| ▼ src | |
| ► basic | |
| ► database | |
| ► insert_statement_generator | |
| InsertGenerator.cc | Insert statement generator |
| InsertGenerator.fwd.hh | Insert statement generator |
| InsertGenerator.hh | Insert statement generator |
| RowData.cc | Column data object for the insert statement generator |
| RowData.fwd.hh | Column data object for the insert statement generator |
| RowData.hh | |
| ► schema_generator | |
| Column.cc | Column class for the schema generator framework |
| Column.fwd.hh | Forward hearder for the Column class in the schema generator framework |
| Column.hh | Column class for the schema generator framework |
| Constraint.cc | |
| Constraint.fwd.hh | Forwaard header for the constraints class in the schema generator framework |
| Constraint.hh | |
| DbDataType.cc | DbDataType class for the schema generator framework |
| DbDataType.fwd.hh | |
| DbDataType.hh | |
| ForeignKey.cc | ForeignKey class for the schema generator framework |
| ForeignKey.hh | ForeignKey class for the schema generator framework |
| Index.cc | Index class for the schema generator framework |
| Index.hh | Index class for the schema generator framework |
| PrimaryKey.cc | PrimaryKey class for the schema generator framework |
| PrimaryKey.hh | PrimaryKey class for the schema generator framework |
| Schema.cc | Construct a database backend independant schema |
| Schema.hh | Table definition for the schema generator framework |
| DatabaseSessionLoader.cc | Load the database session object |
| DatabaseSessionLoader.fwd.hh | Load the database session |
| DatabaseSessionLoader.hh | Load the utility database session |
| DatabaseSessionLoaderCreator.hh | Load the database session |
| DatabaseSessionOptions.cc | Load the database session |
| DatabaseSessionOptions.fwd.hh | Load the database session |
| DatabaseSessionOptions.hh | Load the database session |
| DatabaseSessionOptionsCreator.hh | Load the database session |
| open.cc | Functions for opening database files |
| open.hh | Functions for opening database files |
| sql_utils.cc | Database utility functions |
| sql_utils.hh | |
| ► datacache | |
| BasicDataCache.cc | A DataCache storing objects derived from basic::datacache::CacheableData |
| BasicDataCache.fwd.hh | Forward declaration for BasicDataCache |
| BasicDataCache.hh | A DataCache storing objects derived from basic::datacache::CacheableData |
| CacheableData.fwd.hh | |
| CacheableData.hh | |
| CacheableString.fwd.hh | |
| CacheableString.hh | |
| CacheableStringFloatMap.fwd.hh | |
| CacheableStringFloatMap.hh | |
| CacheableStringMap.fwd.hh | |
| CacheableStringMap.hh | |
| DataCache.fwd.hh | Forward declaration for DataCache |
| DataCache.hh | |
| DataMap.cc | |
| DataMap.fwd.hh | |
| DataMap.hh | |
| DataMapObj.hh | |
| DiagnosticData.fwd.hh | |
| DiagnosticData.hh | |
| HierarchicalDataMap.cc | |
| HierarchicalDataMap.fwd.hh | |
| HierarchicalDataMap.hh | |
| WriteableCacheableData.fwd.hh | |
| WriteableCacheableData.hh | |
| WriteableCacheableDataCreator.cc | |
| WriteableCacheableDataCreator.hh | Base class for WriteableCacheableDataCreators for the WriteableCacheableData load-time factory registration scheme |
| WriteableCacheableDataFactory.cc | |
| WriteableCacheableDataFactory.fwd.hh | |
| WriteableCacheableDataFactory.hh | |
| WriteableCacheableMap.fwd.hh | |
| WriteableCacheableMap.hh | |
| ► gpu | |
| GPU.cc | OpenCL-based GPU scheduler class |
| GPU.hh | OpenCL-based GPU scheduler class |
| Timer.cc | High-resolution Timer (ns resolution) |
| Timer.hh | High-resolution Timer (ns resolution, but on *nix only) |
| ► message_listening | |
| 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 | |
| util.cc | Utility functions for the message listening framework |
| util.hh | |
| ► options | |
| ► keys | |
| 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 | |
| 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.hh | Program options global and initialization function |
| option_macros.hh | |
| options.py | Program options generation script that is run to generate the options |
| options_class.py | Program options generation script classes |
| options_rosetta.py | Program options generation script: Rosetta options encoding |
| PyRosettaFunctions.cc | |
| PyRosettaFunctions.hh | Additional functions to set/get Options from PyRosetta |
| util.cc | |
| util.hh | |
| ► resource_manager | |
| ► fallback_configuration | |
| NativeFallbackConfiguration.cc | |
| NativeFallbackConfiguration.fwd.hh | |
| NativeFallbackConfiguration.hh | |
| NativeFallbackConfigurationCreator.hh | |
| ► locator | |
| DatabaseResourceLocator.cc | |
| DatabaseResourceLocator.fwd.hh | Forward header for DatabaseResourceLocator |
| DatabaseResourceLocator.hh | |
| DatabaseResourceLocatorCreator.hh | Header for DatabaseResourceLocator Creator for the load-time factory registration scheme |
| FileListResourceLocator.cc | |
| FileListResourceLocator.fwd.hh | Forward header for FileListResourceLocator |
| FileListResourceLocator.hh | |
| FileListResourceLocatorCreator.hh | Header for FileSystemResourceLocator Creator for the load-time factory registration scheme |
| FileSystemResourceLocator.cc | |
| FileSystemResourceLocator.fwd.hh | Forward header for FileSystemResourceLocator |
| FileSystemResourceLocator.hh | |
