► brunette | |
| abego_predict.cc | |
| add_xyz_to_pose.py | |
| aln_to_disulf.cc | |
| armEval.cc | |
| calc_ssm_energies_with_structure_profile.cc | |
| calcFractionFolded.cc | |
| cluster_alns.cc | Divide input alns into clusters based on gdtmm comparison of partial models |
| contact_map_from_homologs.cc | |
| convertFragmentType.cc | |
| dumpPhiPsiStats.cc | |
| enumerate_junctions.py | |
| evalFullLength.cc | |
| evalRepeats.cc | |
| extractNativeRepeats.cc | |
| filterAlignments.cc | |
| filterImperfectAln.cc | This takes two sets of alignments. 1 perfect and 1 imperfect. The output is the residues of the imperfect alignment that are correctly aligned |
| findNaturallyOccuringAlphaRepeats.cc | |
| fragments_to_ss.cc | |
| get_junctions_from_legos.py | |
| hle_predict.cc | |
| minimalCstHomology.cc | : Generates the minimal coordinate constraints necessary for fixing homology model. Also creates fasta with virtual. @usage: -in::file::alignment alignment.filt -in::file::template_pdb <pdb names from within the alignment> -in:file:coordCsts <pdb names from within the alignment> -in:file:fasta <fasta name> |
| minimalCstRelax.cc | For the first structure in the alignment compare the deviation between native and the relaxed native structure. Then constraints are modified and coordinate constraints are added. If an alignment is given only the residues from the beginning to end of the alignment are used |
| outputAbego.cc | |
| outputLayerDesignBurial.cc | |
| outputRama.cc | |
| outputSasa.cc | |
| predictedCstFilter.cc | |
| repeat_dock.cc | |
| silents_to_ss.cc | |
| tj_util.hh | |
| unalignedEvaluate.cc | This takes an alignment file, fasta file, and a silent file. It then evaluates the qualities of the loops |
| ► carbohydrates | |
| basic_glycan_sampler.cc | |
| test_glycan_trees.cc | |
| ► chen | |
| simple_dna_regression_test.cc | |
| ► chrisk | |
| byres_data.cc | |
| domain_assemble.cc | |
| hbscan.cc | |
| pep_analysis.cc | |
| pep_gly.cc | |
| pep_nrg.cc | |
| pep_opt.cc | |
| pep_opt_parallel.cc | |
| pep_paapp.cc | |
| pep_prep.cc | |
| pep_prepspec.cc | |
| pep_rama.cc | |
| pep_ref.cc | |
| pep_spec.03-11.cc | |
| pep_spec.06-23.cc | |
| pep_spec.cc | |
| pep_spec_flx.cc | |
| pep_spec_flx.mov.cc | |
| pepspec.cc | |
| pepspec_anchor_dock.cc | |
| rotamer_repack.cc | |
| ► christophe | |
| PCS_main.cc | |
| PCS_main.hh | |
| ► chu | |
| loop_test.cc | |
| zinc_stat.cc | |
| ► cmiles | |
| close_loops_cart.cc | |
| close_loops_ccd.cc | |
| dssp.cc | |
| extend.cc | |
| fragment_rmsd.cc | |
| gdtha.cc | |
| helix_rotate.cc | |
| jumping.cc | |
| kcluster.cc | |
| maxsub.cc | |
| medal.cc | |
| medal_exchange.cc | |
| rmsd_partial_thread.cc | |
| sheet_translate.cc | |
| star_abinitio.cc | |
| windowed_rama.cc | |
| windowed_rmsd.cc | |
| ► colin | |
| backrub_pilot.cc | |
| cterdesign.cc | Backrub Monte Carlo/small phi/psi move/design protocol |
| ig_dump.cc | Tool to calculate and dump out an interaction graph |
| mm_params.cc | |
| ► combss | |
| generate_orbital_statistics.cc | |
| sequencerecovery.cc | A protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper |
| ► csykang | |
| make_retroinverso.cc | Generates a retroinverso version of a pose |
| ► dan | |
| angle_stats.cc | |
| generate_matcher_constraints.cc | |
| kinematic_relax_test.cc | |
| loop_minimize.cc | Minimizes a loop to serve as a starting / target structure for modeling |
| LoopExtend.cc | Loop Extend protocol |
| sidechain_min.cc | Minimizes non-disulfide-bonded side-chains in the input structure |
| ► danpf | |
| mmtf2pdb.cc | Mmtf to pdb file using rosetta |
| mmtfs2mmtf.cc | List of mmtfs to a single mmtf (using models) |
| ► dekim | |
| convert_to_centroid.cc | |
| decoy_features.cc | |
| extended_chain.cc | |
| score_nonlocal_frags.cc | |
| strand_pairings.cc | |
| ► delucasl | |
| generate_ligand_start_position_file.cc | |
| ligand_score.cc | |
| ligands_to_database.cc | |
| params_tester.cc | |
| process_mdl.cc | AtomType and assign neighbor atoms for a list of mdl files, output fixed mdl files and pdbs |
| roc_optimizer.cc | |
| roc_test.cc | |
| RotamerDump.cc | |
| simpleScore.cc | This scores a pose @detail Run this script with the following arguments: 1) in::file::s ) score::weights <name of weight file (without extension)> |
| ► dgront | |
| ► experiments | |
| AllCrmsd.cc | |
| call_mover.cc | |
| call_rdc.cc | |
| convert_frags.cc | |
| CreatePose.cc | |
| DetailedScores.cc | |
| DisulfideBondEnergy.cc | |
| DumpConstraints.cc | |
| GunnTest.cc | |
| print_options.cc | |
| RDCTest.cc | |
| read_profile.cc | |
| TryScoreFilter.cc | |
| welde_chains.cc | |
| ► fragmentpicker | |
| diverse_fragments.cc | |
| fragmentpicker_integration_demo.cc | |
| picker.cc | |
| PickSSE.cc | |
| quotapicker_demo.cc | |
| rescore_fragments.cc | |
| ► saxs | |
| assemble_domains_with_saxs_jd2.cc | |
| call_saxs_score.cc | |
| ComputeSAXSSpectrum.cc | |
| linker_sampler.cc | |
| RescorePDDF.cc | |
| RescoreSAXS.cc | |
| RotateSAXS.cc | |
| ApplicationContext.cc | |
| ApplicationContext.hh | |
| CustomAbinitio.cc | |
| CustomAbinitio.hh | |
| DisulfideTest.cc | |
| DomainAssemblerNDocker.cc | |
| Features.cc | |
| filters_in_abrelax.cc | |
| hierarchical_clustering.cc | |
| IndirectSorter.cc | |
| JumpSpecificAbrelax.cc | |
| JumpSpecificAbrelax.hh | |
| LibraryJumpSetup.cc | |
| LibraryJumpSetup.hh | |
| SaxsSampler.cc | |
| SpecificJumpSetup.cc | |
| SpecificJumpSetup.hh | |
| tnm_sampler.cc | |
| ► doug | |
| ► cu_binder | |
| Cu_binder_model.cc | |
| make_peptoid.cc | |
| ► cyclic_peptoid_peptide | |
| cyclic_peptoid_peptide_test1.cc | |
| ► peptoid_rotlibs | |
| peptoid_rotlib_test1.cc | Test the cyclic peptide/peptoid patches |
| peptoid_rotlib_test2.cc | Test the peptoid rotlibs |
| peptoid_rotlib_test3.cc | |
| betacat_movie.cc | |
| cyclic_pack.cc | |
| Cyclize.cc | |
| get_dihedral_peptide.cc | |
| get_dihedral_peptoid.cc | |
| make_peptoid.cc | |
| make_peptoid_sequence.cc | |
| noah_score_interface.cc | |
| number_of_residuetypes.cc | Simply print the number of ResidueTypes in the default ResidueTypeSet |
| peptoid_movie.cc | Simple app to make a movie |
| peptoid_rotamer_prediction_benchmark.cc | |
| pymolmovertest.cc | |
| rotamer_prediction_benchmark.cc | |
| score_min_rtmin_test.cc | Simple test of scoring and minimization |
| simple_relax.cc | |
| test_chain_sequence.cc | Test the PDBInfo::chain_sequence functionality |
| ► dwkulp | |
| flexibleLoopDesign.cc | |
| reportFragments.cc | |
| ► eva | |
| adapt_rotamers.cc | |
| ► fcchou | |
| adenosine_stack_test.cc | |
| lariat_modeling.cc | |
| non_natural_na.cc | |
| rna_pdb_scoring.cc | |
| rotamer_test.cc | |
| swa_rna_analytical_closure.cc | |
| test.cc | |
| thermal_sampler_alpha.cc | |
| turner_test_double_helix.cc | |
| turner_test_one_chain.cc | |
| turner_two_chain.cc | |
| ► firas | |
| check_burial.cc | |
| ► flo | |
| EnzdesFixBB.cc | |
| SecondaryMatcher.cc | |
| ► fordas | |
| dumpstubinteractions.cc | |
| lsmgridprobe.cc | |
| ► frank | |
| autorb.cc | |
| calc_ssm_energies.cc | |
| cart_refine.cc | |
| cen_relax.cc | |
| cryst_design.cc | @Author Frank Dimaio |
| cryst_gen.cc | |
| cryst_reporters.hh | |
| dock_pdb_into_density.cc | |
| dsrna_grow.cc | |
| extract_silent.cc | |
| fasol_perres.cc | |
| fpd_symmTest.cc | |
| make_rms_filtered_fragfile.cc | |
| map_morph.cc | |
| min_test.cc | |
| mirrorsymm_test.cc | |
| multimodel_gdt.cc | |
| pdb_gen_cryst.cc | |
| pdb_to_map.cc | |
| per_atom_gradients.cc | |
| perturb_structure.cc | |
| pseudo_ca_trace.cc | |
| rb_rms.cc | |
| RBSegMove.cc | |
| redesign_minimize_into_density.cc | |
| relax_viewer.cc | |
| spacegroup.hh | |
| ► frankdt | |
| concatenate_poses.cc | Concatenates poses together end-to-end while transforming them to avoid chainbreaks |
| concatenate_poses.fwd.hh | Concatenates poses together end-to-end while transforming them to avoid chainbreaks |
| concatenate_poses.hh | Concatenates poses together end-to-end while transforming them to avoid chainbreaks |
| SmartSEWINGTester.cc | Testing app for SEWING file IO |
| SmartSEWINGTester.fwd.hh | Testing app for SEWING file IO |
| SmartSEWINGTester.hh | Testing app for SEWING file IO |
| steric_fusion_scan.cc | Concatenates poses together end-to-end while transforming them to avoid chainbreaks |
| steric_fusion_scan.fwd.hh | Searches two proteins for the most sterically hindering fusion |
| steric_fusion_scan.hh | Concatenates poses together end-to-end while transforming them to avoid chainbreaks |
| ► georgkuenze | |
| spinlabel_activity.cc | This pilot app inserts a spin-label residue at a specified position and tests all rotamers for this spin-label. Those romaters which remain after the bump filter (with or without allowing packing of neighboring residues) are written out as SDF files. Finally, the native residue is replaced by the spin-label residue and the mutated pose is written out as a PDB file |
| ► gideonla | |
| CutOutDomain.cc | |
| ► gktaylor | |
| create_constraints.cc | |
| homolog_cst.hh | |
| score_pdb.cc | |
| score_silent.cc | |
| ► grant | |
| AbInitio_MPI.cc | |
| DenovoProteinDesign_Test.cc | |
| RedesignXtal_Silent.cc | |
| RedesignXtal_Test.cc | |
| ► guangfeng | |
| align_substructure.cc | |
| cryst_hbonds.cc | |
| ligand_docking_hbonds.cc | |
| torsion_types.cc | |
| ► guffysl | |
| heme_binding.cc | Application to redesign an enzyme to bind an alternative ligand |
| heme_replace.cc | |
| HemeBindingMover.hh | |
| ► habib | |
| david_align_and_recompute_score_and_rmsd.cc | |
| david_align_append_and_recompute_score_and_rmsd.cc | |
| david_darc_multirun.cc | |
| david_extract_dinucleotide_musashi_reference.cc | |
| david_extract_domain.cc | |
| david_fill_gaps.cc | |
| david_find_best_contact_pocket.cc | |
| david_find_best_pocket.cc | |
| david_find_complex_contacts.cc | |
| david_find_contacts.cc | |
| david_find_exemplar.cc | |
| david_find_pocket_exemplar.cc | |
| david_find_pocket_stabilizing_mutations.cc | |
| david_find_surface_residues.cc | |
| david_open_pocket.cc | |
| david_pocket2PDB.cc | |
| david_pocket_align_and_save.cc | |
| david_pocket_compare.cc | |
| david_recompute_score_and_rmsd.cc | |
| david_rotation_experiment.cc | |
| ► hpark | |
| collect_rotamer_contacts.cc | |
| decompose_GDT.cc | |
| min_test.cc | |
| min_test_hpark.cc | |
| mpi_refinement.cc | |
| NMcorrelation.cc | |
| NMsearch.cc | |
| NMsearch.hh | |
| rama_energy.cc | |
| refit_rotamer_prob.cc | |
| rescore_mutscan.cc | |
| resmap.cc | |
| rotamer_clash.cc | |
| rotamer_energy.cc | |
| sampling_movers.cc | |
| sampling_movers.hh | |
| sampling_utils.cc | |
| sampling_utils.hh | |
| switch_fa.cc | |
| test_bbmc.cc | Run Monte Carlo for sampling protein conformation |
| test_bbmc.org.cc | |
| test_LH.cc | |
| test_mm.cc | |
| test_sampling.cc | |
| testMD.cc | |
| testNM.cc | |
| ► ian | |
| cluster_ligand_poses.cc | Choose several ligand poses for further docking refinement |
| ligand_evis.cc | |
| ligdock_confidence.cc | |
| redo_rms_atomtree_diffs.cc | |
| select_best_unique_ligand_poses_jd1.cc | |
| ► jackmaguire | |
| ► vlmmlr_packer | |
| FixbbSimAnnealer.cc | |
| FixbbSimAnnealer.fwd.hh | |
| FixbbSimAnnealer.hh | |
| benchmark_k_medoids.cc | |
| measure_sequence_similarity_to_native.cc | |
| tensorflow_manager_multi_input_test.cc | See main/tests/integration/tests/tensorflow_manager/multi_input_test/README.md |
| tensorflow_manager_multirun_test.cc | See main/tests/integration/tests/tensorflow_manager/multirun/README.md |
| tensorflow_manager_test1.cc | See main/tests/integration/tests/tensorflow_manager/multirun/README.md |
| tensorflow_test2.cc | See main/tests/integration/tests/tensorflow_simple_model_load_and_evaluate/README.md |
| test_rosetta_thread_manager_preallocation.cc | An application to test the RosettaThreadManager's preallocation API |
| ► jacob | |
| cxdesign.cc | |
| cxdock.cc | |
| ► jadolfbr | |
| ► antibody_design | |
| graft_design_cdrs.cc | Designs an antibody using GraftDesign |
| prob_design_cdrs.cc | Designs CDRs using cluster probabilities. Test App |
| ► bootcamp | |
| raw_pointers.cc | |
| ► cluster_utilities | |
| relax_cdrs.cc | |
| ► testing | |
| class_tests.cc | Just a file for testing various classes |
| test_grafting.cc | |
| AddFrameworkProfilesOperation.cc | |
| AddFrameworkProfilesOperation.fwd.hh | |
| AddFrameworkProfilesOperation.hh | |
| AntibodyDesignMoverGenerator.cc | |
| AntibodyDesignMoverGenerator.fwd.hh | |
| AntibodyDesignMoverGenerator.hh | |
| AntibodyInfoRMLoader.cc | |
| AntibodyInfoRMLoader.fwd.hh | |
| AntibodyInfoRMLoader.hh | |
| AntibodyInfoRMLoaderCreator.hh | |
| AntibodyInfoRMOptions.cc | |
| AntibodyInfoRMOptions.fwd.hh | |
| AntibodyInfoRMOptions.hh | |
| AntibodyInfoRMOptionsCreator.hh | |
| model_antibody_basic.cc | |
| test_neighborhood_selector.cc | Test neighborhood selector |
| test_symmetry.cc | |
| ► james | |
| add_ligand.cc | |
| analyze_casp9.cc | |
| angle_recovery_stats.cc | |
| angles.cc | |
| anneal_align.cc | |
| assemble_domains_jd2.cc | |
| basic_thread.cc | |
| boost_hacks.cc | |
| build_template.cc | |
| burial.cc | |
| ca_build.cc | |
| cartesian.cc | |
| casp9_superdev.cc | |
| compare_features.cc | |
| constraints_matrix.cc | |
| constraints_viewer.cc | |
| copy_hack.cc | |
| cs_align.cc | |
| cst_func.cc | |
| cst_quality.cc | |
| density_grid.cc | |
| design_profile.cc | |
| distances.cc | |
| dp_align.cc | |
| exhaustive_align.cc | |
| fast_cm.cc | |
| filter_sequences.cc | |
| homolog_cst.hh | |
| hybrid.cc | |
| james_util.hh | |
| jcluster.cc | |
| jdock.cc | |
| jidealize.cc | |
| jrelax.cc | |
| jscore.cc | |
| jseq.cc | |
| kdtree_disulf.cc | |
| make_artificial_centroids.cc | Takes an input set of PDBs, creates artificial centroid by averaging coordinates |
| make_profile.cc | |
| mammoth_hack.cc | |
| medal_test.cc | |
| min_cst.cc | |
| model_quality.cc | |
| per_residue_features.cc | |
| phi_hack.cc | |
| pick_frags.cc | |
| prof_search.cc | |
| remap_aln.cc | |
| sc_interaction.cc | |
| score_silent_cst.cc | |
