► C loos::AbstractObserver ► C loos::BasicProgress C loos::PercentProgress Provide feedback by percent-complete C loos::PercentProgressWithTime ► C argparse.Action C all_stacking.FullHelp C hierarchical-cluster.FullHelp C loos.pyloos.options.FullHelper C packing_score_per_res.FullHelp C scattering.FullHelp C set_segids.FullHelp ► C loos::internal::Action Base class for all commands.. C loos::internal::Backbone Shortcut for checking for backbone atoms.. C loos::internal::Hydrogen Shortcut for checking for hydrogens.. C loos::internal::drop Drop the top item from the stack C loos::internal::dup Duplicate the top item on the stack C loos::internal::equals Test for equality: ARG1 ARG == C loos::internal::extractNumber Extracts a number for a string on the stack using a regular expression: ARG1 regexp(S) C loos::internal::greaterThan ARG1 ARG2 > C loos::internal::greaterThanEquals ARG1 ARG2 >= C loos::internal::lessThan Relation operators...: ARG1 ARG2 < C loos::internal::lessThanEquals ARG1 ARG2 <= C loos::internal::logicalAnd ARG1 ARG2 && C loos::internal::logicalNot ARG1 ! C loos::internal::logicalOr ARG1 ARG2 || C loos::internal::logicalTrue Always returns true.. C loos::internal::matchRegex Regular expression matching: ARG1 regexp(S) C loos::internal::matchStringAsRegex Regular expression matching: ARG1 regexp(ARG2) C loos::internal::pushAtomChainId Push atom's chain ID onto the stack C loos::internal::pushAtomId Push atom id onto the stack C loos::internal::pushAtomIndex Push atom index onto the stack C loos::internal::pushAtomName Push atom name onto the stack C loos::internal::pushAtomResid Push atom's residue id onto the stack C loos::internal::pushAtomResname Push atom'ss residue name onto the stack C loos::internal::pushAtomSegid Push atom's segid onto the stack C loos::internal::pushFloat Push a float onto the data stack C loos::internal::pushInt Push an integer onto the data stack C loos::internal::pushString Push a std::string onto the data stack C loos::OptionsFramework::AggregateOptions Combines a set of OptionsPackages C loos::AscendingSort< T > Policy class for sorting in ascending sequence C loos::Atom Basic Atom class for handling atom properties C loos::AtomCoordsEquals Compares two atoms based on name, id, resid, resname, segid, and coords C loos::AtomEquals Compares two atoms based solely on name, id, resid, resname, and segid ► C loos::AtomicGroup Class for handling groups of Atoms (pAtoms, actually) C loos::Amber Class for reading in AMBER parmtop/coord files.. C loos::CHARMM Class for reading a CHARMM coordinate file C loos::Gromacs Implements a GROMACS model file (.gro) C loos::MDTraj Class for reading a MDTraj HDF5 file C loos::MMCIF Class to read pdbx/mmcif files C loos::PDB PDB reading/writing class C loos::PSF Class for reading a subset of the PSF format C loos::TinkerXYZ Class for reading a subset of the TinkerXYZ format C loos::internal::AtomicNumberDeducer ► C loos::AtomSelector Virtual base-class for selecting atoms from a group C loos::AndSelector Combines two selectors with a logical "and" C loos::AtomNameSelector Predicate for selecting atoms based on explicit name matching C loos::BackboneSelector Predicate for selecting backbone C loos::CAlphaSelector Predicate for selecting CA atoms C loos::HeavyAtomSelector Select non-hydrogen atoms C loos::HeavySolventSelector Select only heavy solvent atoms C loos::HydrogenSelector Select hydrogen atoms C loos::IndexSelector Predicate for selecting atoms based on index C loos::KernelSelector Selection predicate that executes a compiled Kernel C loos::NotSelector Negates a selection predicate C loos::OrSelector Combines two selectors with a logical "or" C loos::ResidRangeSelector Predicate for selecting atoms from a range of resid's C loos::SegidSelector Predicate for selecting atoms based on the passed segid string C loos::SolventSelector Predicate for selecting solvent based on common solvent SEGIDs C loos::ZSliceSelector Predicate for selecting atoms