Rosetta 3.3
File List
Here is a list of all files with brief descriptions:
doc/apps/pilot/make_table_of_pilot_apps.py
doc/developer/example_protocol.cc
doc/developer/jd2_example.cc
src/apps/benchmark/benchmark.cc
src/apps/benchmark/benchmark.hh
src/apps/benchmark/Design.bench.hh
src/apps/benchmark/Docking.bench.hhRun a performance benchmark of docking
src/apps/benchmark/init_util.hhInitialization subroutines for Benchmark
src/apps/benchmark/LigandDock.bench.hh
src/apps/benchmark/LigandDockScript.bench.hh
src/apps/benchmark/Minimizer.bench.hh
src/apps/benchmark/score.bench.hh
src/apps/benchmark/ShearMover.bench.hh
src/apps/benchmark/SmallMover.bench.hh
src/apps/benchmark/scientific/ddg_benchmark.cc
src/apps/benchmark/scientific/design_contrast_and_statistic.cc
src/apps/benchmark/scientific/rotamer_recovery.ccThis determines the percent of rotamers correctly predictied during a repack
src/apps/public/AbinitioRelax.cc
src/apps/public/backrub.ccRun backrub Monte Carlo
src/apps/public/cluster.cc
src/apps/public/combine_silent.ccSimple application for combining a number of silent-files into a single silent-file
src/apps/public/extract_pdbs.ccSimple application for extracting PDBs from a silent-file
src/apps/public/fragment_picker.cc
src/apps/public/idealize_jd2.cc
src/apps/public/relax.cc
src/apps/public/sequence_tolerance.ccApp for predicting the sequence tolerance of a structure or set of structures
src/apps/public/SymDock.cc
src/apps/public/analysis/InterfaceAnalyzer.ccQ&D protocol to run InterfaceAnalyzerMover as protocol
src/apps/public/analysis/score.cc
src/apps/public/analysis/score_jd2.cc
src/apps/public/antibody/antibody_mode.cc
src/apps/public/boinc/boinc_mac_app_icon.hh
src/apps/public/boinc/minirosetta.cc
src/apps/public/boinc/minirosetta_graphics.cc
src/apps/public/comparative_modeling/cluster_alns.cc
src/apps/public/comparative_modeling/fix_alignment_to_match_pdb.cc
src/apps/public/comparative_modeling/full_length_model.cc
src/apps/public/comparative_modeling/score_aln.cc
src/apps/public/comparative_modeling/score_aln2.cc
src/apps/public/comparative_modeling/super_aln.cc
src/apps/public/ddg/ddg_monomer.cc
src/apps/public/ddg/minimize_with_cst.cc
src/apps/public/design/fixbb.ccFixed backbone design. Can do side chain minimization after PackRotamers by using the flag -minimize_sidechains. This is SLOW
src/apps/public/design/mpi_msd.cc
src/apps/public/design/sequence_recovery.ccA protocol which outputs sequence recovery statistics ala the table in the "Native sequences are close to optimal" paper
src/apps/public/docking/docking_prepack_protocol.cc
src/apps/public/docking/docking_protocol.cc
src/apps/public/electron_density/loops_from_density.cc
src/apps/public/electron_density/mr_protocols.cc
src/apps/public/enzdes/CstfileToTheozymePDB.cc
src/apps/public/enzdes/enzyme_design.cc
src/apps/public/flexpep_docking/BuildPeptide.cc
src/apps/public/flexpep_docking/FlexPepDocking.cc
src/apps/public/interface_design/anchored_design/AnchoredDesign.ccAnchored Design protocol
src/apps/public/interface_design/anchored_design/AnchoredPDBCreator.ccAnchored Design pre-protocol to make its inputs
src/apps/public/interface_design/anchored_design/AnchorFinder.ccThis 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
src/apps/public/ligand_docking/arls.py
src/apps/public/ligand_docking/arls_impl.py
src/apps/public/ligand_docking/assign_charges.py
src/apps/public/ligand_docking/best_ifaceE.py
src/apps/public/ligand_docking/extract_atomtree_diffs.cc
src/apps/public/ligand_docking/get_scores.py
src/apps/public/ligand_docking/ligand_dock.cc
src/apps/public/ligand_docking/ligand_rpkmin.cc
src/apps/public/ligand_docking/pdb_to_molfile.py
src/apps/public/ligand_docking/prune_atdiff_top5pct.py
src/apps/public/loop_modeling/loopmodel.cc
src/apps/public/match/gen_apo_grids.ccSearch pocket and generate grids
src/apps/public/match/gen_lig_grids.ccGenerate matcher grids for a protein with a ligand
src/apps/public/match/match.cc
src/apps/public/membrane_abinitio/membrane_abinitio2.cc
src/apps/public/pepspec/pepspec.cc
src/apps/public/pepspec/pepspec_anchor_dock.cc
src/apps/public/rna/rna_database.cc
src/apps/public/rna/rna_denovo.cc
src/apps/public/rna/rna_design.cc
src/apps/public/rna/rna_extract.cc
src/apps/public/rosetta_scripts/revert_design_to_native.cc
src/apps/public/rosetta_scripts/rosetta_scripts.ccThe application file for rosetta_scripts, aka jd2_scripting or the parser
src/apps/public/rosettaDNA/rosettaDNA.ccRuns 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
src/apps/public/scenarios/ca_to_allatom.ccAn 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
src/apps/public/scenarios/FloppyTail.ccThis 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
src/apps/public/scenarios/UBQ_E2_thioester.ccThis application is a one-shot for modeling the thioester bond between UBQ and an E2
src/apps/public/symmetry/make_symmdef_file_denovo.py
src/basic/basic.cc
src/basic/basic.hh
src/basic/ComparingTracer.cc
src/basic/ComparingTracer.hhVersion of Tracer calss for to tracking down the source of an instability by compare output with file
src/basic/Emitter.ccLightweight class to ease writting YAML documents
src/basic/Emitter.hhLightweight class to ease writting YAML documents
src/basic/interpolate.cc
src/basic/interpolate.hh
src/basic/MemTracer.cc
src/basic/MemTracer.hh
src/basic/MetricValue.fwd.hh
src/basic/MetricValue.hh
src/basic/MetricValueIO.cc
src/basic/MetricValueIO.hh
src/basic/prof.cc
src/basic/prof.hh
src/basic/Tracer.cc
src/basic/Tracer.fwd.hh
src/basic/Tracer.hhTracer IO system
src/basic/TracerToFile.cc
src/basic/TracerToFile.hhClass for a tracer that writes all output to a file
src/basic/database/open.ccFunctions for opening database files
src/basic/database/open.hhFunctions for opening database files
src/basic/database/sql_utils.cc
src/basic/database/sql_utils.hh
src/basic/datacache/BasicDataCache.ccA DataCache storing objects derived from basic::datacache::CacheableData
src/basic/datacache/BasicDataCache.fwd.hhForward declaration for BasicDataCache
src/basic/datacache/BasicDataCache.hhA DataCache storing objects derived from basic::datacache::CacheableData
src/basic/datacache/CacheableData.fwd.hh
src/basic/datacache/CacheableData.hh
src/basic/datacache/CacheableString.fwd.hh
src/basic/datacache/CacheableString.hh
src/basic/datacache/CacheableStringFloatMap.fwd.hh
src/basic/datacache/CacheableStringFloatMap.hh
src/basic/datacache/CacheableStringMap.fwd.hh
src/basic/datacache/CacheableStringMap.hh
src/basic/datacache/DataCache.fwd.hhForward declaration for DataCache
src/basic/datacache/DataCache.hh
src/basic/datacache/DiagnosticData.fwd.hh
src/basic/datacache/DiagnosticData.hh
src/basic/options/after_opts.ccOption lookup functions emulating Rosetta++ equivalents for transitional use
src/basic/options/after_opts.hhOption lookup functions emulating Rosetta++ equivalents for transitional use
src/basic/options/all.fwd.hhBasic::options package forward declarations
src/basic/options/all.hhBasic::options package declarations