| seqdb_stats.cc | |
| silent_cst_quality.cc | |
| simple_cm.cc | |
| sparta_superdev.cc | |
| super.cc | |
| superdev.cc | |
| thread_fast.cc | |
| ► javierbq | |
| detect_symmetry.cc | |
| domains.cc | |
| fragment_based_design.cc | |
| fragment_sequence_quality.cc | |
| swap_elements.cc | |
| test_serialize.cc | |
| ► jcorn | |
| hbond_connect.cc | |
| hh_test.cc | |
| hotspot_hash.cc | App to find potential hotspot residue placements on the surface of a protein target Method: make a disembodied residue, with option to make residue backbone invisible to the scorefxn centroid dock residue to the target, then full-atom dock and repack the residue only (must use -norepack1) write out all docked residues that contact the target with even a somewhat reasonable energy |
| hshash_utils.cc | Utilites for working with hotspot hash files Functions: 1) Make a subset of a hash based on a percentage or absolute score cutoff 2) Make a list of # of hotspots within 8A of a target residue. Useful for mapping hotspot density onto a target. See RLC's pymol scripts data2bfactor.py and color_b.py |
| PREcst.py | |
| predPRE.py | |
| TwoChainInterface.cc | |
| TwoChainTenANeighbors.cc | |
| ► jd2 | |
| jd2memtest.cc | |
| jd2test.cc | Test for new job distributor - demonstrates most of its functionality |
| ► jeliazkov | |
| calc_cdr_rmsd.cc | Pilot app for two cdr rms + LHOC metric calculation |
| calc_irms_despite_mismatch.cc | |
| ► jianqing | |
| Ncaa_Crosslink.cc | @NCAA utility |
| snugdock.cc | |
| ► jim | |
| optE_test.cc | |
| rotamerize.cc | |
| use_asn_motifs.cc | |
| ► jjgray | |
| antibody_metrics.cc | |
| ► jkleman | |
| add_membrane.cc | |
| input_from_cmd.cc | |
| interface_statistics.cc | Computing interface statistics for membrane protein interfaces |
| mp_find_interface.cc | Sample protein-protein interface in the membrane |
| mp_find_interface_test.cc | |
| mp_parameters.cc | Checking options for MPframework |
| mp_qrtest.cc | |
| mp_quick_relax.cc | Do a quick relax run for a membrane protein |
| mp_relax_partners_separately.cc | |
| mpdocking.cc | Dock two membrane proteins in the membrane |
| mpdocking_setup.cc | Uses MPDockingSetup mover CURRENTLY ONLY WORKS FOR 2 POSES!!! |
| mpfolding.cc | |
| mpframework_test.cc | Testing random small stuff in MPframework |
| mpframework_test1.cc | Testing random small stuff in MPframework |
| mpframework_test2.cc | |
| per_residue_sc_sasa.cc | Computes the SASA of all the sidechains in the protein also computes the relative one |
| range_relax.cc | Relaxes the protein by relaxing in ranges |
| simple_rotamer_recovery.cc | |
| spanfile_from_pdb.cc | Write a spanfile from a PDB file |
| transform_into_membrane.cc | |
| ► johnk | |
| chet_report_rmsd.cc | |
| chet_trp_to_gly.cc | |
| compute_ddgs.cc | |
| constellation_list.cc | |
| david_check_pocket.cc | |
| david_open_pocket.cc | |
| hotspot_test.cc | |
| johnk_docking_protocol.cc | |
| johnk_exact_geometric_solvation.cc | |
| johnk_gapless_threading.cc | |
| johnk_interface_geosol_minimization.cc | |
| johnk_interface_recompute_score_and_rmsd.cc | |
| johnk_parametrize_geometric_solvation.cc | |
| johnk_recompute_score_and_rmsd.cc | |
| justin_identify_holes.cc | |
| justin_local_backrub.cc | |
| metrics_test.cc | |
| nadeem_compensatory_mutation.cc | |
| nadeem_find_destabilizing_mutation.cc | |
| old_test_geosol_minimization.cc | |
| phosphoArg_build_rotamers.cc | |
| phosphoArg_minimize.cc | |
| ragul_backbone_diversity.cc | |
| srirupa_phosphoArg_build_rotamers.cc | |
| srirupa_two_loops.cc | |
| ► josh | |
| motif_loop_build.cc | |
| ► jrporter | |
| inject_hash.cc | |
| topo_driver.cc | Inject proper hashes for cuts into silent structs |
| ► jstev | |
| collect_features.cc | |
| ► jtseffer | |
| SID_rescore.cc | |
| ► kale | |
| ► cyclic_poses | |
| kick_cyclic_pose.cc | |
| load_cyclic_pose.cc | |
| ► detailed_balance | |
| ► analysis | |
| ► styles | |
| __init__.py | |
| blue.py | |
| green.py | |
| rainbow.py | |
| rama.py | |
| red.py | |
| bin_torsions.py | |
| closure_error.py | |
| correlation_time.py | |
| explosion_error.py | |
| progress_bar.py | |
| solution_counts.py | |
| ► jacobian | |
| build_jacobian.f90 | |
| build_jacobian.py | |
| vector.f90 | |
| ► sandbox | |
| 3d_histogram.py | |
| dummy-distribution.py | |
| gaussian-sampling.py | |
| backbone_tests.cc | |
| execute.py | |
| run_backbone.py | |
| run_sidechain.py | |
| sidechain_tests.cc | |
| ► examples | |
| 3d_histogram.py | |
| atom_id_demo.cc | |
| atoms_from_residues.cc | |
| boost_matrix.cc | |
| boost_regex.cc | |
| boost_vector.cc | |
| broken_kick.cc | |
| broken_original_kick.cc | |
| canonical_sampling.cc | |
| chain_break.cc | |
| compute_difference.py | |
| current_example.cc | |
| database_sandbox.cc | |
| dihedral.cc | |
| dof_translator.cc | |
| features_reporter.cc | |
| fold_tree.cc | |
| hello_world.cc | |
| histogram.py | |
| internal_coordinates.py | |
| jd2_state.cc | |
| kic_bug.cc | |
| kic_rama_bias.cc | |
| kick_n_terminus.cc | |
| kick_with_balance.cc | |
| kinematic_closure.cc | |
| local_options.cc | |
| make_comparison.py | |
| partial_pose.cc | |
| pick_from_rama.cc | |
| plot.py | |
| pose_from_pdb.cc | |
| pose_from_residues.cc | |
| pose_from_silent.cc | |
| rama_distribution.cc | |
| rama_function.cc | |
| random_seed.cc | |
| read_cutpoint.cc | |
| reindexing_mover.cc | |
| score_function.cc | |
| silent_output.cc | |
| torsion_id.cc | |
| tracer.cc | |
| vector_math.cc | |
| xyz_from_pose.cc | |
| ► kic_refactor | |
| ► analysis | |
| average_rmsds.py | |
| legacy_score_vs_rmsd.py | |
| percent_subangstrom.py | |
| pivot_selection.py | |
| score_vs_rmsd.py | |
| subloop_histogram.py | |
| ► ideas | |
| easy_kinematic_mover.cc | |
| easy_loop_mover_refine.cc | |
| original_app.cc | |
| ► original | |
| apply.KinematicMover.cc | |
| apply.LoopRelaxMover.cc | |
| apply.perturb_LoopMover_KIC.cc | |
| apply.refine_LoopMover_KIC.cc | |
| kic.LoopRelaxMover.cc | |
| KinematicMover.cc | |
| LoopRelaxMover.cc | |
| perturb_LoopMover_KIC.cc | |
| refine_LoopMover_KIC.cc | |
| simple_apply.KinematicMover.cc | |
| kic_runner.py | |
| KicSandbox.cc | |
| KicSandbox.hh | |
| ► native_ensemble | |
| ► analysis | |
| autocorrelation.py | |
| cache_trajectory.py | |
| delete_job.py | |
| helpers.py | |
| job_manager.py | |
| query_trajectory.cc | |
| schema.py | |
| score_vs_rmsd.py | |
| score_vs_time.py | |
| torsion_vs_time.py | |
| trajectory_movie.cc | |
| wipe_cache.py | |
| app_runner.py | |
| native_ensemble.cc | |
| header_text.cc | |
| pilot_app_settings.py | |
| ► kbarlow | |
| ShapeScoring.cc | |
| ► kdrew | |
| cmaes_minimizer_test.cc | |
| cmaes_test.cc | |
| inverse_rotlib_dump.cc | |
| ld_converter.cc | |
| oop_creator.cc | |
| oop_dock_design.cc | |
| scaffold_matcher.cc | |
| ► kenjung | |
| elscripts.cc | |
| FastGap.cc | |
| fragpdb.cc | |
| loophash_createfiltereddb.cc | |
| lua_test.cc | |
| pose_serialize_test.cc | |
| sixdtreeTEST.cc | |
| symfragrm.cc | |
| ► kevin | |
| ► buriedunsatfinder_test | |
| val2thr.py | |
| buns.cc | |
| bur_nodon_tyr.cc | |
| BuriedUnsatPolarsFinder2.cc | |
| BuriedUnsatPolarsFinder3.cc | |
| hydrate.cc | |
| khSandbox.cc | |
| khSandbox2.cc | |
| khXtal_water_bunsat.cc | |
| read_l_print_pdbinfo.cc | |
| sasa_buns.cc | |
| template.cc | |
| vsasa_buns.cc | |
| vsasa_pdbcode_res.cc | |
| wat_distances.cc | |
| ► kkappel | |
| ► old_ddg_scripts | |
| find_lowest_scoring_relaxed_struct.py | |
| general_RNP_setup_script.py | |
| get_final_ddG_scores.py | |
| mutant_modeler.py | |
| relax_starting_structure.py | |
| setup_for_complex_scoring_general.py | |
| analyze_docked_RNA_motifs.cc | Analyze RNA motifs docked onto proteins to try to design protein binding structures |
| calculate_distances.cc | Calculate distances in RNA/protein structures for score function development |
| check_frag_rmsd.cc | |
| check_rnp_coarse.cc | |
| get_rmsd.cc | |
| move_jump.cc | |
| score_rnp.cc | Align RNA structure using command line input residues |
| score_rnp_lowres.cc | |
| setup_coord_csts.cc | |
| test_rna_protein.cc | |
| ► krishna | |
| ab_binding.cc | |
| antibody_test.cc | |
| mtransferase.cc | |
| pH_docking.cc | |
| pH_neighbor_pack.cc | |
| ► kuichan | |
| design_disulfide.cc | |
| ► kyleb | |
| fragment_extract.cc | |
| ► labonte | |
| debug_labontes_current_work.cc | This is simply a generic pilot app for testing things |
| design_glycans.cc | This application performs a simple "design" of any glycans found with a .pdb |
| glycomutagenesis.cc | This application performs a simulated shotgun glycomutagenesis experiment of an input structure |
| load_crazy_sugars.cc | |
| test_glycan_linkages.cc | This is simple pilot app for testing carbohydrates |
| test_ResidueProperties.cc | This is simple pilot app for testing ResidueProperties |
| test_sugar_torsion_getters_and_setters.cc | This is simple pilot app for testing carbohydrates |
| ► leif | |
| mutate_relax.cc | |
| mutate_relax.h | |
| scratch1.cc | Rosetta exploration code |
| scratch1.hh | Rosetta exploration code |
| ► lemmon | |
| deepMove.cc | This is to illustrate packing residues in a PDB @detail Run this script with the following arguments: 1) in::file::s <list of one PDB with at least 2 residues to pack> 2) in::path::database ) in::file::extra_res_fa <list of extra params files, one per residue type> |
| ligand_design.cc | |
| pack.cc | This is to illustrate packing residues in a PDB @detail Run this script with the following arguments: 1) in::file::s <list of one PDB with at least 2 residues to pack> 2) in::path::database ) in::file::extra_res_fa <list of extra params files, one per residue type> |
| protonatePack.cc | This is to illustrate reading in a ligand with multiple residues and then reassembling the ligand (using Rosetta). @detail Run this script with the following arguments: 1) in::file::s ) in::path::database <root director of minirosetta database> 3) in::file::extra_res_fa <list of extra params files, one per residue type> |
| randomMove.cc | This is to illustrate packing residues in a PDB @detail Run this script with the following arguments: 1) in::file::s <list of one PDB with at least 2 residues to pack> 2) in::path::database ) in::file::extra_res_fa <list of extra params files, one per residue type> |
| readAndWrite.cc | This is to illustrate reading a PDB @detail Run this script with the following arguments: 1) in::file::s ) in::file::extra_res_fa <list of extra params files, one per residue type> |
| rmsd_calculator.cc | |
| simpleScore.cc | This is to illustrate scoring a PDB @detail Run this script with the following arguments: 1) in::file::s ) in::file::extra_res_fa <list of extra params files, one per residue type> |
| undirected_graph.cc | |
| ► lin | |
| SymmAbrelax.cc | |
| SymmSilentFile.cc | |
| ► lior | |
| CycDsulf.cc | |
| CycPepMain.cc | |
| feature_schema_generator.cc | |
| ► liz | |
| close_homolog_refinement.cc | |
| consolidate_clusters.cc | |
| create_hierarchy.cc | |
| ensemble_generator.cc | |
| ensemble_generator_score12_sidechain.cc | |
| ensemble_generator_using_mover.cc | |
| minimize_with_constraints.cc | |
| minimize_with_cst.cc | |
| monomer_ddg.cc | |
| sasa.cc | |
| score_ddgs.cc | |
| test_canonical_mover.cc | |
| test_scmcmover.cc | |
| ► maprahamian | |
| burial_measure_centroid.cc | |
| burial_measure_sphere.cc | |
| per_residue_solvent_exposure.cc | |
| score_test.cc | |
| ► mdsmith | |
| ligand_motifs.cc | |
| motif_ligand_packer_design.cc | Mdsmith, sthyme |
| ► membrane | |
| load_membrane_pose.cc | |
| membrane_ddG.cc | Membrane Framework Application: ddG of Mutation in Membranes |
| membrane_relax.cc | Membrane Framework Application: Membrane Protein Structure Refinement |
| membrane_symdocking.cc | Membrane Framework Application: Symmetric Protein-Protein Docking in Membranes |
| mp_rsd_energies.cc | |
| view_membrane_protein.cc | Membrane Framework Application: Real-Time Visualization of Membrane Proteins |
| ► mike | |
| alignanalyse.cc | |
| batchrelax.cc | |
| crossaln.cc | |
| energy_diff.cc | |
| evolution.cc | |
| geturl_handler.cc | |
| geturl_handler.h | |
| inlinetest.cc | |
| loophash.cc | |
| loophash_analyse.cc | |
| loophash_cenrelax.cc | |
| loophash_createdb.cc | |
| loophash_mpi.cc | |
| loophash_test.cc | |
| make_cst.cc | |
| make_static_database.py | |
| md.cc | |
| mikejd2test.cc | |
| minbench.cc | |
| rama_test.cc | |
| relax_viewer.cc | |
| rosetta_backend.cc | |
| rosetta_native_client.cc | |
| sctrials.cc | |
| shake.cc | |
| silent2cst.cc | |
| silent2frag.cc | |
| testderiv.cc | |
| testloop.cc | |
| testmpi.cc | |
| ► momeara | |
| features_database_schema.cc | Simple application for interconverting Rosetta recognized structure formats |
| format_converter.cc | Simple application for interconverting Rosetta recognized structure formats |
| hbond_param_sweep.cc | Generate geometric conformations of hydrogen bonds |
| hbonds_test.cc | This outputs all relavent information about hbonds for one or many pdbs |
| report_hbonds.cc | Report all data about hydrogen bonds |
| ► monica | |
| dock_test.cc | |
| monica_relax.cc | |
| moves_test.cc | |
| ► mpacella | |
| surface_docking.cc | |
| ► mseetin | |
| convert_pdb_to_silent_file.cc | |
| ► murphp | |
| inv_kin_lig_loop_design.cc | |
| ► nannemdp | |
| params2pdb.cc | |
| ► neil | |
| calc_ddG.cc | |
| char_native.cc | |
| coiled_coil_search.cc | |
| des_pos_ddG.cc | |
| design_symm.bak.110314.cc | |
| design_symm.cc | |
| design_symm_110330_good.cc | |
| design_symm_no_hack_elec.cc | |
| enumeration_test.cc | |
| matdes_design.cc | |
| matdes_design_2comp.cc | |
| matdes_dock.cc | |
| matdes_mutalyze.cc | |
| relax_building_block.cc | |
| symdock_enum.cc | |
| symdock_enum_3_1.cc | |
| ► nikolas | |
| r_segment_rdc.cc | |
| r_SymDock_viewer.cc | |
| ► nir | |
| PeptideDeriver.cc | |
| ► nmarze | |
| elliptical_ip.cc | Pilot app for elliptical initial placement |
| hemagg_trimer.cc | |
| motif_dock.cc | Pilot app for testing motif docking score |
| ► nobuyasu | |