in a specific range of z values C loos::internal::BasicMatrixFormatter< T > C loos::BoundFmt Internal helper class to bind formatting state ► C loos::DensityTools::BulkEstimator C loos::DensityTools::NullEstimator C loos::DensityTools::ZClipEstimator C loos::DensityTools::ZSliceEstimator ► C CalcPropertyBase ► C CalcProperty< double > C CalcDensity C CalcHeight C CalcMolOrder ► C CalcProperty< loos::GCoord > C CalcDipole C CalcOrientVector C CalcProperty< T > ► C loos::Math::ColMajor Class for storing a matrix in column-major order C loos::Math::Matrix< int > C loos::Math::Matrix< T, OrderPolicy, StoragePolicy > Simple matrix template class using policy classes to determine behavior C loos.pyloos.ConvexHull.ConvexHull C loos::Coord< T > Basic 3-D coordinates class C loos::Coord< double > C loos::Coord< int > C loos::DensityTools::DensityGrid< T > A simple 3D grid class of arbitrary types C loos::DensityTools::DensityGrid< double > C loos::DensityTools::DensityGrid< int > C loos::DensityTools::DensityGridPlane< T > Encapsulates an i,j-plane from an DensityGrid C loos::DensityTools::DensityGridRow< T > Encapsulates a j-row from an DensityGrid C loos::DescendingSort< T > Policy class for sorting in descending sequence C DualWorker C loos.Voronoi.Voronoi.Edge ► C ENM::ElasticNetworkModel Interface for all ENMs C ENM::ANM Anisotropic network model C ENM::VSA Vibrational subsystem analysis ENM ► C Exception C loos.Voronoi.Voronoi.VoronoiError ► C std::exception C loos::HBonds::ErrorWithAtom ► C loos::LOOSError Generic LOOS exception C loos::Atom::UnsetProperty DEPRECATED exception class...use loos::UnsetProperty instead C loos::DCD::EndOfFile ► C loos::FileError Errors related to File I/O C loos::FileOpenError Error while opening a file ► C loos::FileReadError Errors that occur while reading a file C loos::FileReadErrorWithLine Errors that occur while reading a text file (where lines are tracked) C loos::FileWriteError Errors while writing to files C loos::NumericalError Exception caused by a blas/atlas error C loos::OptionsError Exception in options C loos::ParseError Exception when parsing input data C loos::TrajectoryError Errors related to trajectory reading and writing C loos::UnsetProperty Exception when trying to use an unset Atom property C loos::XDRDataSizeError Exception indicating internal XDR error ► C FlexLexer C yyFlexLexer C loos::Fmt Output formatter class, adapted from Stroustrup's book C loos::FormFactor C loos::FormFactorSet ► C boost::spirit::qi::grammar C loos::internal::RangeParser< Iterator > ► C Clustering::HAC ► C Clustering::AverageLinkage C Clustering::KGS C loos::HBondDetector Class for detecting hydrogen bonds C Header C loos::AtomicGroup::Iterator Our own simple iterator for stepping over all managed atoms ► C boost::iterator_facade C loos::DensityTools::DensityGridIterator< T, R > Random access iterator using the BOOST facade C loos::Kernel The Kernel (virtual machine) for compiling and executing user-defined atom selections C loos::LineReader Class for reading line-by-line from a file while tracking line numbers and stripping comments C loos.pyloos.options.LoosOptions C Master C loos::Matrix44< T > Specialized 4x4 Matrix class for handling coordinate transforms C loos::MatrixReadImpl< T, P, S > C loos::MatrixReadImpl< T, Math::Triangular, S > Special handling for triangular matrices C loos::MatrixReadImpl< T, P, Math::SparseArray > Special handling for sparse matrices C loos::MatrixWriteImpl< T, P, S, F > C loos::MatrixWriteImpl< T, Math::Triangular, S, F > Write out a triangular matrix C loos::MatrixWriteImpl< T, P, Math::SparseArray, F > Write out a sparse matrix C loos.pyloos.NAMDBin.NAMDBin ► C boost::noncopyable C loos::StreamWrapper Simple wrapper class for caching stream pointers C loos::DensityTools::NonzeroDensity< T > Functor that is true for any non-zero density ► C object C loos.pyloos.trajectories.Trajectory Python-based wrapper for LOOS Trajectories This class turns a loos Trajectory