| FileSystemResourceLocatorCreator.hh | Header for FileSystemResourceLocator Creator for the load-time factory registration scheme |
| NullResourceLocator.cc | |
| NullResourceLocator.fwd.hh | Forward header for NullResourceLocator |
| NullResourceLocator.hh | |
| NullResourceLocatorCreator.hh | Header for NullResourceLocator Creator for the load-time factory registration scheme |
| StringResourceStream.cc | A thin wrapper around an std::stringstream for use with the ResourceManager |
| StringResourceStream.fwd.hh | Forward header for StringResourceStream |
| StringResourceStream.hh | A thin wrapper around an std::stringstream for use with the ResourceManager |
| FallbackConfiguration.cc | |
| FallbackConfiguration.fwd.hh | Forward hearder for FallbackConfiguration class |
| FallbackConfiguration.hh | |
| FallbackConfigurationCreator.cc | |
| FallbackConfigurationCreator.fwd.hh | |
| FallbackConfigurationCreator.hh | Declaration of the FallbackConfigurationCreator class |
| FallbackConfigurationFactory.cc | |
| FallbackConfigurationFactory.fwd.hh | |
| FallbackConfigurationFactory.hh | |
| JobOptions.cc | |
| JobOptions.fwd.hh | Forward hearder for JobOptions class |
| JobOptions.hh | |
| LazyResourceManager.cc | |
| LazyResourceManager.fwd.hh | Forward Header for base class for LazyResourceManager |
| LazyResourceManager.hh | |
| ResourceLoader.cc | |
| ResourceLoader.fwd.hh | |
| ResourceLoader.hh | |
| ResourceLoaderCreator.cc | |
| ResourceLoaderCreator.fwd.hh | |
| ResourceLoaderCreator.hh | |
| ResourceLoaderFactory.cc | |
| ResourceLoaderFactory.hh | |
| ResourceLoaderRegistrator.hh | Declaration of class ResourceLoaderRegistrator |
| ResourceLocator.cc | |
| ResourceLocator.fwd.hh | Forward header for ResourceLocator |
| ResourceLocator.hh | |
| ResourceLocatorCreator.cc | |
| ResourceLocatorCreator.fwd.hh | |
| ResourceLocatorCreator.hh | |
| ResourceLocatorFactory.cc | |
| ResourceLocatorFactory.hh | |
| ResourceLocatorRegistrator.hh | |
| ResourceManager.cc | |
| ResourceManager.fwd.hh | |
| ResourceManager.hh | |
| ResourceManagerCreator.cc | |
| ResourceManagerCreator.fwd.hh | |
| ResourceManagerCreator.hh | |
| ResourceManagerFactory.cc | |
| ResourceManagerFactory.fwd.hh | |
| ResourceManagerFactory.hh | |
| ResourceOptions.cc | |
| ResourceOptions.fwd.hh | |
| ResourceOptions.hh | |
| ResourceOptionsCreator.cc | |
| ResourceOptionsCreator.fwd.hh | |
| ResourceOptionsCreator.hh | |
| ResourceOptionsFactory.cc | |
| ResourceOptionsFactory.hh | |
| ResourceOptionsRegistrator.hh | |
| types.hh | |
| util.hh | |
| ► sampling | |
| ► orientations | |
| QuaternionGrid.cc | Provide an evenly spaced set of rotations |
| QuaternionGrid.fwd.hh | Basic::sampling::orientations::QuaternionGrid forward declaration |
| QuaternionGrid.hh | |
| ► svd | |
| SVD_Solver.cc | SVD solver class ` |
| SVD_Solver.fwd.hh | SVD solver class |
| SVD_Solver.hh | SVD solver class |
| basic.cc | |
| basic.hh | |
| ComparingTracer.cc | |
| ComparingTracer.hh | Version of Tracer calss for to tracking down the source of an instability by compare output with file |
| Emitter.cc | Lightweight class to ease writting YAML documents |
| Emitter.hh | Lightweight class to ease writting YAML documents |
| init.cc | Some statics/funtions helpers for Rosetta init functions |
| init.hh | |
| interpolate.cc | |
| interpolate.hh | |
| MemTracer.cc | |
| MemTracer.hh | |
| MetricValue.fwd.hh | |
| MetricValue.hh | |
| MetricValueIO.cc | |
| MetricValueIO.hh | |
| prof.cc | |
| prof.hh | |
| pymol_chains.cc | Method definitions for a couple PyMOL helper functions |
| pymol_chains.hh | |
| Tracer.cc | |
| Tracer.fwd.hh | |
| Tracer.hh | Tracer IO system |
| TracerToFile.cc | |
| TracerToFile.hh | Class for a tracer that writes all output to a file |
| ► devel | |
| init.cc | |
| init.hh | |
| init.release.cc | Initialization function to ensure all load-time factory registration occurs for classes that live in the devel library. devel::init() calls protocols::init::init(), which in turn calls core::init::init(). Devel library does not exist in release; so the release version of this file is nearly empty |
| init.release.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the devel library. devel::init() calls protocols::init::init(), which in turn calls core::init::init(). Devel library does not exist in release; so the release version of this file is nearly empty |
| svn_version.hh | |
| ► numeric | |
| ► alignment | |
| QCP_Kernel.hh | |
| ► coordinate_fitting | |
| CoordinateArray_RMSD_FlatLookup.hh | |
| FlatLookup.hh | |
| ► crick_equations | |
| BundleParams.cc | Functions implementing the Crick equations for a helical bundle (a helix of helices) |
| BundleParams.hh | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| HelixParams.cc | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| HelixParams.hh | Functions implementing the Crick equations for a straight helix (NOT a helical bundle) |
| ► deriv | |
| angle_deriv.hh | Inline function for computing f1/f2 derivatives for a function of a distance |
| dihedral_deriv.hh | Inline function for computing f1/f2 derivatives for a function of a dihedral |
| distance_deriv.hh | Inline function for computing f1/f2 derivatives for a function of an angle |
| ► expression_parser | |
| Arithmetic.cc | Parse tree for arithmetic operations |