| cluster.cc | |
| fldsgn.cc | |
| flxbb.cc | |
| foldptn.cc | |
| frag2profile.cc | |
| local_rmsd.cc | |
| make_blueprint.cc | Makes blueprint file |
| make_frag_ssdep.cc | |
| ncontact.cc | Nobuyasu Koga |
| pair_distance.cc | |
| pick_bab.cc | |
| pick_lowestscore_pose.cc | |
| rama.cc | |
| sasa.cc | |
| score_delete_segments.cc | |
| ► olli | |
| cloud_app.cc | Check quality of fragments against input structure |
| FragsToAtomDist.cc | |
| helper_code_r_trjconv.cc | |
| r_abrelax.cc | |
| r_assign_clusters.cc | Check quality of fragments against input structure |
| r_broker.cc | |
| r_build_hotspot_loops.cc | |
| r_check_chainbreak.cc | |
| r_convert_frags.cc | |
| r_count_neighbours.cc | Check quality of fragments against input structure |
| r_coupled_sidechain.cc | |
| r_cst_tool.cc | Check quality of fragments against input structure |
| r_dock_tempered.cc | |
| r_fold_cst.cc | |
| r_frag_picker.cc | |
| r_frag_quality.cc | |
| r_local_rdc.cc | |
| r_min_check.cc | Check quality of fragments against input structure |
| r_mpi.cc | Check quality of fragments against input structure |
| r_parse_foldtree.cc | |
| r_pdb2top.cc | Check quality of fragments against input structure |
| r_play_with_etables.cc | |
| r_rmsf.cc | Check quality of fragments against input structure |
| r_score.cc | Check quality of fragments against input structure |
| r_score_rdc.cc | Check quality of fragments against input structure |
| r_tempered_sidechains.cc | |
| r_trjconv.cc | Tool to handle and convert pdb/silent rosetta structure output |
| ► olungu | |
| multidomain_switch.cc | |
| sasa_interface.cc | Calculate metrics over antibody peritopes |
| Superimpose_Pdbs.cc | |
| ► opt_e | |
| optE_simple.cc | |
| ► optE | |
| optE_simple.cc | |
| ► pacheco | |
| design_glycans.cc | This application performs a simple "design" of any glycans found with a .pdb |
| ► parin | |
| parin_test.cc | |
| ► phil | |
| analyze_dna.cc | |
| capri15.cc | |
| capri15_scoring.hh | |
| dimer_relax.cc | |
| dna_design_test.cc | |
| dna_dr_test.cc | |
| dna_relax.cc | |
| dna_spec_test.cc | |
| loop_model.hh | |
| motif_scan.cc | |
| phil.hh | |
| repeat_demo.cc | Example of how to set up a symmetric repeat protein system where you fold through the polypeptide chain |
| simple_dna_regression_test.cc | |
| symtest.cc | |
| test1.cc | Some simple examples of how to use basic functionality + some DNA functionality |
| zf_relax.cc | |
| ► possu | |
| build_repeats.cc | |
| helical_param.cc | |
| ► ptconway | |
| batchrelax_mpi.cc | |
| elec_dens_rot_recov.cc | |
| ► ragul | |
| cstmin.cc | |
| gen_rna_pharmacophore.cc | |
| get_pharmacophore_without_bound_rna.cc | |
| get_rna_pharmacophore.cc | |
| get_rna_pharmacophore_with_water.cc | |
| get_rna_ring_sasa.cc | |
| ragul_analyze_tcr_interface.cc | |
| ragul_calculate_ligand_rmsd.cc | |
| ragul_calculate_residue_rmsd.cc | |
| ragul_darc_minimize.cc | |
| ragul_darc_optimize_weights.cc | |
| ragul_darc_run_with_delphi.cc | |
| ragul_find_all_hbonds.cc | |
| ragul_get_aa_code.cc | |
| ragul_get_connolly_surface.cc | |
| ragul_get_delphi_phimap.cc | |
| ragul_get_ligand_hbonds.cc | |
| ragul_get_ligand_sasa.cc | |
| ragul_get_molecular_surface.cc | |
| ragul_rosetta_dump_pdb.cc | |
| ragul_test_darc.cc | |
| sarah_get_pharmacophores.cc | |
| simon_darc_minimize.cc | |
| ► ralford | |
| ► archive | |
| ► framework_devel | |
| ► scoring | |
| membrane_rsd_energy_breakdown.cc | |
| membrane_sfxn.cc | MP Framework: Read Membrane Pose and Dump Result to PDB |
| mp_scoring_feature_reporter.cc | |
| mp_sfxn_integration.cc | |
| mpframework_score.cc | |
| mpscore_integrate.cc | |
| load_membrane_pose.cc | |
| local_minimize.cc | |
| membrane_foldtree.cc | |
| membrane_foldtree2.cc | |
| membrane_info.cc | |
| membrane_integration.cc | |
| membrane_pose_test.cc | Quick debugging of constructing a membrane pose (enables gdb stuff) |
| mp_database_check.cc | |
| mpframework_integration.cc | |
| mpframework_time_bchmk.cc | |
| pymol_viewer_test.cc | |
| virtual_residue_trees.cc | |
| visualize_membrane.cc | |
| ► old_applications | |
| membrane_ddG.cc | |
| membrane_docking.cc | |
| membrane_relax.cc | |
| membrane_relax2.cc | |
| membrane_sampling.cc | |
| mutate_repack.cc | |
| check_rotation.cc | |
| embed_mp_pose_from_topo.cc | |
| make_canonical_helix.cc | |
| membrane_fa_scorefxn.cc | |
| membrane_scorefxn.cc | |
| mpframework_integration.cc | |
| read_mp_pose.cc | MP Framework: Read Membrane Pose and Dump Result to PDB |
| read_mp_pose_from_seq.cc | |
| read_pose_from_seq.cc | Use the membrane framework reading in a pose from seuqnece. Involves a modified mover that might handle chains differently? Last Modified: 3/27/14 |
| sample_tilt_protocol.cc | |
| test_mp_rmsd.cc | |
| transform_into_mem.cc | |
| transform_into_membrane.cc | |
| translate_membrane_pose.cc | |
| translate_view_membrane.cc | |
| version_mpscorefxn.cc | |
| visualize_membrane.cc | Read in a pose into the membranew framework and dump out the pose with the lipid bilayer present (as VRT atoms) |
| color_by_lipid_type.cc | Utility script - fills the bfactor colum with xyz-dependent fractional hydration values. Can be used to visualize the hydration in PyMOL |
| enumerate_rotamers.cc | Create PDB files for all possible rotamers of D, E, N, and Q |
| find_optimal_hydrophobic_thk.cc | An application for finding the minimum energy hydrophobic thickness of a membrane protein |
| mp_rsd_energies.cc | |
| version_mpscorefxn.cc | |
| ► rayyrw | |
| assemble_placed_fragments.cc | |
| cal_nonoverlap_scores.cc | |
| cal_overlap_scores.cc | |
| clash_score.hh | |
| closability_score.hh | |
| fastrelax_replonly.cc | |
| FragMonteCarlo.hh | |
| min_pack_min.hh | |
| overlap_score.hh | |
| place_fragments_into_density.cc | |
| replonly.cc | |
| rms_util.hh | |
| score_jd2_replonly.cc | |
| util.hh | |
| ► reggiano | |
| density_res_zscores.cc | |
| ► rhiju | |
| ► legacy | |
| add_delete_monte_carlo.cc | |
| erraser_monte_carlo.cc | |
| OLD_TRIAL_protein_helix_assemble.cc | |
| stepwise_test.cc | |
| TRIAL_protein_helix_assemble.cc | |
| turner_rules_test.cc | |
| turner_rules_test_WORKS.cc | |
| benzene_test.cc | |
| block_stack_test.cc | |
| check_cubic_conv.cc | |
| coarse_rna_test.cc | |
| dna_test.cc | |
| easy_target_test.cc | |
| entropy_test.cc | |
| gcc185_test.cc | |
| generalize_gaussian_chain_func_test.cc | |
| get_info.cc | |
| homolog_finder_farna.cc | |
| loop_closure_test.cc | |
| mg_hires_pdbstats.cc | |
| mg_lores_pdbstats.cc | |
| morph_pdbs.cc | |
| pack_phosphates.cc | |
| pack_polar_hydrogens.cc | |
| pdbstats_rnahelix.cc | |
| pdbstats_test.cc | |
| polar_pdbstats.cc | |
| protein_helix_assemble.cc | |
| rb_entropy.cc | |
| read_tensor.cc | Checking if we can read in a tensor from a .bin.gz and associated .json |
| rna_assemble_test.cc | |
| rna_protein_test.cc | |
| rna_test.cc | |
| screen_phosphates.cc | |
| silly_tag_stuff.cc | |
| stepwise_centroid_test.cc | |
| stepwise_helix_test.cc | |
| stepwise_loop_test.cc | |
| stepwise_lores_test.cc | |
| stepwise_template_test.cc | |
| ► rjha | |
| MetalInterface.hh | This header contains helper functions common to metal interface pilot_apps |
| MetalInterfaceStructureCreator.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 |
| NeighborMatch.cc | Finds residues neighboring a given residue across an interface. Intended for creating posfiles suitable for RosettaMatch |
| SurfaceGroups.cc | Defines groups of neighbors on the surface of a pose |
| ZincMatchFilter.cc | This application is designed to help filter through the matches from RosettaMatch. It calculates some of the geometry about the metal atom (currently the metal-ligand atom distances and the tetrahedral coordinations six ligand-metal-ligand angles (all of which should be 109.5). It also outputs a sum of squares for those values |
| ► rmoretti | |
| atom_tree_check.cc | Check retreeing with core::kinematics::tree |
| bcl_type_check.cc | |
| bootstrap_bcl_types.cc | |
| crash_report_test.cc | |
| extract_atomtree_diffs_jd1.cc | |
| ligand_dock_jd1.cc | Old, JD1 version of ligand_dock, kept in case someone really needs it |
| ligand_rpkmin_jd1.cc | |
| molfile_read_test.cc | Check molfile loading in Rosetta |
| restype_kin_output.cc | |
| rosetta_retype_check.cc | Check the rosetta retyping typing scheme in Rosetta |
| rts_check.cc | |
| ► ronj | |
| analyze_ddG.cc | |
| find_position_matches_using_inverse_rotamers.cc | Program which scans for backbone positions in a list of scaffolds with low rmsd to specific positions in a reference structure by building inverse rotamers |
| hydrophobic_patch_stats_calculator.cc | A simple protocol which outputs information about surface residues on the passed in list of PDBs |
| rss_energy_calculator.cc | Functions which iterates over PDBs, chops out fragments and scores them, and then outputs residue energies |
| surface_optE_parallel.cc | |
| surfacescore.cc | |
| ► rpache | |
| calibrate_pdb_via_sidechain_optimization.cc | |
| generate_matcher_constraints.cc | |
| score_protein_ligand_interactions.cc | Score interactions with a given ligand |
| ► rvernon | |
| calc_pair_stats.cc | |
| compute_disulfide_matching_score.cc | |
| create_disulfide_alldata.cc | |
| create_disulfide_angle_statistics.cc | |
| create_disulfide_database.cc | |
| create_disulfide_distance_statistics.cc | |
| create_disulfide_fa_angle_statistics.cc | |
| extract_by_sidechain_sasa_score.py | |
| pcs_distances_for_fragpicker.cc | |
| pcs_fragments_to_distances.cc | |
| pcs_fragments_to_distances2.cc | |
| pcs_fragments_to_distances_wRMS.cc | |
| pcs_score_individual_residues.cc | |
| pcs_score_residues.cc | |
| pcs_score_select.cc | |
| pcs_score_select_helices.cc | |
| print_disulfide_scorefunctions.cc | |
| score_sidechain_sasa.cc | |
| ► sarel | |
| hotspot_stub_constraint_test.cc | For running an integration test |
| ► schaarj | |
| combine_ContactMaps.py | |
| ► scheck | |
| struct_frag.cc | Creating fragments from supplied structures |
| ► sergey | |
| cloud_demo.cc | |
| ColorsDemo.cc | Demo for Tracer Color output |
| ComparingTracerExample.cc | |
| docking.py | |
| GA.cc | Ashworth |
| hal-demo.cc | |
| hal.cc | |
| JSON_Demo.cc | Demo for JSON parser |
| OptionsTest.cc | |
| PDBTest.cc | |
| py_rosetta_test.cc | Various small tests thats mirror PyRosetta unit tests |
| PyEnTest.cc | |
| PyMOLDemo.cc | |
| SharedPtrDemo.cc | Demo for boost shared_ptr |
| TracerTest.cc | |
| ► sevya | |
| find_consensus_mutations.cc | |
| minimization_test.cc | |
| msd.cc | Experimental multi state design implementation. Written to encourage convergence in protein designs occurring simultaneously, rather than enforce that they have identical sequences |
| msd_jd2.cc | Experimental multi state design implementation. Written to encourage convergence in protein designs occurring simultaneously, rather than enforce that they have identical sequences |
| recon_mpi.cc | Multistate design through RECON run through MPI |
| ► shilei | |
| bb_cluster.cc | |
| cluster_hotspot_docking.cc | |
| complex_interface_optimize.cc | |
| compute_Irmsd.cc | |
| docking_inputpatchdock_mpi.cc | |
| docking_parallel.cc | |
| generate_hbond_geometry.cc | |
| lowresdock_patchdock_hotspot_cst.cc | |
| match_disulfide_to_scaffold.cc | |
| read_pose_jump_orientation_repack.cc | |
| score_hotspot_cst.cc | |
| tmalign_cluster.cc | |
| ► shirst | |
| LoophashFilter.cc | Trying to figure how to use loophash as a filter in folding with the TMHTopologySamplerClaimer |
| TestTopologySampler.cc | |
| ► smlewis | |
| ► ascan | |
| AlanineScanner.cc | |
| ► ChemXRW | |
| PDB_diagnostic.cc | This app is meant to report if Rosetta can successfully read a PDB, and if not, help with diagnostics on why it failed. Spiritual child of old AnchorFinder |
| ► hect | |
| HECT.hh | |
| HECT_all.cc | |
| HECT_ubq.cc | |
| Extender.cc | Script to add residues to a PDB. This script is NOT intended to make a good conformation - just the sequence-correct PDB for other modes (loop modeling, etc) |
| FloppyTail_loop.cc | |
| ForgetPDBInfo.cc | |
| LoopAnalyzer.cc | Q&D protocol to run LoopAnalyzerMover as protocol |
| sasa_qd.cc | Q&D protocol to run SasaCalculatorLegacy as protocol (why is this not already there?) |
| UBQ_UBQ_E2.cc | This application is a one-shot for modeling the thioester bond between UBQ and an E2 |
| ► sraman | |
| RBSegMove_test.cc | |
| RBSegMove_test_viewer.cc | |
| RDC_test.cc | |
| ► ssrb19 | |
| adding_peptoids.cc | |
| ► sthyme | |
| dna_motifs_collector.cc | App for collection of protein-DNA interaction motifs |
| ligand_motifs.cc | |
| motif_dna_packer_design.cc | App for motif-biased protein-DNA design |
| pdb2motiffile.cc | Helper app to convert two-residue pdbs into a MotifLibrary text file |
| ► stranges | |
| buried_polar_finder.cc | |
| InterfaceMutMaker.cc | Makes a mutation from a command line flag and outputs wt and mut complex and separated structures |
| min_pack_min.cc | Does cycles of Minimiziation, Repacking, Minimization for interface analysis later no design by default |
| peptide_minimizer.cc | Does stuff |
| simple_interfaceanalyzer.cc | |
| sym_fixbb.cc | Symmetric fixed backbone design |
| xml_task_printer.cc | Takes in a task, outputs it |
| ► thermo | |
| metropolis_hastings.cc | Metropolis-Hastings Monte Carlo app |
| ► tjacobs | |
| BundleDumper.cc | |
| BundlePairRmsdCalculator.cc | |
| BundlePairRmsdCalculatorGPU.cc | |
| CompareBundleToNative.cc | |
| FoldTreeOutputter.cc | |
| FragmentDumper.cc | |
| HelicalAssembly.cc | |
| HelicalPdbGenerator.cc | |
| HelixAssemblyDesigner.cc | |
| InterfaceStrandFinderMover.cc | |
| loophash_createfiltereddb.cc | |
| model_dumper.cc | |
| ModelTrimmer.cc | Silly pilot app that reads a model file, removes models that fail certain criteria, and then dumps it back out. This is hardcoded in lots of terrible ways. Ideally, this concept should be generalized and run strategically during the actual generation of a SEWING construct, but that's for another day/PhD |
| MotifFinder.cc | |