into something more python-like ► C loos.pyloos.trajectories.VirtualTrajectory Virtual trajectory composed of multiple Trajectory objects This class can combine multiple loos.pyloos.Trajectory objects into one big "virtual" trajectory C loos.pyloos.trajectories.AlignedVirtualTrajectory A virtual trajectory that supports iterative alignment ► C loos::OptionsFramework::OptionsPackage Base class for options C Clustering::ClusteringOptions C ToolOptions C ToolOptions C ToolOptions C ToolOptions C ToolOptions C ToolOptions C ToolOptions C loos::OptionsFramework::BasicConvergence C loos::OptionsFramework::BasicOptions Options common to all tools (including –fullhelp) C loos::OptionsFramework::BasicSelection Provides a single LOOS selection (–selection) C loos::OptionsFramework::BasicSplitBy Provides a mechanism for controlling how to split an AtomicGroup C loos::OptionsFramework::BasicTrajectory Basic trajectory with a –skip option C loos::OptionsFramework::BasicWater Options specific to tools that work with water/internal-water C loos::OptionsFramework::ModelWithCoords Request a model with coordinates C loos::OptionsFramework::MultiTrajOptions Multiple trajectories as one trajectory via MultiTrajectory C loos::OptionsFramework::OutputPrefix Gets a string as prefix for output files (–prefix) C loos::OptionsFramework::OutputTrajectoryOptions C loos::OptionsFramework::OutputTrajectoryTypeOptions C loos::OptionsFramework::RequiredArguments Provides simple way to add command-line arguments (required options) C loos::OptionsFramework::TrajectoryWithFrameIndices Trajectory with either a –range or –skip C loos::OptionsFramework::TwoModelsWithCoords Request Two models with coordinates C loos::OptionsFramework::WeightsOptions C loos::internal::OutputTrajectoryNameBindingType C loos::Parser Front-end to the Bison/Flex parser C loos::ParserDriver C loos::PercentTrigger Trigger whenever at least frac percent more iterations have happened C loos::PeriodicBox Class for managing periodic box information C loos::PreciseMatrixFormatter< T > Generic matrix element formatter allowing setting of width and precision C loos::internal::RangeItem C RegexFmt C loos.Voronoi.Voronoi.Region C loos::Remarks Class for handling PDB Remarks C loos::RnaSuite Class for assigning backbone suites to an RNA C loos::Math::RowMajor Class for storing a matrix in row-major order.. ► C std::runtime_error C ENM::BadSpringFunction Bad spring function was requested C ENM::BadSpringParameter Unspecified problem with parameters in SpringFunction C loos::MatrixReadError Generic reading error class C ScanfFmt C loos::ScientificMatrixFormatter< T > Generic matrix element formatter using scientific notation.. C loos::Math::SharedArray< T > Storage policy for a block of memory wrapped in a boost::shared_array pointer ► C SharedArray C loos::Math::Matrix< int > C loos::Math::Matrix< T, OrderPolicy, StoragePolicy > Simple matrix template class using policy classes to determine behavior C loos::SharedPeriodicBox This class manages a shared Periodicbox C loos::HBonds::SimpleAtom ► C loos::SimpleCounter Basic progress counter object, defining the interface.. C loos::EstimatingCounter A progress counter that can estimate how much time is left C loos::ProgressCounter< Trigger, Counter > The progress counter front-end C loos::DensityTools::SimpleMeta Simple class for handling metadata C Simplex< T > Nelder-Meade Simplex Optimizer (based loosely on the NRC (1996) implementation) C SingleWorker C SortDatum C loos::Math::SparseArray< T > Storage policy for a sparse matrix (see important note in the detailed documentation) ► C ENM::SpringFunction Interface for ENM spring functions ► C ENM::UniformSpringFunction Spring functions that are uniform in all directions (ie return a single value) C ENM::ConstBonded Use a spring function that is a constant weight regardless of distance C ENM::DistanceCutoff Basic distance cutoff for "traditional" ENM C ENM::DistanceWeight Distance weighting (i.e. C