| Arithmetic.fwd.hh | Parse tree for arithmetic operations class forward declarations |
| Arithmetic.hh | Parse tree for arithmetic operations |
| ► fourier | |
| FFT.cc | Wrapper class performing ffts on 1,2, and 3 dimensional farrays |
| FFT.hh | |
| kiss_fft.cc | |
| kiss_fft.hh | |
| kiss_fft_state.cc | |
| kiss_fft_state.hh | |
| SHT.cc | A few spherical harmonic transform function: very simple, with support for real, even BW only |
| SHT.hh | A few spherical harmonic transform functions |
| ► geometry | |
| ► hashing | |
| SixDHasher.cc | Implementation of 6D hasher classes |
| SixDHasher.fwd.hh | Forward declaration for classes in 6D hasher |
| SixDHasher.hh | |
| xyzStripeHash.cc | |
| xyzStripeHash.fwd.hh | |
| xyzStripeHash.hh | |
| xyzStripeHashWithMeta.fwd.hh | |
| xyzStripeHashWithMeta.hh | |
| BoundingBox.fwd.hh | Numeric::geometry::BoundingBox forward declaration |
| BoundingBox.hh | 3d axis aligned bounding box |
| ► histograms | |
| OneDHistogram.hh | |
| TwoDHistogram.hh | |
| ► internal | |
| ColPointers.hh | 3x3 matrix column pointers wrapper class |
| ColsPointer.hh | Contiguous column-ordered 3x3 matrix pointer wrapper class |
| ColVectors.hh | 3x3 matrix column vectors wrapper class |
| RowPointers.hh | 3x3 matrix row pointers wrapper class |
| RowsPointer.hh | Contiguous row-ordered 3x3 matrix pointer wrapper class |
| RowVectors.hh | 3x3 matrix row vectors wrapper class |
| ► interpolation | |
| ► periodic_range | |
| ► full | |
| interpolation.hh | Interpolation over periodic range points at full bin width multiples |
| ► half | |
| interpolation.hh | Interpolation over periodic range points at half bin width multiples |
| ► spline | |
| Bicubic_spline.cc | |
| Bicubic_spline.fwd.hh | |
| Bicubic_spline.hh | |
| CompoundInterpolator.cc | Interpolation with cubic splines |
| CompoundInterpolator.hh | Interpolation with cubic splines |
| Cubic_spline.cc | |
| Cubic_spline.fwd.hh | |
| Cubic_spline.hh | |
| Interpolator.cc | |
| Interpolator.hh | |
| PolycubicSpline.cc | |
| PolycubicSpline.fwd.hh | |
| PolycubicSpline.hh | |
| SimpleInterpolator.cc | Interpolation with cubic splines |
| SimpleInterpolator.hh | Interpolation with cubic splines |
| spline_functions.cc | |
| spline_functions.hh | |
| SplineGenerator.cc | Interpolation with cubic splines |
| SplineGenerator.hh | |
| TricubicSpline.cc | |
| TricubicSpline.fwd.hh | |
| TricubicSpline.hh | |
| Histogram.fwd.hh | |
| Histogram.hh | A class for storing histogram data |
| interpolation.hh | Interpolation functions |
| util.cc | |
| util.hh | |
| ► kdtree | |
| calc_distance.cc | |
| calc_distance.hh | |
| constants.hh | Constants used for kd-tree implementation |
| construct_kdtree.cc | |
| construct_kdtree.hh | |
| HyperRectangle.cc | |
| HyperRectangle.fwd.hh | |
| HyperRectangle.hh | |
| KDNode.cc | Implementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| KDNode.fwd.hh | Forward declaration for KDNode class |
| KDNode.hh | Implementation of a node in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| KDPoint.cc | |
| KDPoint.fwd.hh | Forward declaration for KDPoint class |
| KDPoint.hh | Utility functions for kd-tree. See kdtree.hh for more information |
| KDPointList.cc | Definition for a class that keeps track of the best N KDPoint objects by distance |
| KDPointList.hh | Definition for a class that keeps track of the best N KDPoint objects by distance |
| KDTree.cc | |
| KDTree.fwd.hh | Forward declaration for KDTree class |
| KDTree.hh | Implementation of a tree in a kd-tree. See numeric/kdtree/kdtree.hh for more information |
| nearest_neighbors.cc | |
| nearest_neighbors.hh | Utility functions for kd-tree. See kdtree.hh for more information |
| util.cc | |
| util.hh | |
| WrappedPrimitive.hh | |
| WrappedReal.hh | Silly little class to wrap a numeric::Real in an OP |
| ► kinematic_closure | |
| bridgeObjects.cc | Solves the triaxial loop closure problem for a system of atoms |
| bridgeObjects.hh | Header file for bridgeObjects code for ALC |
| closure.cc | |
| closure.hh | |
| dixon.cc | Computes the dixon resultant |
| dixon.f90 | |
| dixon.hh | Header file for dixon code for ALC |
| kinematic_closure_helpers.cc | Helpers for functions associated with bridgeObjects.cc |
| kinematic_closure_helpers.hh | Header file for kinematic_closure_helpers.cc |
| qq.f90 | |
| sturm.cc | Implements sturm chain solver |
| sturm.hh | Implements sturm chain solver |
| types.hh | Define the numeric types that are commonly used in this namespace |
| vector.cc | |
| vector.hh | Implement the primitive vector operations (again) |
| ► linear_algebra | |
| GeneralizedEigenSolver.fwd.hh | Forward header for GeneralizedEigenSolver |
| GeneralizedEigenSolver.hh | Header file for GeneralizedEigenSolver |
| rgg.cc | |
| rgg.hh | Header file for the EISPACK rgg routine |
| ► model_quality | |
| maxsub.cc | Ab-initio fragment assembly protocol for proteins |
| maxsub.hh | |
| rms.cc | |
| rms.hh | RMS functions imported from rosetta++ |
| RmsData.cc | |
| RmsData.hh | |
| ► nls | |
| lmmin.cc | |
| lmmin.hh | |
| ► random | |
| DistributionSampler.hh | |
| mt19937.hh | Mersenne Twister 19937 random number generator |
| random.cc | Random number generator system |
| random.functions.hh | |
| random.fwd.hh | Random number generator system |