| mpi_helixAssembly.cc | |
| NodePairRmsdCalculator.cc | |
| PrepareGraphNodes.cc | |
| SewAppend.cc | Application wrapper for the SEWING protocol. Takes a pre-generated score file and creates backbone assemblies from it |
| SewingAssembler.cc | |
| SmotifHasher.cc | |
| SmotifPairRmsdCalculatorGPU.CC | |
| TestLoophash.cc | |
| ThreeHelixBundleFinder.cc | |
| ► tseng | |
| tseng_minimize.cc | |
| ► vmullig | |
| bettercluster.cc | |
| cycpep_analysis.cc | Simple analysis of N-to-C cyclic peptides |
| design_cycpeptide_MPI.cc | |
| design_truecycpeptide_fromstub.cc | |
| fit_helixparams.cc | Constructs a piece of secondary structure with repeating mainchain torsion values, and fits the Crick parameters for a helix to the structure |
| make_betahelicalbundle.cc | |
| make_helicalbundle.cc | |
| make_ideal_betapeptide.cc | |
| make_mainchain_potential.cc | An app to make a mainchain potential, using MM or QM methods, for an NCAA with an already-generated sidechain potential (Dunbrack library) |
| make_truecyclicpeptide.cc | |
| PCA_internal_test.cc | |
| PCA_visualizer.cc | |
| plot_scoreterm.cc | Plot a given score term as a function to two degrees of freedom for an arbitrary residue type |
| symmetrize_3d_ramamap.cc | Takes a Ramachandran-style data file as input, and spits out a symmetric version (symmetrized by copying the negative phi region of Ramachandran space) |
| symmetrize_new_ramamap.cc | Takes a Ramachandran-style data file as input, and spits out a symmetric version (symmetrized by copying the negative phi region of Ramachandran space) |
| symmetrize_old_ramamap.cc | Takes a Ramachandran-style data file as input, and spits out a symmetric version (symmetrized by copying the negative phi region of Ramachandran space) |
| symmetrize_rotlib.cc | An app that takes a rotamer library that should be symmetric (e.g. a peptoid rotamer library) and generates a symmetrized version |
| tensorflow_test1.cc | Copied verbatim from the Tensorflow website. This is intended to be a quick test of whether we're properly linking the Tensorflow libraries |
| test_cyclic_rama.cc | |
| test_D_scoring.cc | |
| test_KIC_betapeptide.cc | |
| test_makebundle_mover.cc | A test of the mover that makes a helix in a helical bundle |
| test_makebundlehelix_mover.cc | A test of the mover that makes a helix in a helical bundle |
| test_metalloproteins.cc | |
| test_multithreaded_ig_correctness.cc | A cxx11thread application that tests that multithreaded interaction graph computation yields an identical interaction graph to that produced by the single-threaded interaction graph computation |
| test_multithreaded_packing_performance.cc | An app to test the multithreaded performance of the packer |
| test_multithreaded_pdb_load.cc | A pilot app to test the creation of several poses at once (without first initializing anything by having a single thread initialize the pose) |
| test_multithreaded_ramapp_load.cc | A pilot app to test the load of RamaPrePro data when many threads are trying to do this at once |
| test_pose_copy.cc | |
| test_rosetta_thread_manager_advanced_API.cc | An application to test the Rosetta thread manager. This application carries out three levels of requests for threads. Depending on the number of threads launched and the options provided, some might not be possible to field, resulting in the thread manager assigning work to fewer threads than requested |
| test_rosetta_thread_manager_basic_API.cc | An application to test the RosettaThreadManager's default API, which accepts a vector of work |
| test_sidechainKIC.cc | |
| test_tensorflow_graph_convolutional_nn.cc | A pilot app that tests the ability to load and evaluate a graph convolutional neural network made with Tensorflow within Rosetta |
| test_trRosetta.cc | An integration test (with pass/fail functionality) to ensure that trRosetta is properly integrated into Rosetta |
| test_trRosettaConstraintGenerator.cc | A unit test (albeit one in the integration test suite) for the trRosettaConstraintGenerator. This compares the constraints generated by the C++ ConstraintGenerator to known outputs from the original Python version of trRosetta |
| test_trRosettaProtocolMover.cc | A unit test (albeit one in the integration test suite) for the trRosettaProtocolMover. This mainly tests that the native pose is set properly and retained when the mover is cloned |
| ► weitzner | |
| DB_Builder.py | Create SQLite DB for RamachandranEnergy2B energey |
| graphics_demo.cc | |
| long_loop.cc | |
| ► wendao | |
| ► cenrot_scripts | |
| ► build_residue_type | |
| build_restypes.py | |
| ► dunbrack | |
| dbscan_adaptive_kernel_density_bb_dependent_rotlib.py | |
| dbscan_cluster_rotamer.py | |
| kmeans_adaptive_kernel_density_bb_dependent_rotlib.py | |
| kmeans_bb_dependent_rotlib.py | |
| kmeans_common.py | |
| spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib.py | |
| ► env_dep_pair | |
| ► env | |
| cal_env.m | |
| gausswin.m | |
| load_env_table.m | |
| load_env_table_ref.m | |
| load_pair_env_table.m | |
| load_pair_env_table_ref.m | |
| load_tables.m | |
| calc_NtoP.m | |
| calc_pair_matrix.m | |
| calc_Pi.m | |
| calc_Pi_ang.m | |
| calc_Pi_ang_sc.m | |
| calc_Pi_sc.m | |
| calc_Pij.m | |
| draw_gen_env_dep_orient_decompose.m | |
| draw_gen_env_dep_pair.m | |
| draw_gen_env_dep_pair_decompose.m | |
| draw_matrix.m | |
| gausswin.m | |
| gen_env_dep_orient.m | |
| gen_env_dep_orient_decompose.m | |
| gen_env_dep_orient_draw.m | |
| gen_env_dep_pair.m | |
| gen_env_dep_pair_decompose.m | |
| load_angle_r_table.m | |
| load_pair_env_table.m | |
| pre_fill_dfire.m | |
| pre_fill_dfire_2D.m | |
| smooth_2D.m | |
| ► pdbs_counting | |
| cal_NBR_radius.py | |
| cal_vdw_radius_pool.py | |
| gen_vdw_radius.m | |
| gen_vdw_radius_soft.m | |
| hist2d.py | |
| calc_stress_tensor.cc | |
| cenrot_bbsc_demo.cc | |
| cenrot_jd2.cc | Test centroid rot model |
| cyclic_sampler.cc | Run Monte Carlo for sampling protein conformation |
| decoys_frag_quality.cc | |
| fa_to_cenrot_score.cc | Test centroid rot model |
| gen_cav_ball.cc | |
| general_pair_counting.cc | Generate octave "load_table" scripts for calculating env and pair term |
| pairwise_fa_energy.cc | |
| params_opt.cc | |
| test_bbmc.cc | Run Monte Carlo for sampling protein conformation |
| test_cen_rot.cc | |
| test_cluster.cc | |
| test_hpool.cc | |
| ► whitney | |
| whitney_identify_epitope.cc | |
| whitney_local_backrub.cc | |
| whitney_prepare_native.cc | |
| whitney_rebuild_ankyrin.cc | |
| whitney_repack_input.cc | |
| whitney_specificity_switch.cc | |
| ► will | |
| ► old | |
| ► gpu | |
| CL.hh | |
| CL_args.hh | |
| gpu_bb_struct.hh | |
| gpu_bit_utils.hh | |
| gpu_cbdock.cc | |
| gpu_cpu_speedtest.cc | |
| gpu_homog_atom_coords.h | |
| gpu_linker.cc | |
| gpu_mat_vec.hh | |
| gpu_octree_impl_test.cc | |
| gpu_pack14.h | |
| gpu_refold.hh | |
| gpu_refold_test_cpu.hh | |
| gpu_score.cc | |
| gpu_score.hh | |
| gpu_set_args.py | |
| gpu_speedtest.cc | |
| gpu_speedtest.hh | |
| gpu_test.cc | |
| gpu_test.cl.cc | |
| gpu_test_k_square.hh | |
| gpu_test_Mxform.cc | |
| gpu_xforms.hh | |
| tmp.cl.cc | |
| xyzHash_test.hh | |
| ► query_lang | |
| filter.cc | |
| metric.cc | |
| Vec.hh | |
| atom_design.cc | |
| atom_type_rdf.cc | |
| bpy.cc | |
| cluster_cyc_disulf.cc | |
| coiled_coil.cc | |
| coiled_coil_zn.cc | |
| crossmatch.cc | |
| crossmatch_3e.cc | |
| crossmatch_d2.cc | |
| CXdock.cc | |
| cxdock_sheet.cc | |
| CXdock_TMP.cc | |
| cycgly_bbg8t3a.cc | |
| cycgly_canonical.cc | |
| cycgly_superimpose.cc | |
| cycgly_target.cc | |
| cycsamp.cc | |
| d3_bpy_linker.cc | |
| design_DL.cc | |
| design_frags.cc | |
| designability_stats.cc | |
| disulf_frag_match.cc | |
| disulf_frag_search.cc | |
| disulf_stat.cc | |
| dock_asym.cc | |
| dubois.cc | |
| dubois_graft.cc | |
| dump_res.cc | |
| dump_unique_atoms.hh | |
| dxdock.cc | |
| dxdock_movie.cc | |
| fabio.cc | |
| find_pocket.cc | |
| flail.cc | |
| fnd_dutton.cc | |
| for_dkim.cc | |
| for_tim.cc | |
| frag_util.hh | |
| FunGroupTK.cc | |
| FunGroupTK_test.cc | |
| gen3bpy.cc | |
| gen_cyc_gly.cc | |
| gen_cyc_gly_cst.cc | |
| gen_d2.cc | |
| gen_d2_3his_ooc.cc | |
| gen_d2_4his.cc | |
| gen_d2_hhhc.cc | |
| gen_disulf_homodimer.cc | |
| gen_homo_hc.cc | |
| gen_trimer_disulf.cc | |
| gen_xtal_dimer_from_trimer.cc | |
| genI213.cc | |
| genI213_2comp.cc | |
| genI213_2dsf.cc | |
| genI213_gensym.cc | |
| genI213_nocontacts.cc | |
| genmatch.cc | |
| genmatch_3bpy.cc | |
| genmatch_d6_bhhcg.cc | |
| genmatch_d6_bpy.cc | |
| genmatch_m8.cc | |
| genP23.cc | |
| gensym_3bpy_from_dimer.cc | |
| gentetra.cc | |
| gentetra_bpy_from_znhis.cc | |
| gentetra_from_trimer.cc | |
| getDistConstraints.cc | |
| hczndimer.cc | |
| helix_assembly.cc | |
| heterodock.cc | |
| holes2_training_data.cc | |
| holes_pbpdb.cc | |
| holes_test.cc | |
| holes_training_data.cc | |
| hubabinitio.cc | |
| hubdenovo.cc | |
| hubfragdesign.cc | |
| IKFGDB.cc | |
| isct_test.cc | |
| make_symmetric_task_test.cc | |
| match_disulf.cc | |
| minimize.cc | |
| minimize_cavities.cc | |
| mkresfile_i213.cc | |
| motif_denovo_hb.cc | |
| motif_hash_util.cc | |
| nisod.cc | |
| options_will.py | |
| organopv.cc | |
| pack_ddg.cc | |
| pack_stat_energy.cc | |
| pca_simple.hh | |
| pca_simplie.hh | |
| pdb_to_frags.cc | |
| pentcb.cc | |
| pentcb_design.cc | |
| pentcb_test.cc | |
| pick_normal_sampling.hh | |
| pilot_packstat.cc | |
| print_dunscores.cc | |
| rblinker.cc | |
| rblinker2.cc | |
| rblinker2_overlay_bound.cc | |
| rblinker2_test.cc | |
| rescore_i213.cc | |
| rsd_canonical_units.cc | |
| sasa_test.cc | |
| scheme_v0_score.cc | |
| score_pdbs.cc | |
| sf4_hash.cc | |
| sic_fast_x.hh | |
| sic_fast_x_BROKEN.cpp | |
| sicdock.cc | |
| smhybrid.cc | |
| sphere_hierarchy.cc | |
| SphereSample.hh | |
| spiro.cc | |
| sup_test.cc | |
| symdock_enum.cc | |
| symdock_enum_3_1.cc | |
| symdock_hybrid.cc | |
| symdock_hybrid_cc3.cc | |
| symfiles.hh | |
| tcdock.cc | |
| test.cc | |
| test_gradient.cc | |
| test_ikrs.cc | |
| test_ikrs2.cc | |
| test_ikrs_flymake.cc | |
| test_kc.cc | |
| test_leerichards.cc | |
| test_loop_hash.cc | |
| test_rose.cc | |
| test_string.cc | |
| test_sucker_energy.cc | |
| tmp.cpp | |
| unique_atoms.h | |
| ward_design.cc | |
| will_mutalyze.cc | |
| willmatch_2d6_bhe.cc | |
| willmatch_chorismate.cc | |
| willmatch_d6_bpy.cc | |
| xyzStripeHash_dump.cc | |
| xyzStripeHash_test.cc | |
| yeates_align.cc | |
| holes.cc | |
| holes_daball_input.cc | |
| sym_multicomp_test.cc | |
| test_surf_vol.cc | |
| test_threaded_scoring.cc | |
| ► wojtek | |
| FiberDiffractionTest.cc | FiberDiffraction simple test for derivatives |
| ► woodsh | |
| mp_optimize_geometry_params.cc | |
| mp_transition_bfactor.cc | |
| set_radius.cc | |
| ► wujsean | |
| graft_ligand.cc | |
| ► xingjiepan | |
| dna_motif_matcher.cc | App for matching motifs to a protein DNA interface |
| ► yab | |
| buns_report.cc | |
| ufv.cc | |
| vllb.cc | |
| ► yfsong | |
| AlignChunkMover.fwd.hh | |
| AlignChunkMover.hh | Align a random jump to template |
| challenge.cc | Protocol to assign sequence |
| PB_potential.cc | |
| plot_hb.cc | |
| util.hh | Pilot app utilities |
| ► yiliu | |
| AbinitioClassic.cc | |
| combine_silent_test.cc | |
| design_contrast_and_statistic.cc | |
| design_contrast_test.cc | |
| extract_pdbs_test.cc | |
| ► ysrinivasan | |
| mucintypeglycosylation.cc | A protocol to dock glycoprotein glycans in glycosyltransferases at the active site |
| ► zhezhang | |
| cal_metric.cc | |
| extract_CA_coords.cc | Check quality of fragments against input structure |
| extract_replica.cc | Check quality of fragments against input structure |
| fasta2pdb.cc | Check quality of fragments against input structure |
| r_rmsf.cc | Check quality of fragments against input structure |
| ► zibochen | |
| pad_helices.cc | |
| ► public | |
| ► analysis | |
| atom_energy_breakdown.cc | Output score terms for atom self energies and atom-atom interactions as a silent scorefile |
| batch_distances.cc | |
| cl_complex_rescore.cc | |
| contactMap.cc | Simple application for creating a contact map from multiple models of the same protein |
| cst_info.cc | |
| ensemble_analysis.cc | Analyse sets of structures |
| fast_clustering.cc | Analyse sets of structures |
| HDXEnergy.cc | Scores Ab Initio Models using HDX-NMR rate Data |
| interface_energy.cc | |
| InterfaceAnalyzer.cc | Q&D protocol to run InterfaceAnalyzerMover as protocol |
| parcs_ccs_calc.cc | |
| 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 |
| per_residue_solvent_exposure.cc | Determines the per residue solvent exposure using one of the following methods: |
| report_hbonds_for_plugin.cc | |
| residue_energy_breakdown.cc | |
| ResidueDisorder.cc | |
| sc.cc | |
| score.cc | |
| score_jd2.cc | Score a pose! |
| shobuns.cc | |
| SID_ERMS_prediction.cc | |
| ► antibody | |
| antibody.cc | C++ port of Python antibody script |
| antibody_CR_paratope.cc | Calculate metrics over antibody paratopes |
| antibody_designer.cc | |
| antibody_graft.cc | |
| antibody_H3.cc | |
| antibody_legacy.cc | |
| antibody_numbering_converter.cc | App to convert antibodies to a different numbering scheme. Antibodies must have L and/or H chains. Only works on a FAB, currently, just like the rest of RosettaAntibody |
| identify_cdr_clusters.cc | |
| packing_angle.cc | |
| snugdock.cc | |
| ► boinc | |
| boinc_mac_app_icon.hh | |
| minirosetta.cc | |
| minirosetta_graphics.cc | |
| ► carbohydrates | |
| dock_glycans.cc | This application performs a bound-bound dock between an oligosaccharide and a carbohydrate-binding protein |
| glycan_clash_check.cc | |
| glycan_info.cc | |
| GlycanDock.cc | Perform local docking and refinement of a glycoligand into the putative pocket of a protein receptor |
| pose_from_saccharide_sequence.cc | Convert a saccharide sequence into a minimized Pose structure |
| ► clustering | |
| calibur.cc | |
| cluster.cc | |
| energy_based_clustering.cc | Cluster a set of structures using an energy-biased cluster centre selection algorithm |