src/basic/options/option.ccProgram options global and initialization function
src/basic/options/option.cc.gen.hh
src/basic/options/option.cc.include.gen.hh
src/basic/options/option.hhProgram options global and initialization function
src/basic/options/option_macros.hh
src/basic/options/options.pyProgram options generation script that is run to generate the options
src/basic/options/options_class.pyProgram options generation script classes
src/basic/options/options_rosetta.pyProgram options generation script: Rosetta options encoding
src/basic/options/PyRosettaFunctions.cc
src/basic/options/PyRosettaFunctions.hhAdditional functions to set/get Options from PyRosetta
src/basic/options/util.cc
src/basic/options/util.hh
src/basic/options/keys/abinitio.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/abrelax.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/all.fwd.hhBasic::options package keys forward declarations
src/basic/options/keys/all.hhBasic::options package keys declarations
src/basic/options/keys/AnchoredDesign.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/antibody.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/archive.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/assembly.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/backrub.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/batch_relax.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/bbg.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/blivens.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/boinc.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/broker.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/canonical_sampling.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/casp.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/chemical.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/chrisk.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/chunk.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/cluster.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/cm.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/constraints.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/corrections.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/crossmatch.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/ddg.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/DenovoProteinDesign.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/dna.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/docking.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/DomainAssembly.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/dwkulp.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/edensity.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/enzdes.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/evaluation.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/evolution.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fast_loops.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/features.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/filters.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fingerprint.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fldsgn.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/flexpack.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/flexPepDocking.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/flxbb.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fold_and_dock.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fold_cst.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/fold_from_loops.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/frags.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/holes.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/hotspot.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/in.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/inout.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/james.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/jd2.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/jumps.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/krassk.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/lh.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/loopfcst.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/LoopModel.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/loops.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/lp.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/match.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/matdes.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/mc.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/membrane.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/mike.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/MM.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/MonteCarlo.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/motifs.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/ms.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/murphp.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/mysql.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/nonlocal.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/optE.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/optimization.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/OptionKeys.cc.gen0.hh
src/basic/options/keys/OptionKeys.cc.gen1.hh
src/basic/options/keys/OptionKeys.cc.gen2.hh
src/basic/options/keys/OptionKeys.cc.gen3.hh
src/basic/options/keys/OptionKeys.hhBasic::options::OptionKeys collection
src/basic/options/keys/OptionKeys0.cc
src/basic/options/keys/OptionKeys1.cc
src/basic/options/keys/OptionKeys2.cc
src/basic/options/keys/OptionKeys3.cc
src/basic/options/keys/orbitals.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/out.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/packing.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/packstat.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/parser.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/patterson.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/PCS.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/pepspec.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/pH.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/phil.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/pocket_grid.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/pose_metrics.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/qsar.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/RBSegmentRelax.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/rdc.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/relax.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/remodel.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/resample.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/rescore.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/residues.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/rna.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/robert.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/rot_anl.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/run.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/score.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/smhybrid.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/SSrbrelax.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/symmetry.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/templates.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/threadsc.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/ufv.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/options/keys/wum.OptionKeys.gen.hhBasic::options::OptionKeys collection