| random.hh | Random number generator system |
| random_permutation.hh | Reorder the elements in a vector using a RNG object |
| random_xyz.cc | |
| random_xyz.hh | Random vectors and stuff |
| reservoir_sample.hh | Randomly select the best N elements from a stream of elements using one pass over a dataset |
| uniform.fwd.hh | |
| uniform.hh | Uniform random number generator |
| WeightedReservoirSampler.hh | |
| WeightedSampler.cc | Class to generate random positive integers using a given set of weights |
| WeightedSampler.fwd.hh | Forward declarations for class WeightedSampler |
| WeightedSampler.hh | Class to generate random positive integers using a given set of weights |
| ► statistics | |
| functions.cc | |
| functions.hh | Collection of various functions to compute statistics. feel free to add your own |
| agglomerative_hierarchical_clustering.cc | |
| agglomerative_hierarchical_clustering.hh | Hierarchical clustering utilities |
| all.fwd.hh | Numeric package forward declarations |
| angle.functions.hh | Trigonometric functions |
| BodyPosition.fwd.hh | Numeric::BodyPosition forward declarations |
| BodyPosition.hh | Rigid body 3-D position/transform |
| BodyPosition.io.hh | BodyPosition input/output functions |
| Calculator.cc | |
| Calculator.fwd.hh | |
| Calculator.hh | String-input calculator |
| ClusteringTreeNode.cc | |
| ClusteringTreeNode.fwd.hh | |
| ClusteringTreeNode.hh | Node of a hierarchical clustering tree |
| color_util.cc | |
| color_util.hh | |
| constants.cc | Common numeric constants in varying precisions |
| constants.hh | Common numeric constants in varying precisions |
| conversions.hh | Conversions between degrees and radians |
| cyclic_coordinate_descent.cc | Compute the angle that minimizes the deviation between a set of atoms |
| cyclic_coordinate_descent.hh | Compute the angle that minimizes the deviation between a set of atoms |
| EulerAngles.fwd.hh | Numeric::EulerAngles forward declarations |
| EulerAngles.hh | EulerAngles container derived from xyzVector.hh |
| HomogeneousTransform.fwd.hh | Fast coordinate frame container |
| HomogeneousTransform.hh | Fast coordinate frame container |
| interpolate.hh | |
| IntervalSet.fwd.hh | IntervalSet forward declarations |
| IntervalSet.hh | Definition and implementation of IntervalSet class |
| io.hh | Numeric package i/o functions |
| IOTraits.hh | Numerics input/output type traits |
| MathMatrix.hh | |
| MathMatrix_operations.hh | |
| MathNTensor.hh | |
| MathTensor.hh | |
| MathVector.hh | |
| MathVector_operations.hh | |
| MultiDimensionalHistogram.cc | Class for accumulating a histogram of one or more numeric variables |
| MultiDimensionalHistogram.fwd.hh | Forward declarations for class MultiDimensionalHistogram |
| MultiDimensionalHistogram.hh | Class for accumulating a histogram of one or more numeric variables |
| numeric.functions.hh | Numeric functions |
| NumericTraits.hh | Numeric type traits |
| PCA.hh | |
| polynomial.cc | Classes for polynomial evaluation functions |
| polynomial.fwd.hh | Forward header for Polynomial class |
| polynomial.hh | Polynomial evaluation class |
| prob_util.cc | |
| prob_util.hh | |
| Quaternion.fwd.hh | Numeric::Quaternion forward declarations |
| Quaternion.hh | Unit quaternion 3-D orientation representation |
| Quaternion.io.hh | Quaternion input/output functions |
| roc_curve.cc | |
| roc_curve.fwd.hh | |
| roc_curve.hh | |
| sphericalVector.fwd.hh | Numeric::sphericalVector forward declarations |
| sphericalVector.hh | Fast spherical-coordinate numeric vector |
| trig.functions.hh | Trigonometric functions |
| types.hh | Rosetta project type declarations. Should be kept updated with core/types.hh. This exists because numeric can't depend on files in core |
| UniformRotationSampler.fwd.hh | Numeric::UniformRotationSampler forward declarations |
| UniformRotationSampler.hh | |
| util.cc | Small bundle of utilities for dealing with numbers |
| util.hh | Small bundle of utilities for dealing with numbers |
| wrap_angles.hh | Functions to wrap angles in different ranges. author Kale Kundert (kale..nosp@m.kund.nosp@m.ert@u.nosp@m.csf..nosp@m.edu) |
| xyz.functions.fwd.hh | Numeric::xyzVector and numeric::xyzMatrix functions forward declarations |
| xyz.functions.hh | XyzVector and xyzMatrix functions |
| xyz.io.hh | XyzTriple, xyzVector, and xyzMatrix i/o functions |
| xyz.json.hh | |
| 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 | |
| ► platform | |
| ► cygwin | |
| ► platform | |
| types.hh | |
| ► linux | |
| ► GL | |
| freeglut.h | |
| freeglut_ext.h | |
| freeglut_std.h | |
| glut.h | |
| ► platform | |
| types.hh | Platform-specific types for Linux |
| ► macos | |
| ► platform | |
| types.hh | Platform-specific types for MacOS 10.4 on 32-bit PPC with GCC |
| ► windows | |
| ► 32 | |
| ► gcc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with GCC |
| ► icc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with Intel C++ |
| ► msvc | |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows with MS VC++ |
| ► platform | |
| types.hh | Platform-specific types for 32-bit Windows |
| ► 64 | |
| ► gcc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with GCC |
| ► icc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with Intel C++ |