ENM::ExponentialDistance Exponential distance weighting (i.e. C ENM::HCA HCA method (bimodal distance-based function) ► C ENM::SuperBlock This class creates superblocks in a hessian ► C ENM::SuperBlockDecorator SuperBlock decorator base class C ENM::BoundSuperBlock Decorator for switching spring functions based on a matrix of flags C loos.Voronoi.Voronoi.SuperRegion C loos.pyloos.SymmMatrix.SymmMatrix C loos::internal::SystemNameBindingType C Threader< W > C loos::DensityTools::Threshold< T > Functor that is true if value is greater than or equal to threshold C loos::DensityTools::ThresholdRange< T > Functor that is true if value is between low and hi, inclusive C loos::TimeSeries< T > Time Series Class ► C loos::Trajectory Base-class for polymorphic trajectories C loos::AmberNetcdf Class for reading Amber Trajectories in NetCDF format C loos::AmberRst Class for reading amber restart files as a single-frame trajectory C loos::AmberTraj Class for reading amber coordinate trajectories C loos::CCPDB Class for interpreting concatenated PDB files as a Trajectory C loos::DCD Class for reading DCD files C loos::MDTrajTraj Class for reading MDTraj HDF5 coordinate trajectories C loos::MultiTrajectory Combine multiple trajectories (pTraj's) into one large virtual trajectory C loos::PDBTraj Class for intepreting separate PDB files as a single trajectory C loos::TRR Class representing the GROMACS TRR trajectory files C loos::TinkerArc Class for handling Tinker ARC files (concatenation of .xyz files) C loos::XTC Class representing GROMACS reduced precision, compressed trajectories C loos::internal::TrajectoryNameBindingType ► C loos::TrajectoryWriter Base class for writing trajectories C loos::DCDWriter A very lightweight class for writing simple DCDs C loos::XTCWriter Class for writing Gromacs XTC trajectories C loos::Math::Triangular Class for storing a symmetric triangular matrix C loos::TriggerAlways This is a simple "trigger" for use as a default C loos::TriggerEvery Trigger every i-iterations C loos::UniqueStrings Class for uniquifying strings.. C loos::UnitCell This class encapsulates crystallographic unit cell data C loos::unordered_pair_eq< T > Test equality of unordered pair. typename T must have == operator C loos::unordered_pair_hash< T > C loos::UserTimer Policy class for tracking only user process time C loos::internal::Value Value class for the LOOS Kernel (virtual machine) C loos::internal::ValueStack C loos.Voronoi.Voronoi.VoronoiWrapper ► C loos::WallTimer Policy class for tracking wall-time C loos::Timer< loos::WallTimer > C loos::Timer< TimerType > Class for tracking time ► C loos::DensityTools::WaterFilterBase Base interface for water filter/picker C loos::DensityTools::WaterFilterAxis Pick waters that are within a radius of the principal axis for a molecule C loos::DensityTools::WaterFilterBlob Pick waters based on a grid-mask C loos::DensityTools::WaterFilterBox Pick waters inside a bounding box C loos::DensityTools::WaterFilterContacts Pick waters with a minimum number of contacts to protein atoms C loos::DensityTools::WaterFilterCore Pick waters that are within a radius of the core axis for a molecule ► C loos::DensityTools::WaterFilterDecorator Decorator base class for "decorating" the core water filters.. C loos::DensityTools::BulkedWaterFilter Add bulk water back into the mask/map C loos::DensityTools::ZClippedWaterFilter Restrict waters to be within a given z-range C loos::DensityTools::WaterFilterRadius Pick waters within a given radius of a group of atoms C loos::DensityTools::WaterHistogrammer ► C loos::Weights C loos::UniformWeight C loos::WeightsFromFile C loos::internal::XDRReader This class provides some facility for handling XDR data C loos::internal::XDRWriter C loos::DensityTools::XEDMWriter< T > Functor for writing out ASCII formatted X-Plor electron density maps C loos::XForm Matrix class for handling coordinate transforms.. C loos.pyloos.ConvexHull.ZSliceSelector C loos.Voronoi.Voronoi.ZSliceSelector