src/basic/svd/SVD_Solver.ccSVD solver class `
src/basic/svd/SVD_Solver.fwd.hhSVD solver class
src/basic/svd/SVD_Solver.hhSVD solver class
src/numeric/agglomerative_hierarchical_clustering.cc
src/numeric/agglomerative_hierarchical_clustering.hhHierarchical clustering utilities
src/numeric/all.fwd.hhNumeric package forward declarations
src/numeric/all.hhNumeric package declarations
src/numeric/angle.functions.hhTrigonometric functions
src/numeric/BodyPosition.fwd.hhNumeric::BodyPosition forward declarations
src/numeric/BodyPosition.hhRigid body 3-D position/transform
src/numeric/BodyPosition.io.hhBodyPosition input/output functions
src/numeric/ClusteringTreeNode.cc
src/numeric/ClusteringTreeNode.fwd.hh
src/numeric/ClusteringTreeNode.hhNode of a hierarchical clustering tree
src/numeric/constants.ccCommon numeric constants in varying precisions
src/numeric/constants.hhCommon numeric constants in varying precisions
src/numeric/conversions.hhConversions between degrees and radians
src/numeric/gmx_functions.cc
src/numeric/gmx_functions.hh
src/numeric/HomogeneousTransform.fwd.hhFast coordinate frame container
src/numeric/HomogeneousTransform.hhFast coordinate frame container
src/numeric/IntervalSet.fwd.hhIntervalSet forward declarations
src/numeric/IntervalSet.hhDefinition and implementation of IntervalSet class
src/numeric/io.hhNumeric package i/o functions
src/numeric/IOTraits.hhNumerics input/output type traits
src/numeric/MathMatrix.hh
src/numeric/MathMatrix_operations.hh
src/numeric/MathVector.hh
src/numeric/MathVector_operations.hh
src/numeric/MultiDimensionalHistogram.ccClass for accumulating a histogram of one or more numeric variables
src/numeric/MultiDimensionalHistogram.fwd.hhForward declarations for class MultiDimensionalHistogram
src/numeric/MultiDimensionalHistogram.hhClass for accumulating a histogram of one or more numeric variables
src/numeric/numeric.functions.hhNumeric functions
src/numeric/NumericTraits.hhNumeric type traits
src/numeric/Quaternion.fwd.hhNumeric::Quaternion forward declarations
src/numeric/Quaternion.hhUnit quaternion 3-D orientation representation
src/numeric/Quaternion.io.hhQuaternion input/output functions
src/numeric/random.functions.ccRandom number functions
src/numeric/random.functions.hhRandom number functions
src/numeric/sphericalVector.fwd.hhNumeric::sphericalVector forward declarations
src/numeric/sphericalVector.hhFast spherical-coordinate numeric vector
src/numeric/statistics.functions.cc
src/numeric/statistics.functions.hhCollection of various functions to compute statistics. feel free to add your own
src/numeric/trig.functions.hhTrigonometric functions
src/numeric/types.hhRosetta project type declarations. Should be kept updated with core/types.hh. This exists because numeric can't depend on files in core
src/numeric/util.ccSmall bundle of utilities for dealing with numbers
src/numeric/util.hhSmall bundle of utilities for dealing with numbers
src/numeric/xyz.functions.fwd.hhNumeric::xyzVector and numeric::xyzMatrix functions forward declarations
src/numeric/xyz.functions.hhXyzVector and xyzMatrix functions
src/numeric/xyz.io.hhXyzTriple, xyzVector, and xyzMatrix i/o functions
src/numeric/xyzMatrix.fwd.hhNumeric::xyzMatrix forward declarations
src/numeric/xyzMatrix.hhFast 3x3 matrix
src/numeric/xyzMatrix.io.hhXyzMatrix input/output functions
src/numeric/xyzTriple.fwd.hhNumeric::xyzTriple forward declarations
src/numeric/xyzTriple.hhFast (x,y,z)-coordinate vector container
src/numeric/xyzTriple.io.hhXyzTriple input/output functions
src/numeric/xyzVector.fwd.hhNumeric::xyzVector forward declarations
src/numeric/xyzVector.hhFast (x,y,z)-coordinate numeric vector
src/numeric/xyzVector.io.hhXyzVector input/output functions
src/numeric/deriv/angle_deriv.hhInline function for computing f1/f2 derivatives for a function of a distance
src/numeric/deriv/dihedral_deriv.hhInline function for computing f1/f2 derivatives for a function of a dihedral
src/numeric/deriv/distance_deriv.hhInline function for computing f1/f2 derivatives for a function of an angle
src/numeric/fourier/FFT.ccWrapper class performing ffts on 1,2, and 3 dimensional farrays
src/numeric/fourier/FFT.hh
src/numeric/fourier/kiss_fft.cc
src/numeric/fourier/kiss_fft.hh
src/numeric/fourier/kiss_fft_state.cc
src/numeric/fourier/kiss_fft_state.hh
src/numeric/geometry/BoundingBox.fwd.hhNumeric::geometry::BoundingBox forward declaration
src/numeric/geometry/BoundingBox.hh3d axis aligned bounding box
src/numeric/histograms/OneDHistogram.hh
src/numeric/histograms/TwoDHistogram.hh
src/numeric/internal/ColPointers.hh3x3 matrix column pointers wrapper class
src/numeric/internal/ColsPointer.hhContiguous column-ordered 3x3 matrix pointer wrapper class
src/numeric/internal/ColVectors.hh3x3 matrix column vectors wrapper class
src/numeric/internal/RowPointers.hh3x3 matrix row pointers wrapper class
src/numeric/internal/RowsPointer.hhContiguous row-ordered 3x3 matrix pointer wrapper class
src/numeric/internal/RowVectors.hh3x3 matrix row vectors wrapper class
src/numeric/interpolation/all.hhNumeric::interpolation package declarations
src/numeric/interpolation/Histogram.fwd.hh
src/numeric/interpolation/Histogram.hhA class for storing histogram data
src/numeric/interpolation/interpolation.hhInterpolation functions
src/numeric/interpolation/util.cc
src/numeric/interpolation/util.hh
src/numeric/interpolation/full/interpolation.hhInterpolation over points at full bin width multiples
src/numeric/interpolation/periodic_range/full/interpolation.hhInterpolation over periodic range points at full bin width multiples
src/numeric/interpolation/periodic_range/half/interpolation.hhInterpolation over periodic range points at half bin width multiples
src/numeric/interpolation/periodic_range/periodic_value/full/interpolation.hhInterpolation of periodic values over periodic range points at full bin width multiples
src/numeric/interpolation/periodic_range/periodic_value/half/interpolation.hhInterpolation of periodic values over periodic range points at half bin width multiples
src/numeric/interpolation/spline/Bicubic_spline.cc
src/numeric/interpolation/spline/Bicubic_spline.fwd.hh
src/numeric/interpolation/spline/Bicubic_spline.hh
src/numeric/interpolation/spline/CompoundInterpolator.ccInterpolation with cubic splines
src/numeric/interpolation/spline/CompoundInterpolator.hhInterpolation with cubic splines
src/numeric/interpolation/spline/Cubic_spline.cc