| ► msvc | |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows with MS VC++ |
| ► platform | |
| types.hh | Platform-specific types for 64-bit Windows |
| ► PyRosetta | |
| ► platform | |
| types.hh | |
| ► utility | |
| ► boinc | |
| boinc_util.cc | |
| boinc_util.hh | Wrappers to make BOINC work |
| ► excn | |
| Exceptions.cc | |
| Exceptions.hh | |
| EXCN_Base.hh | |
| ► factory | |
| Factory.fwd.hh | Utility::factory::Factory forward declarations |
| Factory.hh | Pluggable factory |
| Registrant.fwd.hh | Utility::factory::Registrant forward declarations |
| Registrant.hh | Factory registrant |
| WidgetFactory.fwd.hh | WidgetFactory forward declaration |
| WidgetFactory.hh | WidgetFactory base class for load-time registration of WidgetCreators to the WidgetFactory |
| WidgetRegistrator.hh | WidgetRegistrator class which registers WidgetCreator classes at load time |
| ► file | |
| file_sys_util.cc | Platform independent operations on files (except I/O) |
| file_sys_util.hh | Platform independent operations on files (except I/O) |
| FileName.cc | |
| FileName.fwd.hh | Utility::file::FileName forward declarations |
| FileName.hh | File name class supporting Windows and UN*X/Linux format names |
| gzip_util.cc | Gzip utility functions |
| gzip_util.hh | Gzip utility functions |
| PathName.cc | |
| PathName.fwd.hh | Utility::file::PathName forward declarations |
| PathName.hh | Path name class supporting Windows and UN*X/Linux format names |
| ► graph | |
| BFS_prune.hh | A breadth first search with pruning for boost graphs |
| DFS_sort.hh | A depth first search with sorting for edge visitation |
| ring_detection.hh | Algorithms for working with rings in boost graphs |
| RingDetection.hh | |
| ► io | |
| all.fwd.hh | Utility::io package forward declarations |
| FileContentsMap.cc | Implementation of the FileContentsMap class, which loads and then maintains the contents of files as strings in memory |
| FileContentsMap.fwd.hh | Forward declaration of a class that maintains file contents in memory as strings |
| FileContentsMap.hh | Declaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed |
| icstream.cc | Input channel stream wrapper base class, |
| icstream.fwd.hh | Utility::io::icstream forward declarations |
| icstream.hh | Input channel stream wrapper class |
| irstream.fwd.hh | Utility::io::irstream forward declarations |
| irstream.hh | Input stream wrapper abstract base class |
| izstream.cc | Input file stream wrapper for uncompressed and compressed files |
| izstream.fwd.hh | Utility::io::izstream forward declarations |
| izstream.hh | Input file stream wrapper for uncompressed and compressed files |
| mpistream.hh | |
| mpistream.ipp | |
| ocstream.cc | Output channel stream wrapper base class, |
| ocstream.fwd.hh | Utility::io::ocstream forward declarations |
| ocstream.hh | Output channel stream wrapper class |
| orstream.fwd.hh | Utility::io::orstream forward declarations |
| orstream.hh | Output stream wrapper abstract base class |
| ozstream.cc | Output file stream wrapper for uncompressed and compressed files |
| ozstream.fwd.hh | Utility::io::ozstream forward declarations |
| ozstream.hh | Output file stream wrapper for uncompressed and compressed files |
| util.cc | General database input/output utility function definitions |
| util.hh | General database input/output utility functions |
| zipstream.hpp | Altered zipstream library header |
| zipstream.ipp | Altered zipstream library implementation |
| ► json_spirit | |
| json_spirit.h | |
| json_spirit_error_position.h | |
| json_spirit_reader.cc | |
| json_spirit_reader.h | |
| json_spirit_reader_template.h | |
| json_spirit_stream_reader.h | |
| json_spirit_tools.cc | Extra utilitiy functions not provided by json spirit library |
| json_spirit_tools.hh | Extra utilitiy functions not provided by json spirit library |
| json_spirit_utils.h | |
| json_spirit_value.cc | |
| json_spirit_value.h | |
| json_spirit_writer.cc | |
| json_spirit_writer.h | |
| json_spirit_writer_options.h | |
| json_spirit_writer_template.h | |
| ► keys | |
| AutoKey.fwd.hh | Utility::keys::AutoKey forward declarations |
| AutoKey.hh | Automatic hidden index key abstract base class |
| ClassKeyMap.fwd.hh | Utility::keys::ClassKeyMap forward declarations |
| ClassKeyMap.hh | Keyed-access map with key subset map for each client class |
| ClassKeyVector.fwd.hh | Utility::keys::ClassKeyVector forward declarations |
| ClassKeyVector.hh | Keyed-access vector with key subset map for each client class |
| Key.fwd.hh | Utility::keys::Key forward declarations |
| Key.hh | Hidden index key interface class |
| Key2Tuple.fwd.hh | Utility::keys::Key2Tuple forward declarations |
| Key2Tuple.hh | 2-tuple meta-key |
| 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 |
| Key3Vector.fwd.hh | Utility::keys::Key3Vector forward declarations |
| Key3Vector.hh | 3-key meta-key |
| Key4Tuple.fwd.hh | Utility::keys::Key4Tuple forward declarations |
| Key4Tuple.hh | 4-tuple meta-key |
| Key4Vector.fwd.hh | Utility::keys::Key4Vector forward declarations |
| Key4Vector.hh | 4-key meta-key |
| KeyCount.fwd.hh | Utility::keys::KeyCount forward declarations |
| KeyCount.hh | Key counter functor |
| KeyLess.fwd.hh | Utility::keys::KeyLess forward declarations |
| KeyLess.hh | Key comparison functor template |
