PROFASI  Version 1.5
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCprf::AtomRepresentation of an atom in PROFASI
oCprf::AtomCoordinatesA class to store the coordinates of an atom
oCprf::AtomDescriptorMinimal information that identifies one atom in a PDB file
oCprf::AtomLabelDictionaryA translator for atom labels from other conventions
oCprf::AtomRecordRecord corresponding to one atom in a PDB file
oCprf::BackboneRepresentation for the protein backbone
oCBasicMCRunConstant temperature Monte Carlo simulations
|oCParTempRunParallel tempering class
|oCRetraceA program to retrace the path of an individual replica of parallel tempering
|oCSimAnnealRunSimulated annealing
|oCSimTempRunSimulated tempering with profasi
|\CWLRunMonte Carlo simulations with the Wang Landau method
oCprf_xml::ChunkA "chunk" of data in an XML file
oCprf::CompositePredicate< T >A composite predicate class
oCprf::CompositePredicate< AtomDescriptor >
oCprf::ContactAn abstraction of a contact
oCprf::ContactFunctionA boolean function object class on Contacts
|oCprf::CaContactA simple contact function based on Calpha separation
|oCprf::HBContactA ContactFunction based on hydrogen bonds
|oCprf::HPContactA Contact function for Hydrophobic contacts
|\Cprf::ProximityA ContactFunction based on spatial proximity
oCprf_utils::CorrelationBoxCorrelationBox finds the correlation coefficient between two data streams
oCprf_utils::CorrelationEvaluator
oCprf::DistanceRestraintA single distance restraint
oCprf::dof_change_typeA structure to hold the most basic information about one change
oCprf::DOF_IndexHelper class for population for DOF management
oCprf::DOF_InfoA structure with 8 integers to characterize a degree of freedom
oCextract_propsCalculating run-time properties from traj files
oCextract_snapshotExtracting a snapshot configuration
oCprf::ExVolBaseHelper class for both ExVol and LocExVol classes
|oCprf::ExVolThe excluded volume term
|\Cprf::LocExVolThird-neighbour excluded volume contribution
oCprf::FindCoordSimple but very useful class used widely in PROFASI to get coordinates
oCprf_utils::His1DThe default histogram utility in ProFASi is based on His1D
|\Cprf_utils::AdaptiveHisA histogram that can adjust its own range according to the data
oCprf_utils::His2DA histogram with 2 independent variables
oCprf::HydrogenBondHydrogenBond base class from which the HBMM and HBMS classes are derived
|oCprf::HBMMThe Backbone-Backbone hydrogen bond term
|\Cprf::HBMSThe Backbone-Sidechain hydrogen bond term
oCprf::LigandAn abstract class providing a base for amino acids and capping groups
|\Cprf::AminoAcidAmino acid base class
oCprf::MCMC class handles the Markov Chain Monte Carlo evolution
oCprf_utils::MeanFinderSimple utility to find the mean of a vector
oCminimizeMinimize an expression over degrees of freedom of a protein molecule
oCprf::NamedAnything that has a name
|oCprf::NodeA Node is (like in graph theory) a meeting point of a few bonds
|oCprf::ObservableAn observable is in principle anything that is named and has a value
|\Cprf::UpdateThe base class for all conformational updates
oCprf::ObsHandlerA handler class for Observables
oCprf_utils::OptBaseBase class for program switches and options
|oCprf_utils::ProgOptOne option that a program may handle
|\Cprf_utils::ProgSwitchA program switch
oCprf::ParTempParallel Tempering
oCprf::PDB_modelAn abstraction of one model in a PDB file
oCprf_utils::PermutationPermutation class originally developed by SM for ALFS
oCprf::PopBaseBase class for a population of representations of proteins
|oCprf::PDBReaderA top level PDB file parser
|\Cprf::PopulationA population of proteins
oCPopulationHandlerHelper class for configuring the protein population
oCprf_traj::prf_raw_confReader for PROFASI's raw binary data format
oCprf_utils::prf_timeAbstraction for some system time function
oCprf_utils::ProgArgsA utility to help manage program parameters
oCprf::ProteinRepresentation for a poly peptide chain
oCprf::RandomNumberBaseBase class for Random number generators for use in PROFASI
|oCprf::MersenneTwisterMersenneTwister is the default random number generator for profasi
|\Cprf::Ran3nEngineRan3nEngine is the default random number generator class for profasi
oCprf_utils::RangeBoxSmall utility class RangeBox
oCregularizerA program to regularize PDB structures
oCprf::RestraintFunctionSimple harmonic potential well for arbitrary variable
|oCprf::CircularNormalCircular normal potential well
|oCprf::FlattenedPLPower law with a small distance cut
|oCprf::GaussianRestraintRestraint of the form of a Gaussian
|\Cprf::PowerLawRestraintGeneric power law potential
oCprf::RMSDRoot Mean Square Deviation
oCprf::RMSD_UtilsThe RMSD_Utils handler class
oCprf::SelResAn abstraction for a residue selected for further processing
oCprf::ShapeRepresents an abstract shape in space defined by a set of points
oCprf::SimplePredicate< T >An extensible composite-capable simple predicate class
oCprf::SimplePredicate< AtomDescriptor >
|oCprf::AtomTypeSelectorA predicate that returns true if the atom is of a certain species
|oCprf::isAtomA trivial predicate to select all atoms
|oCprf::isBackboneAtomA predicate that returns true if the atom is on the backbone
|oCprf::isHeavyAtomA predicate that returns true if the atom is not Hydrogen
|oCprf::LabelSelectorA predicate that returns true if the atom has a certain label
|\Cprf::ResSelectorA predicate that returns true if the atom is in one kind of residue
oCprf_utils::StatBox
oCprf_utils::TimerProFASi's own timer for managing time limited runs
oCprf_traj::TrajectoryPROFASI (multi-segment) trajectories
oCprf_traj::TrajIteratorIterator to browse trajectories
oCprf_traj::TrajSegA segment of a trajectory
oCprf_traj::TrajSnapshotSnapshot of program state
oCUpdatesHandlerA manager for MC updates
oCprf::Vector3A representation of three vectors
oCprf::WangLandauWang Landau iterations
oCprf_xml::XML_MiniA small class to do the book keeping for XML parsing
\Cprf_xml::XML_NodeA class to represent an XML node

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2