| ► comparative_modeling | |
| avrg_silent.cc | |
| cluster_alns.cc | |
| fast_gap.cc | |
| fix_alignment_to_match_pdb.cc | |
| full_length_model.cc | |
| iterhybrid_selector.cc | |
| partial_thread.cc | |
| score_aln.cc | |
| score_aln2.cc | |
| spheregrinder.cc | |
| super_aln.cc | |
| template_features.cc | |
| validate_silent.cc | |
| ► coupled_moves | |
| coupled_moves.cc | |
| ► cyclic_peptide | |
| count_cycpep_sequences.cc | An application to count the number of unique sequences for a cyclic peptide given its symmetry |
| 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 | |
| cartesian_ddg.cc | |
| ddg_monomer.cc | |
| ensemble_generator_score12_sidechain_ver2.cc | |
| minimize_with_cst.cc | |
| ► design | |
| beta_peptide_modeling.cc | |
| create_clash-based_repack_shell.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 |
| 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 | |
| ► DRRAFTER | |
| auto-DRRAFTER_setup.py | |
| auto-DRRAFTER_setup_next_round.py | |
| DRRAFTER.py | |
| drrafter_error_estimation.cc | Calculate error estimates for a set of DRRAFTER models |
| drrafter_rna.py | |
| DRRAFTER_util.py | |
| finalize_models.py | |
| fit_helix_in_map.cc | Fit a helix in a density map at a specific position |
| submit_jobs.py | |
| ► electron_density | |
| denovo_density.cc | |
| density_tools.cc | |
| dgdp.cc | |
| grower_prep.cc | |
| mr_protocols.cc | |
| ► enzdes | |
| CstfileToTheozymePDB.cc | |
| enzyme_design.cc | |
| ► ERRASER | |
| erraser.py | |
| erraser_analysis.py | |
| erraser_option.py | |
| erraser_single_res.py | |
| erraser_single_res_analysis.py | |
| erraser_util.py | |
| erraser_wrapper.py | |
| full_struct_minimize.py | |
| measure_params.py | |
| rna_decompose.py | |
| rna_rosetta_ready_set.py | |
| rna_rosetta_to_pdb.py | |
| seq_rebuild.py | |
| SWA_rebuild.py | |
| ► fiber_diffraction | |
| FiberDiffractionFreeSet.cc | |
| ► flexpep_docking | |
| BuildPeptide.cc | |
| FlexPepDocking.cc | |
| ► helical_bundle | |
| helical_bundle_predict.cc | An application that attempts to predict helical bundle structures, without using PDB fragments |
| ► hydrate | |
| hydrate.cc | Hydrate/SPaDES protocol |
| ► 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 | |
| generate_database_cache.cc | |
| validate_database.cc | |
| ► legacy_sewing | |
| sewing_hasher.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 | |
| loodo.cc | |
| loopmodel.cc | |
| transform_loodo.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 | |
| helix_from_sequence.cc | |
| mp_ddG.py | |
| mp_dock.cc | |
| mp_dock_setup.cc | |
| mp_domain_assembly.cc | Build a full-length membrane protein model from a bunch of poses and a fasta file |
| mp_lipid_acc.cc | |
| mp_mutate_relax.cc | Mutate a residue, then do quick relax for a membrane protein |
| mp_range_relax.cc | |
| mp_seqrecov.cc | Compute recovery statistics that consider the membrane environment |
| mp_span_from_pdb.cc | |
| mp_symdock.cc | |
| mp_transform.cc | |
| mp_viewer.cc | |
| ► membrane_abinitio | |
| membrane_abinitio2.cc | |
| ► motif_dock | |
| make_motif_tables.cc | |
| ► motif_ligand_discovery | |
| identify_ligand_motifs.cc | |
| ligand_discovery_search_protocol.cc | Aginsparg, ipatel, sthyme |
| ► motif_tools | |
| extract_motifs.cc | Application to extract motifs from a set of pdb files |
| incorporate_motifs.cc | |
| ► ncaa_utilities | |
| MakeRotLib.cc | |
| UnfoldedStateEnergyCalculator.cc | |
| ► nmr | |
| calc_nmr_tensor.cc | |
| ligand_transform_with_pcs.cc | Find a ligand position that minimizes experimental PCS data through a grid search and that can be used as starting position for ligand docking |
| 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 | |
| make_exemplar.cc | |
| pocket_measure.cc | |
| pocket_relax.cc | |
| pocket_suggest_target_residues_by_ddg.cc | |
| ► pose_sewing | |
| MakeSegmentFile.cc | App to make segment files |
| MakeSegmentFile.fwd.hh | |
| MakeSegmentFile.hh | |
| ► post-translational_modification | |
| DNA_methylation.cc | This application performs a simulated methylation of an input structure containing DNA |
| glycosyltransfer.cc | This application performs a simulated glycosylation of an input structure |
| N-terminal_acetylation.cc | |
| phosphorylation.cc | This application performs a simulated acetylation at the N-terminus of an input structure |
| ► recces | |
| ► legacy | |
| recces_turner.cc | Legacy version of recces app, to be merged with thermal_sampler by December 2016 |
| thermal_sampler.cc | |
| recces.cc | Legacy version of recces app, to be merged with thermal_sampler by December 2016 |
| ► recon_design | |
| recon.cc | The application file for running RECON multistate design Takes in an XML similar to RosettaScripts and runs RECON from that |
| ► relax_w_allatom_cst | |
| amino_acids.py | |
| clean_pdb_keep_ligand.py | |
| sidechain_cst_3.py | |
| ► rna | |
| ► erraser | |
| erraser2.cc | Single erraser app. no python! |
| erraser_minimizer.cc | |
| ► thread | |
| rna_thread.cc | |
| rna_thread_and_minimize.cc | |
| ► util | |
| analyze_base_pairing.cc | Analyze base pairing patterns in a silent file |
| cs_rosetta_rna.cc | |
| nucleobase_sample_around.cc | |
| rna_cluster.cc | |
| rna_database.cc | |
| rna_extract.cc | |
| rna_features.cc | |
| rna_graft.cc | |
| rna_helix.cc | |
| rna_idealize.cc | |
| rna_minimize.cc | |
| rna_motif.cc | Check if we can annotate U-turns, A-minor motifs, etc. in an RNA |
| rna_predict_chem_map.cc | |
| rna_score.cc | |
| rna_suitename.cc | |
| rna_denovo.cc | |
| rna_design.cc | |
| ► rnp_ddg | |
| combine_pdbs.py | |
| find_lowest_scoring_relaxed_struct.py | |
| general_RNP_setup_script.py | |
| get_final_ddG_scores.py | |
| get_lowest_scoring_relaxed_models.py | |
| mutant_modeler.py | |
| relax_starting_structure.py | |
| rnp_ddg.cc | |
| util.py | |
| ► rosetta_scripts | |
| ► multistage | |
| multistage_rosetta_scripts.cc | |
| reverse_conversion_util.hh | |
| parse_rosetta_script.cc | Using the same command line arguments as the rosetta_scripts application, create all of the objects defined within a RosettaScript using the parse-my-tag and parse-tag functions of those objects – but do not call apply on the resulting ParsedProtocolMover that is produced |
| revert_design_to_native.cc | |
| rosetta_scripts.cc | The application file for rosetta_scripts, aka jd2_scripting or the parser |
| rosetta_scripts_jd3.cc | First implementation of a JD3 app for RosettaScripts |
| validate_rosetta_script.cc | Using the same command line arguments as the rosetta_scripts application, validate the input script against Rosetta's internally-generated XSD |
| ► 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 is intended for modeling the binding of a long unstructured C-terminal tail to some other part of a protein. It will work for internal regions too |
| ► sewing | |
| ► ligand_sewing_tools | |
| backside_hbond_finder.cc | |
| generate_starting_zinc_sites.cc | |
| metal_site_finder.cc | |
| zinc_statistic_generator.cc | |
| edge_file_generator.cc | |
| segment_file_generator.cc | |
| segment_file_generator.fwd.hh | |
| segment_file_generator.hh | |
| ► stepwise | |
| ► legacy | |
| swa_protein_main.cc | |
| swa_rna_main.cc | |
| swa_rna_util.cc | |
| build_full_model.cc | |
| resample_full_model.cc | Stepwise-based seq_rebuild (for erraser) |
| stepwise.cc | |
| ► surface_docking | |
| surface_docking.cc | |
| ► symmetry | |
| make_symmdef_file_denovo.py | |
| ► tcr | |
| tcrmodel.cc | Application for Tcr (T cell receptor) modelling |
| ► trRosetta | |
| trRosetta.cc | |
| ► weight_optimization | |
| optE_parallel.cc | |
| torsional_potential_corrections.cc | |
| AbinitioRelax.cc | |
| backrub.cc | Run backrub Monte Carlo |
| calculate_sasa.cc | |
| combine_silent.cc | Simple application for combining a number of silent-files into a single silent-file |
| constel.cc | |
| dump_capped_residue.cc | Useful utility: given an amino/nucleic acid name, dump a polymerically capped version as PDB |
| extract_pdbs.cc | Simple application for extracting PDBs from a silent-file |
| fragment_picker.cc | |
| idealize_jd2.cc | |
| minimize.cc | Calls the minimizer to energy-relax a pose |
| minimize_ppi.cc | |
| mutate.cc | |
| packstat.cc | |
| pH_protocol.cc | |
| relax.cc | |
| remodel.cc | |
| restype_converter.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_docking.cc | Application source code for testing methods relevant to protein-glycoligand docking |
| 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_coenzymes.cc | |
| test_EnergyMethodOptions.cc | Simply call EnergyMethodOptions::show() |
| test_explicit_membrane_input.cc | Application source code for testing loading of a variety of small-molecule cofactors |
| 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 |
| test_SiteConstraint.cc | Application file for testing SiteConstraint.cc |
| ► basic | |
| ► citation_manager | |
| Citation.cc | Data structure for storing a citation |
| Citation.fwd.hh | Data structure for storing a citation |
| Citation.hh | Data structure for storing a citation |
| CitationCollection.cc | A class for keeping track of a collection of citations for a particular Rosetta module |
| CitationCollection.fwd.hh | A class for keeping track of a collection of citations for a particular Rosetta module |
| CitationCollection.hh | A class for keeping track of a collection of citations for a particular Rosetta module |
| CitationCollectionBase.cc | Base structure for storing citations |
| CitationCollectionBase.fwd.hh | Base structure for storing citations |
| CitationCollectionBase.hh | Base structure for storing citations |
| CitationManager.cc | A class that receives lists of works to cite from Rosetta modules, then returns a list of all works to cite on demand. Threadsafe |
| CitationManager.fwd.hh | A class that receives lists of works to cite from Rosetta modules, then returns a list of all works to cite on demand. Threadsafe |
| CitationManager.hh | |
| UnpublishedModuleAuthor.cc | Authorship information for a single author in an unpublished Rosetta module |
| UnpublishedModuleAuthor.fwd.hh | Authorship information for a single author in an unpublished Rosetta module |
| UnpublishedModuleAuthor.hh | Authorship information for a single author in an unpublished Rosetta module |
| UnpublishedModuleInfo.cc | Authorship information for an unpublished Rosetta module |
| UnpublishedModuleInfo.fwd.hh | Authorship information for an unpublished Rosetta module |
| UnpublishedModuleInfo.hh | Authorship information for an unpublished Rosetta module |
| ► 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 |
| 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 | |
| CacheableResRotPairFloatMap.cc | A CacheableData that stores a std::map<ResRotPair,float> |
| CacheableResRotPairFloatMap.fwd.hh | A CacheableData that stores a std::map<ResRotPair,float> |
| CacheableResRotPairFloatMap.hh | A CacheableData that stores a std::map<ResRotPair,float> |
| CacheableString.cc | |
| CacheableString.fwd.hh | |
| CacheableString.hh | |
| CacheableStringFloatMap.cc | |
| CacheableStringFloatMap.fwd.hh | |
| CacheableStringFloatMap.hh | |
| CacheableStringIntegerMap.cc | |
| CacheableStringIntegerMap.fwd.hh | |
| CacheableStringIntegerMap.hh | |
| CacheableStringMap.cc | |
| CacheableStringMap.fwd.hh | |
| CacheableStringMap.hh | |
| CacheableUint64MathMatrixFloatMap.cc | |
| CacheableUint64MathMatrixFloatMap.fwd.hh | |
| CacheableUint64MathMatrixFloatMap.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.fwd.hh | Forward declaration for DataCache |
| DataCache.hh | |
| DataMap.cc | |
| DataMap.fwd.hh | |
| DataMap.hh | |
| DataMapObj.cc | |
| DataMapObj.fwd.hh | Forward declaration for DataMapObj |
| DataMapObj.hh | |
| DiagnosticData.cc | |
| DiagnosticData.fwd.hh | |
| DiagnosticData.hh | |
| HierarchicalDataMap.cc | |
| HierarchicalDataMap.fwd.hh | |
| HierarchicalDataMap.hh | |
| WriteableCacheableData.cc | |
| 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.cc | |
| 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 |
| cloud.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 |
| constel.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 |
| coupled_moves.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 |
| DisulfideInsertion.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 |
| dump_trajectory.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 |
| enzymes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| epr_deer.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 |
| helical_bundle_predict.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| holes.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| hotspot.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| hydrate.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 |
| jd3.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| jumps.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| krassk.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| legacy_sewing.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 |
| machine_learning.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| magnesium.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| make_mainchain_potential.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 |
| mean_field.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 |
| multithreading.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| murphp.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| mutate.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| nmr.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 |
| partial_thread.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 |
| PDB_diagnostic.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 |
| ralford.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 |
| recces.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| recon.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 |