src/numeric/interpolation/spline/Cubic_spline.fwd.hh
src/numeric/interpolation/spline/Cubic_spline.hh
src/numeric/interpolation/spline/Interpolator.hh
src/numeric/interpolation/spline/SimpleInterpolator.ccInterpolation with cubic splines
src/numeric/interpolation/spline/SimpleInterpolator.hhInterpolation with cubic splines
src/numeric/interpolation/spline/spline_functions.cc
src/numeric/interpolation/spline/spline_functions.hh
src/numeric/interpolation/spline/SplineGenerator.ccInterpolation with cubic splines
src/numeric/interpolation/spline/SplineGenerator.hh
src/numeric/kdtree/calc_distance.cc
src/numeric/kdtree/calc_distance.hh
src/numeric/kdtree/constants.hhConstants used for kd-tree implementation
src/numeric/kdtree/construct_kdtree.cc
src/numeric/kdtree/construct_kdtree.hh
src/numeric/kdtree/HyperRectangle.cc
src/numeric/kdtree/HyperRectangle.fwd.hh
src/numeric/kdtree/HyperRectangle.hh
src/numeric/kdtree/KDNode.ccImplementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information
src/numeric/kdtree/KDNode.fwd.hhForward declaration for KDNode class
src/numeric/kdtree/KDNode.hhImplementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information
src/numeric/kdtree/KDPoint.cc
src/numeric/kdtree/KDPoint.fwd.hhForward declaration for KDPoint class
src/numeric/kdtree/KDPoint.hhUtility functions for kd-tree. See kdtree.hh for more information
src/numeric/kdtree/KDPointList.ccDefinition for a class that keeps track of the best N KDPoint objects by distance
src/numeric/kdtree/KDPointList.hhDefinition for a class that keeps track of the best N KDPoint objects by distance
src/numeric/kdtree/KDTree.cc
src/numeric/kdtree/KDTree.fwd.hhForward declaration for KDTree class
src/numeric/kdtree/KDTree.hhImplementation of a tree in a kd-tree. See numeric/kdtree/kdtree.hh for more information
src/numeric/kdtree/nearest_neighbors.cc
src/numeric/kdtree/nearest_neighbors.hhUtility functions for kd-tree. See kdtree.hh for more information
src/numeric/kdtree/util.cc
src/numeric/kdtree/util.hh
src/numeric/kdtree/WrappedChar.hh
src/numeric/kdtree/WrappedPrimitive.hh
src/numeric/kdtree/WrappedReal.hhSilly little class to wrap a numeric::Real in an OP
src/numeric/kdtree/WrappedType.hh
src/numeric/model_quality/maxsub.ccAb-initio fragment assembly protocol for proteins
src/numeric/model_quality/maxsub.hh
src/numeric/model_quality/rms.cc
src/numeric/model_quality/rms.hhRMS functions imported from rosetta++
src/numeric/model_quality/RmsData.cc
src/numeric/model_quality/RmsData.hh
src/numeric/model_quality/util.hhUtilities for calculated model-quality statistics
src/numeric/random/mt19937.hhMersenne Twister 19937 random number generator
src/numeric/random/random.ccRandom number generator system
src/numeric/random/random.fwd.hhRandom number generator system
src/numeric/random/random.hhRandom number generator system
src/numeric/random/random_permutation.hhReorder the elements in a vector using a RNG object
src/numeric/random/reservoir_sample.hhRandomly select the best N elements from a stream of elements using one pass over a dataset
src/numeric/random/uniform.fwd.hh
src/numeric/random/uniform.hhUniform random number generator
src/numeric/random/WeightedSampler.ccClass to generate random positive integers using a given set of weights
src/numeric/random/WeightedSampler.fwd.hhForward declarations for class WeightedSampler
src/numeric/random/WeightedSampler.hhClass to generate random positive integers using a given set of weights
src/ObjexxFCL/array.iterator.hh
src/ObjexxFCL/byte.fwd.hh
src/ObjexxFCL/byte.hh
src/ObjexxFCL/CArray.fwd.hh
src/ObjexxFCL/CArray.hh
src/ObjexxFCL/CArray.io.hh
src/ObjexxFCL/CArrayP.fwd.hh
src/ObjexxFCL/CArrayP.hh
src/ObjexxFCL/CArrayP.io.hh
src/ObjexxFCL/char.functions.cc
src/ObjexxFCL/char.functions.hh
src/ObjexxFCL/Chunk.hh
src/ObjexxFCL/ChunkExponent.hh
src/ObjexxFCL/ChunkVector.fwd.hh
src/ObjexxFCL/ChunkVector.hh
src/ObjexxFCL/ChunkVector.io.hh
src/ObjexxFCL/Cstring.cc
src/ObjexxFCL/Cstring.fwd.hh
src/ObjexxFCL/Cstring.hh
src/ObjexxFCL/Dimension.cc
src/ObjexxFCL/Dimension.fwd.hh
src/ObjexxFCL/Dimension.hh
src/ObjexxFCL/DimensionExpression.cc
src/ObjexxFCL/DimensionExpression.hh
src/ObjexxFCL/DimensionExpressionCon.hh
src/ObjexxFCL/DimensionExpressionCube.hh
src/ObjexxFCL/DimensionExpressionDiv.hh
src/ObjexxFCL/DimensionExpressionMax.hh
src/ObjexxFCL/DimensionExpressionMin.hh
src/ObjexxFCL/DimensionExpressionMul.hh
src/ObjexxFCL/DimensionExpressionPow.hh
src/ObjexxFCL/DimensionExpressionRef.cc
src/ObjexxFCL/DimensionExpressionRef.hh
src/ObjexxFCL/DimensionExpressions.hh
src/ObjexxFCL/DimensionExpressionSquare.hh
src/ObjexxFCL/DimensionExpressionSub.hh
src/ObjexxFCL/DimensionExpressionSum.hh
src/ObjexxFCL/DynamicIndexRange.cc
src/ObjexxFCL/DynamicIndexRange.fwd.hh
src/ObjexxFCL/DynamicIndexRange.hh
src/ObjexxFCL/FArray.all.fwd.hh
src/ObjexxFCL/FArray.all.hh
src/ObjexxFCL/FArray.fwd.hh
src/ObjexxFCL/FArray.hh
src/ObjexxFCL/FArray.io.hh
src/ObjexxFCL/FArray1.all.fwd.hh
src/ObjexxFCL/FArray1.all.hh
src/ObjexxFCL/FArray1.fwd.hh
src/ObjexxFCL/FArray1.hh
src/ObjexxFCL/FArray1.io.hh
src/ObjexxFCL/FArray1A.fwd.hh
src/ObjexxFCL/FArray1A.hh
src/ObjexxFCL/FArray1D.fwd.hh
src/ObjexxFCL/FArray1D.hh
src/ObjexxFCL/FArray1P.fwd.hh
src/ObjexxFCL/FArray1P.hh
src/ObjexxFCL/FArray2.all.fwd.hh
src/ObjexxFCL/FArray2.all.hh
src/ObjexxFCL/FArray2.fwd.hh
src/ObjexxFCL/FArray2.hh
src/ObjexxFCL/FArray2.io.hh
src/ObjexxFCL/FArray2A.fwd.hh
src/ObjexxFCL/FArray2A.hh
src/ObjexxFCL/FArray2D.fwd.hh
src/ObjexxFCL/FArray2D.hh
src/ObjexxFCL/FArray2P.fwd.hh
src/ObjexxFCL/FArray2P.hh
src/ObjexxFCL/FArray3.all.fwd.hh
src/ObjexxFCL/FArray3.all.hh
src/ObjexxFCL/FArray3.fwd.hh
src/ObjexxFCL/FArray3.hh
src/ObjexxFCL/FArray3.io.hh
src/ObjexxFCL/FArray3A.fwd.hh
src/ObjexxFCL/FArray3A.hh
src/ObjexxFCL/FArray3D.fwd.hh
src/ObjexxFCL/FArray3D.hh
src/ObjexxFCL/FArray3P.fwd.hh
src/ObjexxFCL/FArray3P.hh
src/ObjexxFCL/FArray4.all.fwd.hh
src/ObjexxFCL/FArray4.all.hh
src/ObjexxFCL/FArray4.fwd.hh
src/ObjexxFCL/FArray4.hh
src/ObjexxFCL/FArray4.io.hh
src/ObjexxFCL/FArray4A.fwd.hh
src/ObjexxFCL/FArray4A.hh
src/ObjexxFCL/FArray4D.fwd.hh
src/ObjexxFCL/FArray4D.hh
src/ObjexxFCL/FArray4P.fwd.hh
src/ObjexxFCL/FArray4P.hh
src/ObjexxFCL/FArray5.all.fwd.hh
src/ObjexxFCL/FArray5.all.hh
src/ObjexxFCL/FArray5.fwd.hh
src/ObjexxFCL/FArray5.hh
src/ObjexxFCL/FArray5.io.hh
src/ObjexxFCL/FArray5A.fwd.hh
src/ObjexxFCL/FArray5A.hh
src/ObjexxFCL/FArray5D.fwd.hh
src/ObjexxFCL/FArray5D.hh
src/ObjexxFCL/FArray5P.fwd.hh
src/ObjexxFCL/FArray5P.hh
src/ObjexxFCL/FArray6.all.fwd.hh
src/ObjexxFCL/FArray6.all.hh
src/ObjexxFCL/FArray6.fwd.hh
src/ObjexxFCL/FArray6.hh
src/ObjexxFCL/FArray6.io.hh
src/ObjexxFCL/FArray6A.fwd.hh
src/ObjexxFCL/FArray6A.hh
src/ObjexxFCL/FArray6D.fwd.hh
src/ObjexxFCL/FArray6D.hh
src/ObjexxFCL/FArray6P.fwd.hh
src/ObjexxFCL/FArray6P.hh
src/ObjexxFCL/FArrayInitializer.fwd.hh
src/ObjexxFCL/FArrayInitializer.hh
src/ObjexxFCL/FArraySection.fwd.hh
src/ObjexxFCL/FArraySection.hh
src/ObjexxFCL/FArrayTraits.fwd.hh
src/ObjexxFCL/FArrayTraits.hh
src/ObjexxFCL/floops.hh