| KeyLookup.functors.hh | Utility::keys::KeyLookup functor declarations |
| KeyLookup.functors.ii | Lookup functors |
| 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 | |
| ► lua | |
| LuaIterator.cc | A wrapper around a luabind::iterator has skey() and ikey() functions that return a string or int conversion of the key |
| LuaIterator.fwd.hh | A wrapper around a luabind::iterator has skey() and ikey() functions that return a string or int conversion of the key |
| LuaIterator.hh | A wrapper around a luabind::iterator has skey() and ikey() functions that return a string or int conversion of the key |
| LuaObject.cc | A wrapper around a luabind::object has bool conversion, [] support, nested table support, and a .to<T>() conversion function since a luabind::object is actually a pointer to the stack of a luastate object, if the luastate object is destroyed, before this wrapper class is destroyed, i don't know what will happen |
| LuaObject.fwd.hh | A wrapper around a luabind::object has bool conversion, [] support, nested table support, and a .to<T>() conversion function since a luabind::object is actually a pointer to the stack of a luastate object, if the luastate object is destroyed, before this wrapper class is destroyed, i don't know what will happen |
| LuaObject.hh | A wrapper around a luabind::object has bool conversion, [] support, nested table support, and a .to<T>() conversion function since a luabind::object is actually a pointer to the stack of a luastate object, if the luastate object is destroyed, before this wrapper class is destroyed, i don't know what will happen |
| ► options | |
| ► keys | |
| all.fwd.hh | Utility::options package keys forward declarations |
| all.hh | Utility::options package keys declarations |
| AnyOptionKey.fwd.hh | Utility::options::AnyOptionKey forward declarations |
| AnyOptionKey.hh | Automatic hidden index key for any scalar-valued options |
| AnyVectorOptionKey.fwd.hh | Utility::options::AnyVectorOptionKey forward declarations |
| AnyVectorOptionKey.hh | Automatic hidden index key for any vector-valued options |
| BooleanOptionKey.fwd.hh | Utility::options::BooleanOptionKey forward declarations |
| BooleanOptionKey.hh | Automatic hidden index key for boolean options |
| BooleanVectorOptionKey.fwd.hh | Utility::options::BooleanVectorOptionKey forward declarations |
| BooleanVectorOptionKey.hh | Automatic hidden index key for boolean options |
| FileOptionKey.fwd.hh | Utility::options::FileOptionKey forward declarations |
| FileOptionKey.hh | Automatic hidden index key for file options |
| FileVectorOptionKey.fwd.hh | Utility::options::FileVectorOptionKey forward declarations |
| FileVectorOptionKey.hh | Automatic hidden index key for file options |
| IntegerOptionKey.fwd.hh | Utility::options::IntegerOptionKey forward declarations |
| IntegerOptionKey.hh | Automatic hidden index key for integer options |
| IntegerVectorOptionKey.fwd.hh | Utility::options::IntegerVectorOptionKey forward declarations |
| IntegerVectorOptionKey.hh | Automatic hidden index key for integer options |
| OptionKey.fwd.hh | Utility::options::OptionKey forward declarations |
| OptionKey.hh | Abstract automatic hidden index key for options |
| OptionKeys.cc | Utility::options::OptionKeys collection |
| OptionKeys.hh | Utility::options::OptionKeys collection |
| PathOptionKey.fwd.hh | Utility::options::PathOptionKey forward declarations |
| PathOptionKey.hh | Automatic hidden index key for path options |
| PathVectorOptionKey.fwd.hh | Utility::options::PathVectorOptionKey forward declarations |
| PathVectorOptionKey.hh | Automatic hidden index key for path options |
| RealOptionKey.fwd.hh | Utility::options::RealOptionKey forward declarations |
| RealOptionKey.hh | Automatic hidden index key for real options |
| RealVectorOptionKey.fwd.hh | Utility::options::RealVectorOptionKey forward declarations |
| RealVectorOptionKey.hh | Automatic hidden index key for real options |
| ResidueChainVectorOptionKey.fwd.hh | Utility::options::ResidueChainVectorOptionKey forward declarations |
| ResidueChainVectorOptionKey.hh | Automatic hidden index key for integer options |
| ScalarOptionKey.fwd.hh | Utility::options::ScalarOptionKey forward declarations |
| ScalarOptionKey.hh | Abstract automatic hidden index key for scalar-valued options |
| StringOptionKey.fwd.hh | Utility::options::StringOptionKey forward declarations |
| StringOptionKey.hh | Automatic hidden index key for string options |
| StringVectorOptionKey.fwd.hh | Utility::options::StringVectorOptionKey forward declarations |
| StringVectorOptionKey.hh | Automatic hidden index key for string options |
| VectorOptionKey.fwd.hh | Utility::options::VectorOptionKey forward declarations |
| VectorOptionKey.hh | Abstract automatic hidden index key for vector-valued options |
| AnyOption.fwd.hh | Utility::options::AnyOption forward declarations |
| AnyOption.hh | Program any scalar-valued option abstract base class |
| AnyVectorOption.fwd.hh | Utility::options::AnyVectorOption forward declarations |
| AnyVectorOption.hh | Program any vector-valued option abstract base class |
| BooleanOption.fwd.hh | Utility::options::BooleanOption forward declarations |
| BooleanOption.hh | Program boolean option class |