| simple_metrics.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| smhybrid.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| solvent_exposure.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 |
| tcrmodel.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| templates.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| testing.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| threadsc.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| trRosetta.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| ufv.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| unfolded_state.OptionKeys.gen.hh | Basic::options::OptionKeys collection |
| view.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 | |
| ► random | |
| init_random_generator.cc | Functions to initialize the random generator |
| init_random_generator.hh | Functions to initialize the random generator |
| RandomGeneratorSettings.cc | A class to store settings from the options system for the random generator. Moved from core to basic |
| RandomGeneratorSettings.fwd.hh | Forward declarations for a class to store settings from the options system for the random generator. Moved from core to basic |
| RandomGeneratorSettings.hh | A class to store settings from the options system for the random generator. Moved from core to basic |
| ► resource_manager | |
| ► 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 |
| locator_schemas.cc | |
| locator_schemas.hh | |
| 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 |
| loader_schemas.cc | |
| loader_schemas.hh | |
| ResourceLoader.cc | |
| ResourceLoader.fwd.hh | |
| ResourceLoader.hh | |
| ResourceLoaderCreator.cc | |
| ResourceLoaderCreator.fwd.hh | |
| ResourceLoaderCreator.hh | |
| ResourceLoaderFactory.cc | |
| ResourceLoaderFactory.fwd.hh | Forward declaration for ResourceLoaderFactory |
| 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.fwd.hh | Forward declaration for ResourceLocatorFactory |
| 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 | |
| types.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 |
| ► tensorflow_manager | |
| RosettaTensorflowManager.cc | A manager class for loading Tensorflow sessions and controlling mapping to the CPU or GPU |
| RosettaTensorflowManager.fwd.hh | A manager class for loading Tensorflow sessions and controlling mapping to the CPU or GPU |
| RosettaTensorflowManager.hh | |
| RosettaTensorflowProtocolBase.cc | A pure virtual base class for storing Tensorflow sessions and the code for executing them and returning a result. Derived classes will be protocol-specific, and will accept a RosettaTensorflowInput and produce a RosettaTensorflowOutput |
| RosettaTensorflowProtocolBase.fwd.hh | A pure virtual base class for storing Tensorflow sessions and the code for executing them and returning a result. Derived classes will be protocol-specific, and will accept a RosettaTensorflowInput and produce a RosettaTensorflowOutput |
| RosettaTensorflowProtocolBase.hh | A pure virtual base class for storing Tensorflow sessions and the code for executing them and returning a result. Derived classes will be protocol-specific, and will accept a RosettaTensorflowInput and produce a RosettaTensorflowOutput |
| RosettaTensorflowSessionContainer.cc | A container for Rosetta Tensorflow sessions, allowing sessions to be loaded once and stored in the global Tensorflow session manager |
| RosettaTensorflowSessionContainer.fwd.hh | A container for Rosetta Tensorflow sessions, allowing sessions to be loaded once and stored in the global Tensorflow session manager |
| RosettaTensorflowSessionContainer.hh | A container for Rosetta Tensorflow sessions, allowing sessions to be loaded once and stored in the global Tensorflow session manager |
| RosettaTensorflowSessionContainer.tmpl.hh | A container for Rosetta Tensorflow sessions, allowing sessions to be loaded once and stored in the global Tensorflow session manager |
| RosettaTensorflowTensorContainer.cc | A container class for Tensorflow's TF_Tensor objects, which manages access, creation, and destruction in a way that prevents memory leaks |
| RosettaTensorflowTensorContainer.fwd.hh | A container class for Tensorflow's TF_Tensor objects, which manages access, creation, and destruction in a way that prevents memory leaks |
| RosettaTensorflowTensorContainer.hh | A container class for Tensorflow's TF_Tensor objects, which manages access, creation, and destruction in a way that prevents memory leaks |
| RosettaTensorflowTensorContainer.tmpl.hh | A container class for Tensorflow's TF_Tensor objects, which manages access, creation, and destruction in a way that prevents memory leaks |
| TFDataTypeDetector.hh | |
| util.cc | Utility functions for the tensorflow manager |
| util.hh | Utility functions for the tensorflow manager |
| ► thread_manager | |
| RosettaThread.cc | A container for a thread in a RosettaThreadPool. The thread idles continuously until loaded with a function to execute. It then executes the function and returns to the idle state |
| RosettaThread.fwd.hh | A container for a thread in a RosettaThreadPool. The thread idles continuously until loaded with a function to execute. It then executes the function and returns to the idle state |
| RosettaThread.hh | A container for a thread in a RosettaThreadPool. The thread idles continuously until loaded with a function to execute. It then executes the function and returns to the idle state |
| RosettaThreadAllocation.cc | |
| RosettaThreadAllocation.fwd.hh | |
| RosettaThreadAllocation.hh | |
| RosettaThreadAssignmentInfo.cc | A class for storing information about the threads to which a function has been assigned by the RosettaThreadManager |
| RosettaThreadAssignmentInfo.fwd.hh | A class for storing information about the threads to which a function has been assigned by the RosettaThreadManager |
| RosettaThreadAssignmentInfo.hh | A class for storing information about the threads to which a function has been assigned by the RosettaThreadManager |
| RosettaThreadManager.cc | A manager that maintains a threadpool and handles requests for threads for multithreaded execution of functions. This allows multithreading at many different levels in the Rosetta library hierarchy, from job-level parallel execution down to parallel computation of a score, gradient vector, or interaction graph |
| RosettaThreadManager.fwd.hh | A manager that maintains a threadpool and handles requests for threads for multithreaded execution of functions. This allows multithreading at many different levels in the Rosetta library hierarchy, from job-level parallel execution down to parallel computation of a score, gradient vector, or interaction graph |
| RosettaThreadManager.hh | |
| RosettaThreadManagerAdvancedAPIKey.fwd.hh | A class containing no private member data and only a constructor as a private member function, with friendship to only those classes that should be able to access the advanced RosettaThreadManager API. Since the advanced API requires an instance of a RosettaThreadManagerAdvancedAPIKey, this ensures that only those classes can access the advanced API |
| RosettaThreadManagerAdvancedAPIKey.hh | A class containing no private member data and only a constructor as a private member function, with friendship to only those classes that should be able to access the advanced RosettaThreadManager API. Since the advanced API requires an instance of a RosettaThreadManagerAdvancedAPIKey, this ensures that only those classes can access the advanced API.' |
| RosettaThreadManagerInitializationTracker.cc | A singleton that tracks whether we have already launched threads or not |
| RosettaThreadManagerInitializationTracker.fwd.hh | A singleton that tracks whether we have already launched threads or not |
| RosettaThreadManagerInitializationTracker.hh | |
| RosettaThreadPool.cc | A container for a pool of threads. Threads idle continuously until loaded with a function to execute. A subset of threads then execute the function synchronously and then return to the idle state |
| RosettaThreadPool.fwd.hh | A container for a pool of threads. Threads idle continuously until loaded with a function to execute. A subset of threads then execute the function synchronously and then return to the idle state |
| RosettaThreadPool.hh | A container for a pool of threads. Threads idle continuously until loaded with a function to execute. A subset of threads then execute the function synchronously and then return to the idle state |
| 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.fwd.hh | |
| prof.hh | |
| pymol_chains.cc | Method definitions for a couple PyMOL helper functions |
| pymol_chains.hh | |
| report.cc | Report and Reporter |
| report.fwd.hh | Report and Reporter |
| report.hh | Report and Reporter |
| Tracer.cc | |
| Tracer.fwd.hh | |
| Tracer.hh | Tracer IO system |
| TracerImpl.cc | |
| TracerImpl.fwd.hh | Tracer IO system |
| TracerImpl.hh | |
| TracerToFile.cc | |
| TracerToFile.hh | Class for a tracer that writes all output to a file |
| ► numeric | |
| ► alignment | |
| QCPKernel.hh | |
| rmsd_calc.cc | |
| rmsd_calc.hh | |
| rmsd_calc.impl.hh | |
| rmsd_calc.py.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 | |
| MinimalClashHash.cc | Minimal hashing class to find clashes as fast as possible |
| MinimalClashHash.fwd.hh | Minimal hashing class to find clashes as fast as possible |
| MinimalClashHash.hh | Minimal hashing class to find clashes as fast as possible |
| 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 | |
| projection_area.cc | |
| projection_area.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 | |
| BicubicSpline.cc | |
| BicubicSpline.fwd.hh | |
| BicubicSpline.hh | |
| CompoundInterpolator.cc | Interpolation with cubic splines |
| CompoundInterpolator.hh | Interpolation with cubic splines |
| CubicSpline.cc | |
| CubicSpline.fwd.hh | |
| CubicSpline.hh | |
| Interpolator.cc | |
| Interpolator.fwd.hh | |
| Interpolator.hh | |
| PolycubicSpline.cc | |
| PolycubicSpline.fwd.hh | Forward declaration of PolycubicSpline class, and declaration of (templated) owning pointers |
| PolycubicSpline.hh | |
| PolycubicSpline.tmpl.hh | |
| PolycubicSplineBase.fwd.hh | Forward declaration of PolycubicSplineBase class, and declaration of (templated) owning pointers |
| PolycubicSplineBase.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.fwd.hh | |
| 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 |
| InterpolatedPotential.fwd.hh | |
| InterpolatedPotential.hh | An n-dimensional bicubic-interpolated potential |
| InterpolatedPotential.tmpl.hh | |
| interpolation.hh | Interpolation functions |
| polycubic_catmull_rom.hh | |
| 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 | Utility functions for kd-tree. See 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 |
| bridgeObjects_nonredundant.cc | Non-redundant bridgeObject function |
| bridgeObjects_nonredundant.hh | Non-redundant bridgeObject function. @detail The origional bridgeObject function need some redundant inputs which are just place holders and never used in actual calculation. Here I wrote a wrapper of the original function such that no redundant information are needed. However, this wrapper means even more moving around redundant data. TODO: rewrite the function such that redundant data don't appear at all |
| 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 | |
| EllipseParameters.cc | Container class for ellipse parameters |
| EllipseParameters.fwd.hh | Container class for ellipse parameters |
| EllipseParameters.hh | Container class for ellipse parameters |
| GeneralizedEigenSolver.fwd.hh | Forward header for GeneralizedEigenSolver |
| GeneralizedEigenSolver.hh | Header file for GeneralizedEigenSolver |
| minimum_bounding_ellipse.cc | Given a set of points, calculate the minimum bounding ellipse |
| minimum_bounding_ellipse.hh | Given a set of points, calculate the minimum bounding ellipse |
| 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 | |
| functions.cc | |
| functions.hh | |
| 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.fwd.hh | Forward declarations for class DistributionSampler |
| 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 |
| angle.functions.hh | Trigonometric functions |
| AxisRotationSampler.fwd.hh | Numeric::AxisRotationSampler forward declarations |
| AxisRotationSampler.hh | |
| 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 |
| cubic_polynomial.cc | Functions to evaluate cubic polynomials and cubic polynomial derivatives |
| cubic_polynomial.fwd.hh | Forward header for CubicPolynomial class |
| cubic_polynomial.hh | Functions to evaluate cubic polynomials and cubic polynomial derivatives |
| 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 |
| DiscreteIntervalEncodingTree.cc | |
| DiscreteIntervalEncodingTree.fwd.hh | Forward header for DiscreteIntervalEncodingTree class |
| DiscreteIntervalEncodingTree.hh | Definition of a discrete interval encoding tree ("DIET") as described by Martin Erwig https://web.engr.oregonstate.edu/~erwig/papers/Diet_JFP98.pdf |
| 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.fwd.hh | Forward header for MathMatrix |
| MathMatrix.hh | |
| MathMatrix.srlz.cc | Serlialization routines for MathMatrix |
| MathMatrix.srlz.hh | Serlialization routines for MathMatrix |
| MathMatrix_operations.hh | |
| MathNTensor.fwd.hh | Owning pointer declarations for MathNTensor template class |
| MathNTensor.hh | |
| MathNTensor_io.hh | |
| MathNTensorBase.fwd.hh | Owning pointer declarations for MathNTensorBase template class |
| MathNTensorBase.hh | |
| MathTensor.hh | |
| MathVector.fwd.hh | Forward header for MathVector |
| 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 |
| VoxelArray.fwd.hh | |
| VoxelArray.hh | N-dimensional array class to store values at float offsets |
| VoxelGrid.fwd.hh | Forward declaration for class VoxelGrid |
| VoxelGrid.hh | Class that provides optimal space hashing for rapid identification of neighbors |
| VoxelGrid.impl.hh | Implementation file for VoxelGrid class |