src/ObjexxFCL/Fmath.hh
src/ObjexxFCL/format.cc
src/ObjexxFCL/format.hh
src/ObjexxFCL/Fstring.cc
src/ObjexxFCL/Fstring.fwd.hh
src/ObjexxFCL/Fstring.hh
src/ObjexxFCL/IndexRange.cc
src/ObjexxFCL/IndexRange.fwd.hh
src/ObjexxFCL/IndexRange.hh
src/ObjexxFCL/InitializerSentinel.hh
src/ObjexxFCL/KeyFArray1D.fwd.hh
src/ObjexxFCL/KeyFArray1D.hh
src/ObjexxFCL/KeyFArray2D.fwd.hh
src/ObjexxFCL/KeyFArray2D.hh
src/ObjexxFCL/KeyFArray3D.fwd.hh
src/ObjexxFCL/KeyFArray3D.hh
src/ObjexxFCL/KeyFArray4D.fwd.hh
src/ObjexxFCL/KeyFArray4D.hh
src/ObjexxFCL/KeyFArray5D.fwd.hh
src/ObjexxFCL/KeyFArray5D.hh
src/ObjexxFCL/KeyFArray6D.fwd.hh
src/ObjexxFCL/KeyFArray6D.hh
src/ObjexxFCL/ObjexxFCL.2-3.py
src/ObjexxFCL/ObjexxFCL.fwd.hh
src/ObjexxFCL/ObjexxFCL.hh
src/ObjexxFCL/ObjexxFCL.Project.hh
src/ObjexxFCL/Observer.cc
src/ObjexxFCL/Observer.fwd.hh
src/ObjexxFCL/Observer.hh
src/ObjexxFCL/ObserverGraph.cc
src/ObjexxFCL/ObserverGraph.hh
src/ObjexxFCL/ObserverMediator.cc
src/ObjexxFCL/ObserverMediator.hh
src/ObjexxFCL/ObserverMulti.cc
src/ObjexxFCL/ObserverMulti.hh
src/ObjexxFCL/ObserverSingle.hh
src/ObjexxFCL/proxy_const_assert.hh
src/ObjexxFCL/ProxySentinel.hh
src/ObjexxFCL/rvalue_cast.hh
src/ObjexxFCL/sbyte.fwd.hh
src/ObjexxFCL/sbyte.hh
src/ObjexxFCL/SetWrapper.fwd.hh
src/ObjexxFCL/SetWrapper.hh
src/ObjexxFCL/Star.cc
src/ObjexxFCL/Star.fwd.hh
src/ObjexxFCL/Star.hh
src/ObjexxFCL/StaticIndexRange.fwd.hh
src/ObjexxFCL/StaticIndexRange.hh
src/ObjexxFCL/string.functions.cc
src/ObjexxFCL/string.functions.hh
src/ObjexxFCL/Time_Date.cc
src/ObjexxFCL/Time_Date.hh
src/ObjexxFCL/TypeTraits.hh
src/ObjexxFCL/ubyte.fwd.hh
src/ObjexxFCL/ubyte.hh
src/platform/cygwin/platform/types.hh
src/platform/linux/GL/freeglut.h
src/platform/linux/GL/freeglut_ext.h
src/platform/linux/GL/freeglut_std.h
src/platform/linux/GL/glut.h
src/platform/linux/platform/types.hhPlatform-specific types for Linux
src/platform/macos/platform/types.hhPlatform-specific types for MacOS 10.4 on 32-bit PPC with GCC
src/platform/windows/32/gcc/platform/types.hhPlatform-specific types for 32-bit Windows with GCC
src/platform/windows/32/icc/platform/types.hhPlatform-specific types for 32-bit Windows with Intel C++
src/platform/windows/32/msvc/platform/types.hhPlatform-specific types for 32-bit Windows with MS VC++
src/platform/windows/32/platform/types.hhPlatform-specific types for 32-bit Windows
src/platform/windows/64/gcc/platform/types.hhPlatform-specific types for 64-bit Windows with GCC
src/platform/windows/64/icc/platform/types.hhPlatform-specific types for 64-bit Windows with Intel C++
src/platform/windows/64/msvc/platform/types.hhPlatform-specific types for 64-bit Windows with MS VC++
src/platform/windows/64/platform/types.hhPlatform-specific types for 64-bit Windows
src/python/apps/pilot/colin/backrub.py
src/python/apps/pilot/colin/fork_example.py
src/python/apps/public/amino_acids.py
src/python/apps/public/color_pdb.py
src/python/apps/public/color_pdb_byatom.py
src/python/apps/public/get_pdb.py
src/python/apps/public/molfile_to_params.py
src/python/apps/public/parallel.py
src/python/apps/public/pdb2fasta.py
src/python/apps/public/sd.py
src/python/apps/public/rmsd_score_pymol_plotter/rmsd_score_pymol_plotter.py
src/python/bindings/BuildBindings.py
src/python/bindings/docking.py
src/python/bindings/exclude.pyFunctions to exclude varios elements from Python buidings
src/python/bindings/loops.py
src/python/bindings/loops_kic.py
src/python/bindings/NetLink.py
src/python/bindings/PyMOL_demo.py
src/python/bindings/PyMOLPyRosettaServer.py
src/python/bindings/PyRosetta-PyMol.py
src/python/bindings/SetLibPaths.py
src/python/bindings/TestBindings.pyRun bindings test scrips
src/python/bindings/src/__init__.py
src/python/bindings/src/core/_core__by_hand.cc
src/python/bindings/src/core/chemical/orbitals/_orbitals__by_hand.cc
src/python/bindings/src/core/import_pose/_import_pose__by_hand.c
src/python/bindings/src/core/io/__init__.py
src/python/bindings/src/core/pose/_pose__by_hand.cc
src/python/bindings/src/core/scoring/_scoring__by_hand.cc
src/python/bindings/src/core/scoring/constraints/_constraints__by_hand.cc
src/python/bindings/src/numeric/_numeric__by_hand.cc
src/python/bindings/src/protocols/__init__.py
src/python/bindings/src/protocols/abinitio/_abinitio__by_hand.cc
src/python/bindings/src/protocols/jobdist/_jobdist__by_hand.cc
src/python/bindings/src/protocols/moves/_moves__by_hand.cc
src/python/bindings/src/utility/_utility__by_hand.cc
src/python/bindings/test/__init__.py
src/python/bindings/test/T000_Imports.py
src/python/bindings/test/T005_Bindings.py
src/python/bindings/test/T010_LoadPDB.py
src/python/bindings/test/T100_Basic.py
src/python/bindings/test/T200_Scoring.py
src/python/bindings/test/T400_Refinement.py
src/python/bindings/test/T500_Packing.py
src/python/bindings/test/T600_Docking.py
src/python/bindings/test/T650_LoopsKIC.py
src/python/bindings/test/T660_LoopBuilding.py
src/python/bindings/test/T700_FoldTree.py
src/python/bindings/test/T800_ClassicRelax.py
src/python/bindings/test/T850_SubClassing.py
src/python/bindings/test/T900_Other.py
src/python/bindings/tools/__init__.py
src/python/bindings/tools/CppParser.pyParse C++ code and wrap it in Python
src/python/bindings/tools/dox_extract.pyExtract Doxygen comments from C++ files
src/python/bindings/tools/doxygen.pyExtract Doxygen comments from C++ files
src/python/bindings/tools/DoxygenExtractorPyPP.py
src/python/rosetta_py/__init__.py
src/python/rosetta_py/io/__init__.py
src/python/rosetta_py/io/mdl_molfile.py
src/python/rosetta_py/io/pdb.py
src/python/rosetta_py/utility/__init__.py
src/python/rosetta_py/utility/ForkManager.py
src/python/rosetta_py/utility/r3.py
src/python/rosetta_py/utility/rankorder.py
src/utility/all.fwd.hhUtility package forward declarations
src/utility/all.hhUtility package declarations
src/utility/assert.hh
src/utility/basic_sys_util.ccAll system functions in utility that have no other home
src/utility/basic_sys_util.hhAll system functions in utility that have no other home
src/utility/BitSet.fwd.hhUtility::BitSet forward declarations
src/utility/BitSet.hhSimple bit set
src/utility/BitVector.fwd.hhUtility::BitVector forward declarations
src/utility/BitVector.hhSimple bit vector
src/utility/Bound.fwd.hhUtility::Bound forward declarations
src/utility/Bound.hhBound value class
src/utility/DereferenceIterator.hhClass 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() );
src/utility/down_cast.hhFast polymorphic down-casting functions
src/utility/exit.ccProgram exit functions and macros
src/utility/exit.hhProgram exit functions and macros
src/utility/fix_boinc_read.hh
src/utility/fixedsizearray1.fwd.hh
src/utility/fixedsizearray1.hh
src/utility/FixedSizeLexicographicalIterator.fwd.hh
src/utility/FixedSizeLexicographicalIterator.hhClass 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
src/utility/FixedSizeLexicographicalIterator.tmpl.hh
src/utility/heap.ccClass definition for a heap object based on Charlie Strauss's heap code ported over from rosetta++
src/utility/heap.fwd.hhForward class definition of class heap
