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Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
 CPLMD::ActionBase class for all the input Actions
 CPLMD::ActionOptionsThis class is used to bring the relevant information to the Action constructor
 CPLMD::ActionRegisterRegister holding all the allowed keywords
 CPLMD::AngleClass to compute angles
 CPLMD::AtomNumberSimple class to store the index of an atom
 CPLMD::AtomsClass containing atom related quantities from the MD code
 CPLMD::BiasRepresentationThis class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias
 CPLMD::CH3ShiftsProvides the keyword CH3SHIFTS
 CPLMD::CInterpolation
 CPLMD::CitationsClass taking care of bibliography
 CPLMD::analysis::ClassicalScaling
 CPLMD::CLToolThis is the abstract base class to use for implementing new command line tool, within it there is information as to how to go about implemneting a new tool
 CPLMD::CLToolOptions
 CPLMD::CLToolRegisterSame as ActionRegister, but for CLTools
 CPLMD::CommunicatorClass containing wrappers to MPI
 CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_rowSmall utility class which just contains a pointer to the T and the row number
 CPLMD::Communicator::ConstDataConst version of Communicator::Data See Communicator::Data documentation
 CPLMD::CS2BackboneProvides the keyword CS2BACKBONE
 CPLMD::Communicator::DataStructure defining a buffer for MPI
 CPLMD::DLLoaderClass taking care of dynamic loading
 CPLMD::DynamicList< T >A class for storing a list that changes which members are active as a function of time
 CPLMD::DynamicList< PLMD::AtomNumber >
 CPLMD::DynamicList< unsigned >
 Cstd::exceptionSTL class
 CPLMD::ExchangePatterns
 CFieldBase
 CPLMD::FileBase::FieldBaseInternal tool
 CPLMD::FileBaseBase class for dealing with files
 CPLMD::function::FilesHandler
 CPLMD::molfile::fio_iovec
 CPLMD::FlexibleBin
 CPLMD::bias::MetaD::Gaussian
 CPLMD::Grid
 CPLMD::HistogramBeadA class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \)
 CPLMD::colvar::PathMSDBase::ImagePathThis class is a general container for path stuff
 CPLMD::colvar::PathMSDBase::imgOrderByDist
 CPLMD::colvar::PathMSDBase::imgOrderBySimilarity
 CPLMD::Kearsley
 CPLMD::KernelFunctions
 CPLMD::Keywords::KeyTypeThis class lets me pass keyword types easily
 CPLMD::KeywordsThis class holds the keywords and their documentation
 CPLMD::analysis::LandmarkRegister
 CPLMD::analysis::LandmarkSelectionBase
 CPLMD::analysis::LandmarkSelectionOptions
 CPLMD::LatticeReductionClass implementing algorithms for lattice reduction
 CPLMD::LinkCellsA class for doing link cells
 CPLMD::crystallization::LOCAL_Q3Provides the keyword LOCAL_Q3
 CPLMD::crystallization::LOCAL_Q4Provides the keyword LOCAL_Q4
 CPLMD::crystallization::LOCAL_Q6Provides the keyword LOCAL_Q6
 CPLMD::MatrixSquareBracketsAccess< T, C, I, J >Utility class to add [][] access
 CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double >
 CPLMD::MatrixSquareBracketsAccess< Matrix< int >, int >
 CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::SwitchingFunction >, PLMD::SwitchingFunction >
 CPLMD::MatrixSquareBracketsAccess< Matrix< T >, T >
 CPLMD::MatrixSquareBracketsAccess< TensorGeneric< n, m >, double >
 CPLMD::molfile::md_atom
 CPLMD::molfile::md_box
 CPLMD::molfile::md_file
 CPLMD::molfile::md_header
 CPLMD::molfile::md_ts
 CPLMD::MDAtomsBaseClass containing interface to MDAtomsTyped
 CPLMD::MetricRegister
 CPLMD::MolDataClassThis class provides information on various kinds of molecules for instance the kinds of residues that are in a protein the atoms involved in the backbone of a particular residue etc
 CPLMD::molfile::molfile_atom_tPer-atom attributes and information
 CPLMD::molfile::molfile_graphics_tIndividual graphics object/element data