| 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.functions.PyRosetta.hh | Explicit instantiation of some numeric template functions for PyRosetta |
| 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 | |
| zscores.cc | |
| zscores.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.fwd.hh | |
| FArray.hh | |
| FArray.io.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.fwd.hh | |
| FArray2.hh | |
| FArray2.io.hh | |
| FArray2A.fwd.hh | |
| FArray2A.hh | |
| FArray2D.fwd.hh | |
| FArray2D.hh | |
| FArray2P.fwd.hh | |
| FArray2P.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.fwd.hh | |
| FArray4.hh | |
| FArray4.io.hh | |
| FArray4A.fwd.hh | |
| FArray4A.hh | |
| FArray4D.fwd.hh | |
| FArray4D.hh | |
| FArray4P.fwd.hh | |
| FArray4P.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.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 | |
| 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 | |
| missing_stl.hh | Missing STL functions |
| 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 |
| ► msvc | |
| ► platform | |
| types.hh | Platform-specific types for Windows using MSVC |
| ► PyRosetta | |
| ► platform | |
| types.hh | |
| ► python | |
| ► PyRosetta | |
| ► binder | |
| ► documentation | |
| conf.py | |
| ► examples | |
| ► example_struct | |
| ► include | |
| ► test_struct | |
| test_struct.hpp | |
| myts.hpp | |
| make_bindings_via_cmake.py | |
| reference_all_includes.hpp | |
| ► source | |
| ► fmt | |
| chrono.h | |
| color.h | |
| compile.h | |
| core.h | |
| format-inl.h | |
| format.cc | |
| format.h | |
| locale.h | |
| os.cc | |
| os.h | |
| ostream.h | |
| posix.h | |
| printf.h | |
| ranges.h | |
| binder.cpp | |
| binder.hpp | |
| class.cpp | |
| class.hpp | |
| config.cpp | |
| config.hpp | |
| context.cpp | |
| context.hpp | |
| enum.cpp | |
| enum.hpp | |
| function.cpp | |
| function.hpp | |
| main.cpp | |
| options.cpp | |
| options.hpp | |
| stl_binders.hpp | |
| type.cpp | |
| type.hpp | |
| util.cpp | |
| util.hpp | |
| ► test | |
| diffbinder.cpp | |
| self-test.py | Script to run Binder tool self-test |
| T00.basic.hpp | Binder self-test file. Basic functionality |
| T00.basic.ref.cpp | |
| T01.enum.hpp | Binder self-test file. Bindings of enum's functionality |
| T01.enum.ref.cpp | |
| T02.function.hpp | Binder self-test file. Bindings for functions |
| T02.function.ref.cpp | |
| T05.default.hpp | Binder self-test file. Bindings of functions with default arguments |
| T05.default.ref.cpp | |
| T07.class.hpp | Binder self-test file. Bindings of classes data members functionality |
| T07.class.match_args.hpp | |
| T07.class.match_args.ref.cpp | |
| T07.class.ref.cpp | |
| T08.constructor.hpp | Binder self-test file. Bindings of classes constructors |
| T08.constructor.ref.cpp | |
| T09.overload.hpp | Binder self-test file. Test for function overloads in Python |
| T09.overload.ref.cpp | |
| T10.inheritance.hpp | Binder self-test file. Bindings tests for class hierarchy’s |
| T10.inheritance.ref.cpp | |
| T10.virtual_inheritance.hpp | |
| T10.virtual_inheritance.ref.cpp | |
| T11.override.hpp | |
| T11.override.ref.cpp | |
| T12.insertion_operator.hpp | Binder self-test file. Bindings for insertion operator |
| T12.insertion_operator.ref.cpp | |
| T12.operator.hpp | Binder self-test file. Bindings for various operators |
| T12.operator.ref.cpp | |
| T15.copy.hpp | Binder self-test file. Binding for copy constuctors |
| T15.copy.ref.cpp | |
| T15.inner_class.fwd.hpp | Binder self-test file. Tests for bindings of forward declared inner functions |
| T15.inner_class.fwd.ref.cpp | |
| T15.inner_class.hpp | Binder self-test file. Bindings of classes data members with inner classes |
| T15.inner_class.ref.cpp | |
| T17.anonymous.hpp | Binder self-test file. Bindings of classes/functions in anonymous namespace |
| T17.anonymous.ref.cpp | |
| T20.template.hpp | Binder self-test file. Bindings of temlate classes and functions functionality |
| T20.template.ref.cpp | |
| T20.template.variadic.hpp | Binder self-test file. Bindings of variadic temlate classes functionality |
| T20.template.variadic.ref.cpp | |
| T30.include.hpp | Binder self-test file. Tests for include-request functionality |
| T30.include.ref.cpp | |
| T31.include_for_class.hpp | |
| T31.include_for_class.ref.cpp | |
| T32.call_guard.hpp | |
| T32.call_guard.ref.cpp | |
| T33.buffer_protocol.hpp | |
| T33.buffer_protocol.ref.cpp | |
| T40.stl.hpp | Binder self-test file. Tests for bindings of STL classes |
| T40.stl.ref.cpp | |
| T42.stl.names.hpp | Binder self-test file. Tests for bindings of STL classes |
| T42.stl.names.map.hpp | Binder self-test file. Tests for bindings of STL classes |
| T42.stl.names.map.ref.cpp | |
| T42.stl.names.multi.hpp | Binder self-test file. Tests for bindings of STL classes multiset/multimap |
| T42.stl.names.multi.ref.cpp | |
| T42.stl.names.multimap.hpp | Binder self-test file. Tests for bindings of STL classes multiset/multimap |
| T42.stl.names.multimap.ref.cpp | |
| T42.stl.names.multiset.hpp | Binder self-test file. Tests for bindings of STL classes multiset/multimap |
| T42.stl.names.multiset.ref.cpp | |
| T42.stl.names.ref.cpp | |
| T42.stl.names.set.hpp | Binder self-test file. Tests for bindings of STL classes |
| T42.stl.names.set.ref.cpp | |
| T43.stl.pybind11_include_stl.hpp | |
| T43.stl.pybind11_include_stl.ref.cpp | |
| T50.add_on_binder.hpp | |
| T50.add_on_binder.ref.cpp | |
| T50.namespace_binder.hpp | |
| T50.namespace_binder.ref.cpp | |
| T60.custom_shared.hpp | |
| T60.custom_shared.ref.cpp | |
| T60.pybind11.hpp | |
| T60.pybind11.ref.cpp | |
| T70.module_local.hpp | |
| T70.module_local.ref.cpp | |
| T70.options.hpp | |
| T70.options.ref.cpp | |
| T71.module_local.hpp | |
| T71.module_local.ref.cpp | |
| T80.custom_trampoline.hpp | |
| T80.custom_trampoline.ref.cpp | |
| T81.custom_trampoline_with_args.hpp | |
| T81.custom_trampoline_with_args.ref.cpp | |
| build-and-run-tests.py | Script to build Binder and run Binder self-test's |
| build.py | Script to build Binder |
| sphinx-doc-generator.py | Script to generate Sphinx documentation files out of Binder output |
| ► documentation | |
| ► source | |
| conf.py | |
| ► include | |
| rosetta_binders.hpp | Support for custom binders for some Rosetta template classes |
| ► src | |
| ► 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 | |
| ► pyrosetta | |
| ► bindings | |
| __init__.py | |
| energies.py | |
| homogeneous_transform.py | |
| pose.py | |
| rt.py | |
| utility.py | |
| ► distributed | |
| ► cluster | |
| __init__.py | |
| base.py | |
| config.py | |
| converter_tasks.py | |
| converters.py | |
| core.py | |
| exceptions.py | |
| initialization.py | |
| io.py | |
| logging_support.py | |
| multiprocessing.py | |
| toolkit.py | |
| tools.py | |
| utilities.py | |
| validators.py | |
| ► dask | |
| __init__.py | |
| worker.py | |
| ► docs | |
| __init__.py | |
| ► packed_pose | |
| __init__.py | |
| core.py | |
| pandas.py | |
| ► tasks | |
| __init__.py | |
| rosetta_scripts.py | |
| score.py | |
| taskbase.py | |
| ► utility | |
| __init__.py | |
| log.py | |
| pickle.py | |
| ► viewer | |
| ► presets | |
| __init__.py | |
| __init__.py | |
| core.py | |
| modules.py | |
| __init__.py | |
| io.py | |
| ► io | |
| __init__.py | |
| silent_file_map.py | |
| ► network | |
| __init__.py | |
| rosetta_udp_to_tcp_bridge.py | |
| ► numeric | |
| ► alignment | |
| __init__.py | |
| rmsd_calc.py | |
| __init__.py | |
| ► protocols | |
| ► structure_search | |
| __init__.py | |
| alignment.py | |
| __init__.py | |
| h5_fragment_store_provider.py | |
| h5_importer.py | |
| h5_structure_store_provider.py | |
| ► tests | |
| ► bindings | |
| ► core | |
| __init__.py | |
| test_pose.py | |
| __init__.py | |
| ► distributed | |
| ► cluster | |
| __init__.py | |
| skip_command_line_test.py | |
| test_logging.py | |
| test_reproducibility.py | |
| test_smoke.py | |
| __init__.py | |
| test_concurrency.py | |
| test_dask.py | |
| test_dask_worker.py | |
| test_gil.py | |
| test_smoke.py | |
| test_viewer.py | |
| ► numeric | |
| __init__.py | |
| test_alignment.py | |
| ► protocols | |
| ► indexed_structure_store | |
| ► data | |
| __init__.py | |
| __init__.py | |
| test_search.py | |
| __init__.py | |
| __init__.py | |
| __main__.py | |
| ► toolbox | |
| __init__.py | |
| atom_pair_energy.py | |
| cleaning.py | |
| extract_coords_pose.py | |
| generate_resfile.py | |
| load_ligand.py | |
| mutants.py | |
| numpy_utils.py | |
| py_jobdistributor.py | |
| rcsb.py | |
| ► utility | |
| __init__.py | |
| array.py | |
| __init__.py | |
| logging_support.py | |
| mpi.py | |
| PyMOLRosettaServer.py | |
| teaching.py | |
| ► rosetta | |
| __init__.py | |
| ► test | |
| __init__.py | |
| C001_Carbohydrates_Demo01.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 | |
| T006_Options.py | |
| T007_TracerIO.py | |
| T008_Serialization.py | |
| T009_Exceptions.py | |
| T010_LoadPDB.py | |
| T020_Pose_Bindings.py | |
| T040_Types.py | Tests for bindings for various types |
| T100_basic.py | |
| T110_numeric.py | |
| T120_core.RotamerSets.py | |
| T150_PyMOL_Integration.py | |
| T190_Bindings_Utility.py | |
| T200_Scoring.py | |
| T201_Scoring_pre_talaris.py | Test to trigger creation of database/rotamer/bbdep02.May.sortlib.Dunbrack02.lib.bin |
| T220_AtomAtomPairEnergies.py | |
| T250_Constraints.py | |
| T300_PyJobDistributor.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 | |
| T900_distributed.py | |
| Workshop2test.py | |
| Workshop3test.py | |
| Workshop4test.py | |
| Workshop5test.py | |
| Workshop6test.py | |
| Workshop7test.py | |
| Workshop8test.py | |
| Workshop9_my_shapes.py | |
| Workshop9test.py | |
| ez_setup.py | |
| PyMOL-Rosetta-relay-client.python2.py | |
| PyMOL-Rosetta-relay-client.python3.py | |
| PyMOL-RosettaServer.py | |
| PyMOL-RosettaServer.python3.py | |
| self-test.py | Run bindings test and demo scrips |
| setup.py | |
| build.py | Build PyRosetta |
| ► ui | |
| ► apps | |
| ► pilot | |
| ► awatkins | |
| ► rna_denovo | |
| main.cpp | Main function for the stepwise interface project |
| mainwindow.cpp | Main window class for the stepwise interface project |
| mainwindow.h | Headers for main window class for the stepwise GUI project |
| ► stepwise_interface | |
| main.cpp | Main function for the stepwise interface project |
| mainwindow.cpp | Main window class for the stepwise interface project |
| mainwindow.h | Headers for main window class for the stepwise GUI project |
| ► sergey | |
| ► pose_viewer | |
| main.cpp | |
| ► sergey_pilot_app_test | |
| main.cpp | |
| mainwindow.cpp | |
| mainwindow.h | |
| ► vmullig | |
| ► bundle_gui | |
| main.cpp | Main function for the bundle GUI project |
| mainwindow.cpp | Main window class for the bundle GUI project |
| mainwindow.h | Headers for main window class for the bundle GUI project |
| ► simple_pose_draw | |
| main.cpp | |
| mainwindow.cpp | |
| mainwindow.h | |
| ► tests | |
| ► functor | |
| functor_test.cpp | |
| ► task | |
| node_test.cpp | |
| ► workbench | |
| main.cpp | |
| mainwindow.cpp | |
| mainwindow.h | |
| ► config | |
| config_dialog.cpp | |
| config_dialog.h | |
| util.cpp | |
| util.h | |
| ► network | |
| .attic.bowman_model.index_pack.cpp | |
| .attic.bowman_model.index_pack.h | |
| argument.cpp | |
| argument.fwd.h | |
| argument.h | |
| bowman.cpp | |
| bowman.h | |
| bowman_model.cpp | |
| bowman_model.h | |
| bowman_thread.cpp | |
| bowman_thread.h | |
| bowman_view.cpp | |
| bowman_view.h | |
| function_setup_dialog.cpp | |
| function_setup_dialog.h | |
| ► task | |
| .attic.project_model.cpp | |
| .attic.project_model.h | |
| file.cpp | |
| file.fwd.h | |
| file.h | |
| functor.cpp | |
| functor.fwd.h | |
| functor.h | |
| job_submit.cpp | |
| job_submit.h | |
| job_view.cpp | |
| job_view.h | |
| node.cpp | Node class for ui library |
| node.h | Node class for ui library |
| project.cpp | Project class for ui library |
| project.fwd.h | Project class for ui library |
| project.h | Project class for ui library |
| project_model.cpp | Project model class for ui library |
| project_model.h | Project model class for ui library |
| project_view.cpp | Project view class for ui library |
| project_view.h | Project view class for ui library |
| task.cpp | Task class for ui library |
| task.fwd.h | |
| task.h | Task class for ui library |
| task_cancel_dialog.cpp | |
| task_cancel_dialog.h | |
| task_submit.cpp | |
| task_submit.h | |
| task_syncer.cpp | |
| task_syncer.fwd.h | |
| task_syncer.h | |
| task_view.cpp | |
| task_view.h | |
| util.cpp | |
| util.h | |
| ► ui_core | |
| ► pose_draw | |
| SimplePoseDrawOpenGLWidget.cpp | |
| SimplePoseDrawOpenGLWidget.fwd.h | |
| SimplePoseDrawOpenGLWidget.h | |
| ► ui_protocols | |
| ► helical_bundle | |
| HelicalBundleDialogueWidget.cpp | |
| HelicalBundleDialogueWidget.fwd.h | |
| HelicalBundleDialogueWidget.h | |
| HelicalBundlePoseDrawOpenGLWidget.cpp | |
| HelicalBundlePoseDrawOpenGLWidget.fwd.h | |
| HelicalBundlePoseDrawOpenGLWidget.h | |
| HelixOptionWidget.cpp | |
| HelixOptionWidget.fwd.h | |
| HelixOptionWidget.h | |
| ► util | |
| exception.h | |
| serialization.h | |
| tree_node.h | |
| ► viewers | |
| score_file_view.cpp | |
| score_file_view.h | |
| ► widgets | |
| pose_editor.cpp | |
| pose_editor.h | |
| config.devel.py | |
| ui_lib_test.cpp | Unit tests for the ui library |
| ui_lib_test.h | Headers for ui library unit tests |
| update_ui_project.py | Create/update ui project files |
| ► 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 |
| ► 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 | |
| ArrayPool.cc | ArrayPool class declaration and implementation |
| ArrayPool.fwd.hh | Forward declaration for ArrayPool classes |
| ArrayPool.hh | ArrayPool class declaration and implementation |
| BFS_prune.hh | A breadth first search with pruning for boost graphs |
| DFS_sort.hh | A depth first search with sorting for edge visitation |
| Digraph.cc | Directed graph base classes |
| Digraph.fwd.hh | Directed graph base class forward declarations |