src/utility/heap.hhClass 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
src/utility/in_place_list.fwd.hh
src/utility/in_place_list.hhDoubly linked list where elements are shuffled in place
src/utility/IndirectSorter.hhIndirect sort : sorts a container with some data without altering it
src/utility/inline_file_provider.cc
src/utility/inline_file_provider.hh
src/utility/integer_mapping.ccA set of useful classes to map between two enumerations. So far, only a subset mapping is implemented
src/utility/integer_mapping.fwd.hh
src/utility/integer_mapping.hhA set of useful classes to map between two enumerations. So far, only a subset mapping is implemented
src/utility/LexicographicalIterator.cc
src/utility/LexicographicalIterator.fwd.hh
src/utility/LexicographicalIterator.hhClass 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
src/utility/make_static_database.py
src/utility/minmax.hh
src/utility/mpi_util.cc
src/utility/mpi_util.hh
src/utility/OrderedTuple.fwd.hhForward declaration of OrderedTuple class
src/utility/OrderedTuple.hhClass for compairing/sorting data where sort-precidence is in descending order from begin() to end()
src/utility/PeriodicSplineReader.fwd.hhUtility::PeriodicSplineReader forward declarations
src/utility/PeriodicSplineReader.hhClass for reading in Splines and Calculating values of a function, first order derivatives
src/utility/PyAssert.hh
src/utility/PyHelper.hh
src/utility/random.functions.hhRandom number generation functions
src/utility/Show.hhUniformed printing functionality for data types
src/utility/sort_predicates.hh
src/utility/static_database.hh
src/utility/stream_util.hh
src/utility/string_util.ccSome std::string helper functions
src/utility/string_util.hhSome std::string helper functions
src/utility/TopScoreSelector.fwd.hhClass for keeping the N top-scoring objects
src/utility/TopScoreSelector.hhClass for keeping the N top-scoring objects
src/utility/utility.functions.hhNumeric functions (to avoid dependency on numeric package)
src/utility/vector0.fwd.hhUtility::vector0 forward declarations
src/utility/vector0.hhVector0: std::vector with assert-checked bounds
src/utility/vector0_bool.hhVector0: std::vector with assert-checked bounds: bool specialization
src/utility/vector1.functions.hhSome useful functions for vector1 that I'm tired of rewriting
src/utility/vector1.fwd.hhUtility::vector1 forward declarations
src/utility/vector1.hhVector1: std::vector with 1-based indexing
src/utility/vector1_bool.hhVector1: std::vector with 1-based indexing: bool specialization
src/utility/vectorL.fwd.hhUtility::vectorL forward declarations
src/utility/vectorL.hhVectorL: std::vector with L-based indexing
src/utility/vectorL_bool.hhVectorL: std::vector with L-based indexing: bool specialization
src/utility/vectorL_Selector.hhVectorL lower index selectors
src/utility/boinc/boinc_util.cc
src/utility/boinc/boinc_util.hhWrappers to make BOINC work
src/utility/excn/Exceptions.cc
src/utility/excn/Exceptions.hh
src/utility/excn/EXCN_Base.hh
src/utility/factory/Factory.fwd.hhUtility::factory::Factory forward declarations
src/utility/factory/Factory.hhPluggable factory
src/utility/factory/Registrant.fwd.hhUtility::factory::Registrant forward declarations
src/utility/factory/Registrant.hhFactory registrant
src/utility/factory/WidgetFactory.fwd.hhWidgetFactory forward declaration
src/utility/factory/WidgetFactory.hhWidgetFactory base class for load-time registration of WidgetCreators to the WidgetFactory
src/utility/factory/WidgetRegistrator.hhWidgetRegistrator class which registers WidgetCreator classes at load time
src/utility/file/file_sys_util.ccPlatform independent operations on files (except I/O)
src/utility/file/file_sys_util.hhPlatform independent operations on files (except I/O)
src/utility/file/FileName.cc
src/utility/file/FileName.fwd.hhUtility::file::FileName forward declarations
src/utility/file/FileName.hhFile name class supporting Windows and UN*X/Linux format names
src/utility/file/gzip_util.ccGzip utility functions
src/utility/file/gzip_util.hhGzip utility functions
src/utility/file/PathName.cc
src/utility/file/PathName.fwd.hhUtility::file::PathName forward declarations
src/utility/file/PathName.hhPath name class supporting Windows and UN*X/Linux format names
src/utility/io/all.fwd.hhUtility::io package forward declarations
src/utility/io/all.hhUtility::io package declarations
src/utility/io/icstream.ccInput channel stream wrapper base class,
src/utility/io/icstream.fwd.hhUtility::io::icstream forward declarations
src/utility/io/icstream.hhInput channel stream wrapper class
src/utility/io/irstream.fwd.hhUtility::io::irstream forward declarations
src/utility/io/irstream.hhInput stream wrapper abstract base class
src/utility/io/izstream.ccInput file stream wrapper for uncompressed and compressed files
src/utility/io/izstream.fwd.hhUtility::io::izstream forward declarations
src/utility/io/izstream.hhInput file stream wrapper for uncompressed and compressed files
src/utility/io/mpistream.hh
src/utility/io/mpistream.ipp
src/utility/io/ocstream.ccOutput channel stream wrapper base class,
src/utility/io/ocstream.fwd.hhUtility::io::ocstream forward declarations
src/utility/io/ocstream.hhOutput channel stream wrapper class
src/utility/io/orstream.fwd.hhUtility::io::orstream forward declarations
src/utility/io/orstream.hhOutput stream wrapper abstract base class
src/utility/io/ozstream.ccOutput file stream wrapper for uncompressed and compressed files
src/utility/io/ozstream.fwd.hhUtility::io::ozstream forward declarations
src/utility/io/ozstream.hhOutput file stream wrapper for uncompressed and compressed files
src/utility/io/util.hh
src/utility/io/zipstream.hppAltered zipstream library header
src/utility/io/zipstream.ippAltered zipstream library implementation
src/utility/keys/all.fwd.hhUtility::keys package forward declarations
src/utility/keys/all.hhUtility::keys package declarations
src/utility/keys/AutoKey.fwd.hhUtility::keys::AutoKey forward declarations
src/utility/keys/AutoKey.hhAutomatic hidden index key abstract base class
src/utility/keys/ClassKeyMap.fwd.hhUtility::keys::ClassKeyMap forward declarations
src/utility/keys/ClassKeyMap.hhKeyed-access map with key subset map for each client class
src/utility/keys/ClassKeyVector.fwd.hhUtility::keys::ClassKeyVector forward declarations
src/utility/keys/ClassKeyVector.hhKeyed-access vector with key subset map for each client class
src/utility/keys/Key.fwd.hhUtility::keys::Key forward declarations
src/utility/keys/Key.hhHidden index key interface class
src/utility/keys/Key2Tuple.fwd.hhUtility::keys::Key2Tuple forward declarations
src/utility/keys/Key2Tuple.hh2-tuple meta-key
src/utility/keys/Key2Vector.fwd.hhUtility::keys::Key2Vector forward declarations
src/utility/keys/Key2Vector.hh2-key meta-key
src/utility/keys/Key3Tuple.fwd.hhUtility::keys::Key3Tuple forward declarations
src/utility/keys/Key3Tuple.hh3-tuple meta-key
src/utility/keys/Key3Vector.fwd.hhUtility::keys::Key3Vector forward declarations
src/utility/keys/Key3Vector.hh3-key meta-key