| BooleanVectorOption.fwd.hh | Utility::options::BooleanVectorOption forward declarations |
| BooleanVectorOption.hh | Program boolean vector option class |
| FileOption.fwd.hh | Utility::options::FileOption forward declarations |
| FileOption.hh | Program file option class |
| FileVectorOption.fwd.hh | Utility::options::FileVectorOption forward declarations |
| FileVectorOption.hh | Program file vector option class |
| IntegerOption.fwd.hh | Utility::options::IntegerOption forward declarations |
| IntegerOption.hh | Program integer option class |
| IntegerVectorOption.fwd.hh | Utility::options::IntegerVectorOption forward declarations |
| IntegerVectorOption.hh | Program integer vector option class |
| mpi_stderr.cc | |
| mpi_stderr.hh | |
| Option.fwd.hh | Utility::options::Option forward declarations |
| Option.hh | Program option interface class |
| OptionCollection.cc | Program options collection |
| OptionCollection.fwd.hh | Utility::options::OptionCollection forward declarations |
| OptionCollection.hh | Program options collection |
| PathOption.fwd.hh | Utility::options::PathOption forward declarations |
| PathOption.hh | Program path option class |
| PathVectorOption.fwd.hh | Utility::options::PathVectorOption forward declarations |
| PathVectorOption.hh | Program path vector option class |
| RealOption.fwd.hh | Utility::options::RealOption forward declarations |
| RealOption.hh | Program real option class |
| RealVectorOption.fwd.hh | Utility::options::RealVectorOption forward declarations |
| RealVectorOption.hh | Program real vector option class |
| ResidueChainVectorOption.cc | |
| ResidueChainVectorOption.fwd.hh | Utility::options::ResidueChainVectorOption forward declarations |
| ResidueChainVectorOption.hh | Program integer vector option class |
| ScalarOption.fwd.hh | Utility::options::ScalarOption forward declarations |
| ScalarOption.hh | Program scalar-valued option interface class |
| ScalarOption_T_.fwd.hh | Utility::options::ScalarOption_T_ forward declarations |
| ScalarOption_T_.hh | Program scalar-valued option abstract base class |
| StringOption.fwd.hh | Utility::options::StringOption forward declarations |
| StringOption.hh | Program string option class |
| StringVectorOption.fwd.hh | Utility::options::StringVectorOption forward declarations |
| StringVectorOption.hh | Program string vector option class |
| VariantOption.fwd.hh | Utility::options::VariantOption forward declarations |
| VariantOption.hh | Variant option class |
| VectorOption.fwd.hh | Utility::options::VectorOption forward declarations |
| VectorOption.hh | Program vector-valued option interface class |
| VectorOption_T_.fwd.hh | Utility::options::VectorOption_T_ forward declarations |
| VectorOption_T_.hh | Program vector-valued option abstract base class |
| ► pointer | |
| ► boost | |
| access_ptr.hh | Non-owning access smart pointer |
| owning_ptr.hh | Owning smart pointer using C++11 |
| ReferenceCount.fwd.hh | |
| ReferenceCount.hh | Dummy base class |
| ► std | |
| access_ptr.hh | Non-owning access smart pointer |
| owning_ptr.hh | Owning smart pointer using C++11 |
| ReferenceCount.fwd.hh | |
| ReferenceCount.hh | Dummy base class |
| access_ptr.fwd.hh | Non-owning access smart pointer – dispatch class |
| access_ptr.hh | Non-owning access smart pointer – dispatch class |
| owning_ptr.functions.hh | |
| owning_ptr.fwd.hh | Non-owning owning smart pointer – dispatch class |
| owning_ptr.hh | Non-owning access smart pointer – dispatch class |
| ReferenceCount.fwd.hh | Utility::pointer::ReferenceCount forward declarations |
| ReferenceCount.hh | ReferenceCount base class – dispatch class |
| ► py | |
| Inheritance.hh | |
| PyAssert.hh | |
| PyExitCallback.cc | |
| PyExitCallback.fwd.hh | |
| PyExitCallback.hh | |
| PyHelper.hh | |
| ► signals | |
| BufferedSignalHub.fwd.hh | Forward declaration for utility::signals::BufferedSignalHub |
| BufferedSignalHub.hh | SignalHub capable of buffering while blocking |
| Link.fwd.hh | Forward declaration for utility::signals::Link |
| Link.hh | Class storing the link between observers and subjects |
| LinkUnit.fwd.hh | Forward declaration for utility::signals::LinkUnit |
| LinkUnit.hh | Class specifying actual link data between observers and subjects |
| PausableSignalHub.fwd.hh | Forward declaration for utility::signals::PausableSignalHub |
| PausableSignalHub.hh | BufferedSignalHub capable of pausing and waiting for stdin |
| SignalHub.fwd.hh | Forward declaration for utility::signals::SignalHub |
| SignalHub.hh | Primary class for function based implementation of observer pattern |
| TokenHub.fwd.hh | Forward declaration for utility::signals::TokenHub |
| TokenHub.hh | BufferedSignalHub capable of passing observers |
| ► sql_database | |
| DatabaseSessionManager.cc | |
| DatabaseSessionManager.fwd.hh | |
| DatabaseSessionManager.hh | |
| types.cc | |
| types.hh | |
| util.hh | |
| ► tag | |
| Tag.cc | An object for reading/writing a simple xml-like language |
| Tag.fwd.hh | |
| Tag.hh | An object for reading/writing a simple xml-like language |
| ► thread | |
| backwards_thread_local.hh | File to provide backwards compatibility for the thread_local keyword |
| ReadWriteMutex.cc | Classes to manage data that can be read by multiple threads and written to by only one thread |