 CPLMD::molfile::molfile_metadata_tFile level comments, origin information, and annotations
 CPLMD::molfile::molfile_plugin_tMain file reader API
 CPLMD::molfile::molfile_qm_basis_tData for QM basis set
 CPLMD::molfile::molfile_qm_hessian_tData from QM Hessian/normal mode runs
 CPLMD::molfile::molfile_qm_metadata_tSizes of various QM-related, timestep independent data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data
 CPLMD::molfile::molfile_qm_sysinfo_tQM run info
 CPLMD::molfile::molfile_qm_tQM related information that is timestep independent
 CPLMD::molfile::molfile_qm_timestep_metadataSizes of various QM-related, per-timestep data arrays which must be allocated by the caller (VMD) so that the plugin can fill in the arrays with data
 CPLMD::molfile::molfile_qm_timestep_tQM per trajectory timestep info Note that each timestep can contain multiple wavefunctions
 CPLMD::molfile::molfile_qm_wavefunction_tQM wavefunction
 CPLMD::molfile::molfile_timestep_metadata
 CPLMD::molfile::molfile_timestep_t
 CPLMD::molfile::molfile_volumetric_tMetadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading
 CPLMD::setup::MolInfoProvides the keyword MOLINFO
 CPLMD::MPI_CommSurrogate of MPI_Comm when MPI library is not available
 CPLMD::MPI_DatatypeSurrogate of MPI_Datatype when MPI library is not available
 CPLMD::MPI_RequestSurrogate of MPI_Request when MPI library is not available
 CPLMD::MPI_StatusSurrogate of MPI_Status when MPI library is not available
 CPLMD::MultiReferenceBase
 CPLMD::NeighborListA class that implements neighbor lists from two lists or a single list of atoms
 CPLMD::OptimalAlignmentA class that is intended to include or combine various optimal alignment algorithms
 CPLMD::function::FuncPathMSD::ordering
 CPLMD::function::FuncPathMSD::pairordering
 CPLMD::Pbc
 CPLMD::PDBMinimalistic pdb parser
 CplumedMain plumed object
 CPLMD::PlumedC++ wrapper for plumed
 Cplumed_function_holderHolder for function pointer
 Cplumed_plumedmain_function_holderContainer for plumedmain function pointers (create, cmd and finalize)
 CPLMD::PlumedMainInitializerStatic object which registers Plumed
 CPLMD::Random
 CPLMD::ReferenceConfiguration
 CPLMD::ReferenceConfigurationOptionsAbstract base class for calculating the distance from a reference configuration
 CPLMD::Communicator::RequestWrapper class for MPI_Request
 CPLMD::RMSDA class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame
 CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::RowSmall utility class which just contains a pointer to the T and the row number
 CPLMD::Communicator::StatusWrapper class for MPI_Status
 CPLMD::StopwatchClass implementing stopwatch to time execution
 CPLMD::SwitchingFunctionSmall class to compure switching functions
 CPLMD::TargetDist
 CPLMD::TensorChecksSmall auxiliary class
 CPLMD::Stopwatch::TimeClass to hold the value of absolute time
 CPLMD::ToolsEmpty class which just contains several (static) tools
 CPLMD::TorsionClass to compute torsional angles
 CPLMD::molfile::trx_hdr
 CPLMD::UnitsSmall utility class that contains information about units
 CPLMD::ValueA class for holding the value of a function together with its derivatives
 Cstd::vector< T >STL class
 CPLMD::VectorChecksSmall auxiliary class
 CPLMD::VectorGeneric< n >Class implementing fixed size vectors of doubles
 CPLMD::vesselbase::Vessel
 CPLMD::vesselbase::VesselOptionsThis class is used to pass the input to Vessels
 CPLMD::vesselbase::VesselRegister
 CPLMD::molfile::vmdplugin_tTypedef for generic plugin header, individual plugins can make their own structures as long as the header info remains the same as the generic plugin header, most easily done by using the vmdplugin_HEAD macro
 CPLMD::Stopwatch::WatchClass to store a single stopwatch
 CPLMD::WeightBase
 CPLMD::WithCmdBase for classes with cmd() method