src/utility/keys/Key4Tuple.fwd.hhUtility::keys::Key4Tuple forward declarations
src/utility/keys/Key4Tuple.hh4-tuple meta-key
src/utility/keys/Key4Vector.fwd.hhUtility::keys::Key4Vector forward declarations
src/utility/keys/Key4Vector.hh4-key meta-key
src/utility/keys/KeyCount.fwd.hhUtility::keys::KeyCount forward declarations
src/utility/keys/KeyCount.hhKey counter functor
src/utility/keys/KeyLess.fwd.hhUtility::keys::KeyLess forward declarations
src/utility/keys/KeyLess.hhKey comparison functor template
src/utility/keys/KeyLookup.functors.hhUtility::keys::KeyLookup functor declarations
src/utility/keys/KeyLookup.functors.iiUtility::keys::KeyLookup functor declarations
src/utility/keys/KeyLookup.fwd.hhUtility::keys::KeyLookup forward declarations
src/utility/keys/KeyLookup.hhKey lookup map and collection and functors
src/utility/keys/KeyMapTraits.hhKeyMap traits class
src/utility/keys/KeySetTraits.hhKeySet traits class
src/utility/keys/KeyVector.fwd.hhUtility::keys::KeyVector forward declarations
src/utility/keys/KeyVector.hhKeyed-access vector
src/utility/keys/KeyVectorTraits.hhKeyVector traits class
src/utility/keys/NoClient.fwd.hhUtility::keys::NoClient forward declarations
src/utility/keys/NoClient.hhDefault key policy class when no client is needed to distinguish key type
src/utility/keys/SmallKeyMap.fwd.hhUtility::keys::SmallKeyMap forward declarations
src/utility/keys/SmallKeyMap.hhKeyed-access map with key subset map
src/utility/keys/SmallKeyVector.fwd.hhUtility::keys::SmallKeyVector forward declarations
src/utility/keys/SmallKeyVector.hhKeyed-access vector with key subset map
src/utility/keys/UserKey.fwd.hhUtility::keys::UserKey forward declarations
src/utility/keys/UserKey.hhUser-created hidden index key abstract base class
src/utility/keys/VariantKey.fwd.hhUtility::keys::VariantKey forward declarations
src/utility/keys/VariantKey.hhVariant key class
src/utility/options/all.fwd.hhUtility::options package forward declarations
src/utility/options/all.hhUtility::options package declarations
src/utility/options/AnyOption.fwd.hhUtility::options::AnyOption forward declarations
src/utility/options/AnyOption.hhProgram any scalar-valued option abstract base class
src/utility/options/AnyVectorOption.fwd.hhUtility::options::AnyVectorOption forward declarations
src/utility/options/AnyVectorOption.hhProgram any vector-valued option abstract base class
src/utility/options/BooleanOption.fwd.hhUtility::options::BooleanOption forward declarations
src/utility/options/BooleanOption.hhProgram boolean option class
src/utility/options/BooleanVectorOption.fwd.hhUtility::options::BooleanVectorOption forward declarations
src/utility/options/BooleanVectorOption.hhProgram boolean vector option class
src/utility/options/FileOption.fwd.hhUtility::options::FileOption forward declarations
src/utility/options/FileOption.hhProgram file option class
src/utility/options/FileVectorOption.fwd.hhUtility::options::FileVectorOption forward declarations
src/utility/options/FileVectorOption.hhProgram file vector option class
src/utility/options/IntegerOption.fwd.hhUtility::options::IntegerOption forward declarations
src/utility/options/IntegerOption.hhProgram integer option class
src/utility/options/IntegerVectorOption.fwd.hhUtility::options::IntegerVectorOption forward declarations
src/utility/options/IntegerVectorOption.hhProgram integer vector option class
src/utility/options/mpi_stderr.cc
src/utility/options/mpi_stderr.hh
src/utility/options/Option.fwd.hhUtility::options::Option forward declarations
src/utility/options/Option.hhProgram option interface class
src/utility/options/OptionCollection.ccProgram options collection
src/utility/options/OptionCollection.fwd.hhUtility::options::OptionCollection forward declarations
src/utility/options/OptionCollection.hhProgram options collection
src/utility/options/PathOption.fwd.hhUtility::options::PathOption forward declarations
src/utility/options/PathOption.hhProgram path option class
src/utility/options/PathVectorOption.fwd.hhUtility::options::PathVectorOption forward declarations
src/utility/options/PathVectorOption.hhProgram path vector option class
src/utility/options/RealOption.fwd.hhUtility::options::RealOption forward declarations
src/utility/options/RealOption.hhProgram real option class
src/utility/options/RealVectorOption.fwd.hhUtility::options::RealVectorOption forward declarations
src/utility/options/RealVectorOption.hhProgram real vector option class
src/utility/options/ScalarOption.fwd.hhUtility::options::ScalarOption forward declarations
src/utility/options/ScalarOption.hhProgram scalar-valued option interface class
src/utility/options/ScalarOption_T_.fwd.hhUtility::options::ScalarOption_T_ forward declarations
src/utility/options/ScalarOption_T_.hhProgram scalar-valued option abstract base class
src/utility/options/StringOption.fwd.hhUtility::options::StringOption forward declarations
src/utility/options/StringOption.hhProgram string option class
src/utility/options/StringVectorOption.fwd.hhUtility::options::StringVectorOption forward declarations
src/utility/options/StringVectorOption.hhProgram string vector option class
src/utility/options/VariantOption.fwd.hhUtility::options::VariantOption forward declarations
src/utility/options/VariantOption.hhVariant option class
src/utility/options/VectorOption.fwd.hhUtility::options::VectorOption forward declarations
src/utility/options/VectorOption.hhProgram vector-valued option interface class
src/utility/options/VectorOption_T_.fwd.hhUtility::options::VectorOption_T_ forward declarations
src/utility/options/VectorOption_T_.hhProgram vector-valued option abstract base class
src/utility/options/keys/all.fwd.hhUtility::options package keys forward declarations
src/utility/options/keys/all.hhUtility::options package keys declarations
src/utility/options/keys/AnyOptionKey.fwd.hhUtility::options::AnyOptionKey forward declarations
src/utility/options/keys/AnyOptionKey.hhAutomatic hidden index key for any scalar-valued options
src/utility/options/keys/AnyVectorOptionKey.fwd.hhUtility::options::AnyVectorOptionKey forward declarations
src/utility/options/keys/AnyVectorOptionKey.hhAutomatic hidden index key for any vector-valued options
src/utility/options/keys/BooleanOptionKey.fwd.hhUtility::options::BooleanOptionKey forward declarations
src/utility/options/keys/BooleanOptionKey.hhAutomatic hidden index key for boolean options
src/utility/options/keys/BooleanVectorOptionKey.fwd.hhUtility::options::BooleanVectorOptionKey forward declarations
src/utility/options/keys/BooleanVectorOptionKey.hhAutomatic hidden index key for boolean options
src/utility/options/keys/FileOptionKey.fwd.hhUtility::options::FileOptionKey forward declarations
src/utility/options/keys/FileOptionKey.hhAutomatic hidden index key for file options
src/utility/options/keys/FileVectorOptionKey.fwd.hhUtility::options::FileVectorOptionKey forward declarations
src/utility/options/keys/FileVectorOptionKey.hhAutomatic hidden index key for file options