| Digraph.hh | Generic directed graph class header |
| DisjointSets.cc | |
| DisjointSets.fwd.hh | DisjointSets class forward declaration |
| DisjointSets.hh | |
| Graph.cc | Graph base classes |
| Graph.fwd.hh | Graph base class forward declarations |
| Graph.hh | Generic graph class header |
| graph_util.cc | |
| graph_util.hh | Generic graph class header |
| LowMemGraph.cc | A lower memory version of utility::graph::Graph with three key limitations |
| LowMemGraph.fwd.hh | A lower memory version of utility::graph::Graph with three key limitations |
| LowMemGraph.hh | A lower memory version of utility::graph::Graph with three key limitations |
| ring_detection.hh | Algorithms for working with rings in boost graphs |
| RingDetection.hh | |
| unordered_object_pool.fwd.hpp | |
| unordered_object_pool.hpp | |
| UpperEdgeGraph.fwd.hh | |
| UpperEdgeGraph.hh | Templated graph for fast edge additions |
| UpperEdgeGraph.srlz.hh | Templated graph for fast edge additions |
| ► io | |
| base64.cc | |
| base64.hh | |
| 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 |
| GeneralFileManager.cc | A singleton class for managing arbitrary files to ensure that they are loaded once and only once from disk |
| GeneralFileManager.fwd.hh | A singleton class for managing arbitrary files to ensure that they are loaded once and only once from disk |
| GeneralFileManager.hh | A singleton class for managing arbitrary files to ensure that they are loaded once and only once from disk |
| 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.cc | Auto-generated serialization template functions |
| 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 |
| Key4Tuple.srlz.cc | Serlialization routines for Key4Tuples |
| Key4Tuple.srlz.hh | Serlialization routines for Key4Tuples |
| 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.cc | Auto-generated serialization template functions |
| AnyOptionKey.fwd.hh | Utility::options::AnyOptionKey forward declarations |
| AnyOptionKey.hh | Automatic hidden index key for any scalar-valued options |
| AnyVectorOptionKey.cc | Auto-generated serialization template functions |
| AnyVectorOptionKey.fwd.hh | Utility::options::AnyVectorOptionKey forward declarations |
| AnyVectorOptionKey.hh | Automatic hidden index key for any vector-valued options |
| BooleanOptionKey.cc | Auto-generated serialization template functions |
| BooleanOptionKey.fwd.hh | Utility::options::BooleanOptionKey forward declarations |
| BooleanOptionKey.hh | Automatic hidden index key for boolean options |
| BooleanVectorOptionKey.cc | Auto-generated serialization template functions |
| BooleanVectorOptionKey.fwd.hh | Utility::options::BooleanVectorOptionKey forward declarations |
| BooleanVectorOptionKey.hh | Automatic hidden index key for boolean options |
| FileOptionKey.cc | Auto-generated serialization template functions |
| FileOptionKey.fwd.hh | Utility::options::FileOptionKey forward declarations |
| FileOptionKey.hh | Automatic hidden index key for file options |
| FileVectorOptionKey.cc | Auto-generated serialization template functions |
| FileVectorOptionKey.fwd.hh | Utility::options::FileVectorOptionKey forward declarations |
| FileVectorOptionKey.hh | Automatic hidden index key for file options |
| IntegerOptionKey.cc | Auto-generated serialization template functions |
| IntegerOptionKey.fwd.hh | Utility::options::IntegerOptionKey forward declarations |
| IntegerOptionKey.hh | Automatic hidden index key for integer options |
| IntegerVectorOptionKey.cc | Auto-generated serialization template functions |
| IntegerVectorOptionKey.fwd.hh | Utility::options::IntegerVectorOptionKey forward declarations |
| IntegerVectorOptionKey.hh | Automatic hidden index key for integer options |
| OptionKey.cc | Auto-generated serialization template functions |
| OptionKey.fwd.hh | Utility::options::OptionKey forward declarations |
| OptionKey.hh | Abstract automatic hidden index key for options |
| OptionKeyList.cc | Functions for adding option keys into an OptionKeyList |
| OptionKeyList.fwd.hh | |
| OptionKeyList.hh | Functions for adding option keys into an OptionKeyList |
| OptionKeys.cc | Utility::options::OptionKeys collection |
| OptionKeys.hh | Utility::options::OptionKeys collection |
| PathOptionKey.cc | Auto-generated serialization template functions |
| PathOptionKey.fwd.hh | Utility::options::PathOptionKey forward declarations |
| PathOptionKey.hh | Automatic hidden index key for path options |
| PathVectorOptionKey.cc | Auto-generated serialization template functions |
| PathVectorOptionKey.fwd.hh | Utility::options::PathVectorOptionKey forward declarations |
| PathVectorOptionKey.hh | Automatic hidden index key for path options |
| RealOptionKey.cc | Auto-generated serialization template functions |
| RealOptionKey.fwd.hh | Utility::options::RealOptionKey forward declarations |
| RealOptionKey.hh | Automatic hidden index key for real options |
| RealVectorOptionKey.cc | Auto-generated serialization template functions |
| RealVectorOptionKey.fwd.hh | Utility::options::RealVectorOptionKey forward declarations |
| RealVectorOptionKey.hh | Automatic hidden index key for real options |
| ResidueChainVectorOptionKey.cc | Auto-generated serialization template functions |
| ResidueChainVectorOptionKey.fwd.hh | Utility::options::ResidueChainVectorOptionKey forward declarations |
| ResidueChainVectorOptionKey.hh | Automatic hidden index key for integer options |
| ScalarOptionKey.cc | Auto-generated serialization template functions |
| ScalarOptionKey.fwd.hh | Utility::options::ScalarOptionKey forward declarations |
| ScalarOptionKey.hh | Abstract automatic hidden index key for scalar-valued options |
| StringOptionKey.cc | Auto-generated serialization template functions |
| StringOptionKey.fwd.hh | Utility::options::StringOptionKey forward declarations |
| StringOptionKey.hh | Automatic hidden index key for string options |
| StringVectorOptionKey.cc | Auto-generated serialization template functions |
| StringVectorOptionKey.fwd.hh | Utility::options::StringVectorOptionKey forward declarations |
| StringVectorOptionKey.hh | Automatic hidden index key for string options |
| VectorOptionKey.cc | Auto-generated serialization template functions |
| 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.cc | Auto-generated serialization template functions |
| BooleanOption.fwd.hh | Utility::options::BooleanOption forward declarations |
| BooleanOption.hh | Program boolean option class |
| BooleanVectorOption.cc | Auto-generated serialization template functions |
| BooleanVectorOption.fwd.hh | Utility::options::BooleanVectorOption forward declarations |
| BooleanVectorOption.hh | Program boolean vector option class |
| FileOption.cc | Auto-generated serialization template functions |
| FileOption.fwd.hh | Utility::options::FileOption forward declarations |
| FileOption.hh | Program file option class |
| FileVectorOption.cc | Auto-generated serialization template functions |
| FileVectorOption.fwd.hh | Utility::options::FileVectorOption forward declarations |
| FileVectorOption.hh | Program file vector option class |
| IntegerOption.cc | Auto-generated serialization template functions |
| IntegerOption.fwd.hh | Utility::options::IntegerOption forward declarations |
| IntegerOption.hh | Program integer option class |
| IntegerVectorOption.cc | Auto-generated serialization template functions |
| IntegerVectorOption.fwd.hh | Utility::options::IntegerVectorOption forward declarations |
| IntegerVectorOption.hh | Program integer vector option class |
| mpi_stderr.cc | |
| mpi_stderr.hh | |
| Option.cc | Auto-generated serialization template functions |
| 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.cc | Auto-generated serialization template functions |
| PathOption.fwd.hh | Utility::options::PathOption forward declarations |
| PathOption.hh | Program path option class |
| PathVectorOption.cc | Auto-generated serialization template functions |
| PathVectorOption.fwd.hh | Utility::options::PathVectorOption forward declarations |
| PathVectorOption.hh | Program path vector option class |
| RealOption.cc | Auto-generated serialization template functions |
| RealOption.fwd.hh | Utility::options::RealOption forward declarations |
| RealOption.hh | Program real option class |
| RealVectorOption.cc | Auto-generated serialization template functions |
| 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.cc | Auto-generated serialization template functions |
| 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.cc | Auto-generated serialization template functions |
| StringOption.fwd.hh | Utility::options::StringOption forward declarations |
| StringOption.hh | Program string option class |
| StringVectorOption.cc | Auto-generated serialization template functions |
| 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.cc | Program vector-valued option interface 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 |
| memory.hh | |
| owning_ptr.hh | Owning smart pointer using boost header-only libraries |
| ► std | |
| access_ptr.hh | Non-owning access smart pointer |
| memory.hh | Header for boost make_shared |
| owning_ptr.hh | Owning smart pointer using C++11 |
| access_ptr.hh | Non-owning access smart pointer – dispatch class |
| deep_copy.hh | |
| memory.hh | Dispatch header for make_shared |
| owning_ptr.hh | Non-owning access smart pointer – dispatch 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 | |
| AutoBool.hh | Enum class that can be used for booleans with an automatic "let Rosetta decide" option |
| 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 |
| util.cc | Utility functions for schema generation |
| util.hh | Utility functions for schema generation |
| xml_schema_group_initialization.hh | Templated function for the initialization of xml schema groups designed to be used by factories that contain maps of pointers to WidgetCreators |
| 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 | Declaration of the classes used to define an XML Schema |
| XMLSchemaValidation.cc | Functions and classes needed to validate an XML file against a schema |
| XMLSchemaValidation.fwd.hh | Functions and classes needed to validate an XML file against a schema |
| XMLSchemaValidation.hh | Functions and classes needed to validate an XML file against a schema |
| ► thread | |
| backwards_thread_local.hh | File to provide backwards compatibility for the thread_local keyword |
| mutable_cache.hh | A key:value cache intended to be used for (threadsafe) mutable caching of values |
| ReadWriteMutex.cc | Classes to manage data that can be read by multiple threads and written to by only one thread |
| ReadWriteMutex.fwd.hh | |
| ReadWriteMutex.hh | Declaration of the ReadWriteMutex class |
| shared_thread_local_data.hh | SharedThreadLocalData class, - container for data that needs to instantiated as single, shared instance per-thread |
| shared_thread_local_data.impl.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 | |
| ► type_traits | |
| has_insertion_operator.fwd.hh | Implemention of type traits related to Rosetta types, forward declarations |
| has_insertion_operator.hh | |
| is_string_constructible.hh | Implemention of type traits related to Rosetta types, forward declarations |
| ► xsd_util | |
| util.cc | General utility functions for parsing an XSD without needing access to Rosetta's higher libraries. Useful for UI development |
| util.hh | General utility functions for parsing an XSD without needing access to Rosetta's higher libraries. Useful for UI development |
| assert.hh | |
| backtrace.cc | Instead of printing a backtrace inside of an assertion failure, throw an exception |
| backtrace.hh | Programmatic backtrace whenever you want it |
| 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 |
| crash_report.cc | |
| crash_report.hh | |
| 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 |
| cxx_versioning_macros.hh | Macros for using function attributes in a portable way |
| dating.cc | Definitions for utility functions involving calendar dates, not for finding new romantic partners |
| dating.hh | Declarations for utility functions involving calendar dates, not for finding new romantic partners |
| deep_copy_vector1.hh | A vector1 which does a deep copy of its contents |
| DenseBoolMap.hh | Provides a memory efficient way to store a large number of boolean values |
| 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 | |
| iterators.hh | Iterator utilities |
| json_utilities.cc | |
| json_utilities.hh | Bag of utility functions for nlohmann::json (the one at external/include/json.hpp) |
| 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.hh | Utility functions for std::maps |
| minmax.hh | |
| modulo.hh | Calculates modulo for integer, since C++ '' operator has weird behavior for negative numbers |
| 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 |
| small_vector1.hh | Boost::container::small_vector with 1-based indexing |
| sort.functions.hh | Functions related to sorting |
| sort_predicates.hh | Sort predicates for using std::pair in std::sort |
| static_database.cc | |
| static_database.hh | |
| stream_util.fwd.hh | Implemention of ostream operator << for various common types, forward declarations |
| 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 |
| strong_aliasing.hh | |
| sys_util.cc | All system functions in utility that have no other home |
| sys_util.hh | All system functions in utility that have no other home |
| utility.functions.hh | Numeric functions (to avoid dependency on numeric package) |
| VBWrapper.fwd.hh | A Base class for _______________________ |
| VBWrapper.hh | A class derived from VirtualBase for wrapping a primative |
| 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 |
| version.hh | |
| VirtualBase.fwd.hh | A Base class for virtual inheritance hierarchies |
| VirtualBase.hh | A Base class for virtual inheritance hierarchies |
| VirtualBase.srlz.cc | |
| VirtualBase.srlz.hh | Faux serialization routines for the VirtualBase base class |
1.9.1