| ReadWriteMutex.hh | Classes to manage data that can be read by multiple threads and written to by only one thread |
| threadsafe_creation.fwd.hh | |
| threadsafe_creation.hh | |
| ► tools | |
| make_map.hh | Common function to build vector, vector0, vector1, map |
| make_templates.py | Program that generate make_vector.hh and make_map.hh files |
| make_vector.hh | Common function to build vector, vector0, vector1, map |
| make_vector1.hh | |
| assert.hh | |
| backtrace.hh | Programmatic backtrace whenever you want it |
| basic_sys_util.cc | All system functions in utility that have no other home |
| basic_sys_util.hh | All system functions in utility that have no other home |
| Binary_Util.cc | |
| Binary_Util.hh | |
| BitSet.fwd.hh | Utility::BitSet forward declarations |
| BitSet.hh | Simple bit set |
| BitVector.fwd.hh | Utility::BitVector forward declarations |
| BitVector.hh | Simple bit vector |
| Bound.fwd.hh | Utility::Bound forward declarations |
| Bound.hh | Bound value class |
| CSI_Sequence.cc | Terminal ASCII codes |
| CSI_Sequence.fwd.hh | Terminal ASCII codes |
| CSI_Sequence.hh | Terminal ASCII codes |
| curl.cc | Implements a OO interface to CURL wrapping and hiding the ugly C callbacks |
| curl.hh | Implements a OO interface to CURL wrapping and hiding the ugly C callbacks |
| DereferenceIterator.hh | Class for Iterating across a container of OPs if the function expects iterators of the dereferenced objects. example: if you have a loop that iterates on decoys via SilentFileData::begin()... SilentFileData::end() it uses the dereferenced objects: i.e., it->fill_pose() SilentFileData sfd; my_func( sfd.begin(), sfd.end() ); |
| down_cast.hh | Fast polymorphic down-casting functions |
| exit.cc | Program exit functions and macros |
| exit.hh | Program exit functions and macros |
| Factory.hh | A singleton templated factory, is is usually created by protocols/init/init.cc object generated by factory must have name() and create() Factory< Outputter > and Factory< Inputter > are two examples of this factory in use Wonder if there is a way to do lazy initialization of this singleton |
| fix_boinc_read.hh | |
| fixedsizearray1.fwd.hh | |
| fixedsizearray1.hh | |
| FixedSizeLexicographicalIterator.fwd.hh | |
| FixedSizeLexicographicalIterator.hh | Class for iterating across all words of a compile-time-known fixed-length, composed of letters from varying alphabets, where each alphabet is represented by its size. This iteration is performed in lexicographical order. All allocation of a FixedSizeLexicographicalIterator takes place on the stack, and is therefore much faster than a regular LexigographicalIterator |
| FixedSizeLexicographicalIterator.tmpl.hh | |
| heap.cc | Class definition for a heap object based on Charlie Strauss's heap code ported over from rosetta++ |
| heap.fwd.hh | Forward class definition of class heap |
| heap.hh | Class definition for a heap object based on Charlie Strauss's heap code ported over from rosetta++. Stores a sorted list of integers based on floating-point values |
| in_place_list.fwd.hh | |
| in_place_list.hh | Doubly linked list where elements are shuffled in place |
| inline_file_provider.cc | |
| inline_file_provider.hh | |
| integer_mapping.cc | A set of useful classes to map between two enumerations. So far, only a subset mapping is implemented |
| integer_mapping.fwd.hh | |
| integer_mapping.hh | A set of useful classes to map between two enumerations. So far, only a subset mapping is implemented |
| iter_util.hh | |
| LexicographicalIterator.cc | |
| LexicographicalIterator.fwd.hh | |
| LexicographicalIterator.hh | Class for iterating across all words of a fixed-length, composed of letters from varying alphabets, where each alphabet is represented by its size. This iteration is performed in lexicographical order |
| make_static_database.py | |
| minmax.hh | |
| mpi_util.cc | |
| mpi_util.hh | |
| numbers.hh | Brief utility classes for numeric usage |
| OrderedTuple.fwd.hh | Forward declaration of OrderedTuple class |
| OrderedTuple.hh | Class for compairing/sorting data where sort-precidence is in descending order from begin() to end() |
| recent_history_queue.cc | A queue for holding the history in which certain members of a set are promoted to the front of the queue before eventually falling off the end of the queue |
| recent_history_queue.hh | A queue for holding the history in which certain members of a set are promoted to the front of the queue before eventually falling off the end of the queue |
| Show.hh | Uniformed printing functionality for data types |
| SimulateMPI.cc | |
| SimulateMPI.fwd.hh | |
| SimulateMPI.hh | |
| SingletonBase.hh | A base class for all singltons using CRTP and managing the complexity of safely initializing singltons in a thread-safe way |
| sort_predicates.hh | |
| static_database.cc | |
| static_database.hh | |
| stream_util.hh | |
| string_util.cc | Some std::string helper functions |
| string_util.hh | Some std::string helper functions |
| utility.functions.hh | Numeric functions (to avoid dependency on numeric package) |
| vector0.fwd.hh | Utility::vector0 forward declarations |
| vector0.hh | Vector0: std::vector with assert-checked bounds |
| vector0_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_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 |
1.8.7