src/utility/options/keys/IntegerOptionKey.fwd.hhUtility::options::IntegerOptionKey forward declarations
src/utility/options/keys/IntegerOptionKey.hhAutomatic hidden index key for integer options
src/utility/options/keys/IntegerVectorOptionKey.fwd.hhUtility::options::IntegerVectorOptionKey forward declarations
src/utility/options/keys/IntegerVectorOptionKey.hhAutomatic hidden index key for integer options
src/utility/options/keys/OptionKey.fwd.hhUtility::options::OptionKey forward declarations
src/utility/options/keys/OptionKey.hhAbstract automatic hidden index key for options
src/utility/options/keys/OptionKeys.ccUtility::options::OptionKeys collection
src/utility/options/keys/OptionKeys.hhUtility::options::OptionKeys collection
src/utility/options/keys/PathOptionKey.fwd.hhUtility::options::PathOptionKey forward declarations
src/utility/options/keys/PathOptionKey.hhAutomatic hidden index key for path options
src/utility/options/keys/PathVectorOptionKey.fwd.hhUtility::options::PathVectorOptionKey forward declarations
src/utility/options/keys/PathVectorOptionKey.hhAutomatic hidden index key for path options
src/utility/options/keys/RealOptionKey.fwd.hhUtility::options::RealOptionKey forward declarations
src/utility/options/keys/RealOptionKey.hhAutomatic hidden index key for real options
src/utility/options/keys/RealVectorOptionKey.fwd.hhUtility::options::RealVectorOptionKey forward declarations
src/utility/options/keys/RealVectorOptionKey.hhAutomatic hidden index key for real options
src/utility/options/keys/ScalarOptionKey.fwd.hhUtility::options::ScalarOptionKey forward declarations
src/utility/options/keys/ScalarOptionKey.hhAbstract automatic hidden index key for scalar-valued options
src/utility/options/keys/StringOptionKey.fwd.hhUtility::options::StringOptionKey forward declarations
src/utility/options/keys/StringOptionKey.hhAutomatic hidden index key for string options
src/utility/options/keys/StringVectorOptionKey.fwd.hhUtility::options::StringVectorOptionKey forward declarations
src/utility/options/keys/StringVectorOptionKey.hhAutomatic hidden index key for string options
src/utility/options/keys/VectorOptionKey.fwd.hhUtility::options::VectorOptionKey forward declarations
src/utility/options/keys/VectorOptionKey.hhAbstract automatic hidden index key for vector-valued options
src/utility/pointer/access_ptr.fwd.hhUtility::pointer::access_ptr forward declarations
src/utility/pointer/access_ptr.hhNon-owning access smart pointer
src/utility/pointer/all.fwd.hhUtility::pointer package forward declarations
src/utility/pointer/all.hhUtility::pointer package declarations
src/utility/pointer/owning_ptr.functions.hhOwning_ptr acquire and release functions
src/utility/pointer/owning_ptr.fwd.hhUtility::pointer::owning_ptr forward declarations
src/utility/pointer/owning_ptr.hhShared-ownership intrusive reference-counted smart pointer
src/utility/pointer/pointer.functions.hhPointer utility functions
src/utility/pointer/ReferenceCount.cc
src/utility/pointer/ReferenceCount.fwd.hhUtility::pointer::ReferenceCount forward declarations
src/utility/pointer/ReferenceCount.hhBase class for reference-counted single inheritance polymorphic classes
src/utility/pointer/ReferenceCountMI.fwd.hhUtility::pointer::ReferenceCountMI forward declarations
src/utility/pointer/ReferenceCountMI.hhInterface class for reference-counted multiple inheritance polymorphic classes
src/utility/pointer/ReferenceCountMI_.ccBase class for reference-counted multiple inheritance polymorphic classes
src/utility/pointer/ReferenceCountMI_.fwd.hhUtility::pointer::ReferenceCountMI_ forward declarations
src/utility/pointer/ReferenceCountMI_.hhBase class for reference-counted multiple inheritance polymorphic classes
src/utility/query/all.hh
src/utility/query/Filter.hh
src/utility/query/Metric.hh
src/utility/query/types.hh
src/utility/signals/BufferedSignalHub.fwd.hhForward declaration for utility::signals::BufferedSignalHub
src/utility/signals/BufferedSignalHub.hhSignalHub capable of buffering while blocking
src/utility/signals/Link.fwd.hhForward declaration for utility::signals::Link
src/utility/signals/Link.hhClass storing the link between observers and subjects
src/utility/signals/LinkUnit.fwd.hhForward declaration for utility::signals::LinkUnit
src/utility/signals/LinkUnit.hhClass specifying actual link data between observers and subjects
src/utility/signals/PausableSignalHub.fwd.hhForward declaration for utility::signals::PausableSignalHub
src/utility/signals/PausableSignalHub.hhBufferedSignalHub capable of pausing and waiting for stdin
src/utility/signals/SignalHub.fwd.hhForward declaration for utility::signals::SignalHub
src/utility/signals/SignalHub.hhPrimary class for function based implementation of observer pattern
src/utility/signals/TokenHub.fwd.hhForward declaration for utility::signals::TokenHub
src/utility/signals/TokenHub.hhBufferedSignalHub capable of passing observers
src/utility/sql_database/DatabaseSessionManager.cc
src/utility/sql_database/DatabaseSessionManager.fwd.hh
src/utility/sql_database/DatabaseSessionManager.hh
src/utility/sql_database/sqlite3_connection_manager.ccEasy Access to sqlite3 database; manage connections
src/utility/sql_database/sqlite3_connection_manager.fwd.hh
src/utility/sql_database/sqlite3_connection_manager.hhEasy Access to sqlite3 database; manage connections
src/utility/sql_database/sqlite3_interface.cc
src/utility/sql_database/sqlite3_interface.fwd.hhUtility::sql_database::sqlite3_interface forward declarations
src/utility/sql_database/sqlite3_interface.hhEasy Access to sqlite3 database
src/utility/sql_database/dbi/dbixx_example.cc
src/utility/tag/Tag.ccAn object for reading/writing a simple xml-like language
src/utility/tag/Tag.fwd.hh
src/utility/tag/Tag.hhAn object for reading/writing a simple xml-like language
src/utility/tools/make_map.hh
src/utility/tools/make_templates.pyProgram that generate make_vector.hh and make_map.hh files
src/utility/tools/make_vector.hhCommon function to build vector, vector0, vector1, map
src/utility/tools/make_vector0.hh
src/utility/tools/make_vector1.hh
test/scientific/cluster/ligand_docking/yaml/__init__.py
test/scientific/cluster/ligand_docking/yaml/composer.py
test/scientific/cluster/ligand_docking/yaml/constructor.py
test/scientific/cluster/ligand_docking/yaml/cyaml.py
test/scientific/cluster/ligand_docking/yaml/dumper.py
test/scientific/cluster/ligand_docking/yaml/emitter.py
test/scientific/cluster/ligand_docking/yaml/error.py
test/scientific/cluster/ligand_docking/yaml/events.py
test/scientific/cluster/ligand_docking/yaml/loader.py
test/scientific/cluster/ligand_docking/yaml/nodes.py
test/scientific/cluster/ligand_docking/yaml/parser.py
test/scientific/cluster/ligand_docking/yaml/reader.py
test/scientific/cluster/ligand_docking/yaml/representer.py
test/scientific/cluster/ligand_docking/yaml/resolver.py
test/scientific/cluster/ligand_docking/yaml/scanner.py
test/scientific/cluster/ligand_docking/yaml/serializer.py
test/scientific/cluster/ligand_docking/yaml/tokens.py
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