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  a  
FlexibleBin (PLMD)    PathBase (PLMD::mapping)   
Flush (PLMD::generic)    PathMSD (PLMD::colvar)   
ABMD (PLMD::bias)    ForwardDecl (PLMD)    PathMSDBase (PLMD::colvar)   
Action (PLMD)    FourierTransform (PLMD::gridtools)    PathReparameterization (PLMD::mapping)   
ActionAnyorder (PLMD)    FretEfficiency (PLMD::isdb)    PathTools (PLMD::mapping)   
ActionAtomistic (PLMD)    FuncPathGeneral (PLMD::function)    Pbc (PLMD)   
ActionOptions (PLMD)    FuncPathMSD (PLMD::function)    PBMetaD (PLMD::bias)   
ActionPilot (PLMD)    FuncSumHills (PLMD::function)    PCA (PLMD::dimred)   
ActionRegister (PLMD)    Function (PLMD::function)    PCARMSD (PLMD::colvar)   
ActionSet (PLMD)    FunctionVessel (PLMD::vesselbase)    PCAVars (PLMD::mapping)   
ActionSetup (PLMD)    Funnel (PLMD::funnel)    PDB (PLMD)   
ActionShortcut (PLMD)    FUNNEL_PS (PLMD::funnel)    PdbRenumber (PLMD::cltools)   
ActionVolume (PLMD::multicolvar)   
  g  
PesMD (PLMD::cltools)   
ActionWithArguments (PLMD)    Piecewise (PLMD::function)   
ActionWithAveraging (PLMD::vesselbase)    PBMetaD::Gaussian (PLMD::bias)    PIV (PLMD::piv)   
ActionWithGrid (PLMD::gridtools)    MetaD::Gaussian (PLMD::bias)    Plumed (PLMD::generic)   
ActionWithInputGrid (PLMD::gridtools)    GenericMolInfo (PLMD)    plumed   
ActionWithInputMatrix (PLMD::adjmat)    GenExample (PLMD::cltools)    Plumed (PLMD)   
ActionWithInputVessel (PLMD::vesselbase)    GenTemplate (PLMD::cltools)    PlumedMain::plumed_error_handler (PLMD)   
ActionWithIntegral (PLMD::gridtools)    Ghost (PLMD::vatom)    plumed_function_holder   
ActionWithValue (PLMD)    Gradient (PLMD::crystallization)    plumed_nothrow_handler   
ActionWithVessel (PLMD::vesselbase)    GradientVessel (PLMD::crystallization)    plumed_plumedmain_function_holder   
ActionWithVirtualAtom (PLMD)    GREX (PLMD)    plumed_symbol_table_type   
AdaptivePath (PLMD::mapping)    Grid (PLMD)    PlumedHandle (PLMD)   
AdjacencyMatrixBase (PLMD::adjmat)    GridBase (PLMD)    PlumedMain (PLMD)   
AdjacencyMatrixVessel (PLMD::adjmat)    GridIntegrationWeights (PLMD::ves)    PlumedMainInitializer (PLMD)   
AlignedMatrixBase (PLMD::adjmat)    GridLinearInterpolation (PLMD::ves)    PolymerAngles (PLMD::crystallization)   
AlphaBeta (PLMD::multicolvar)    GridPrintingBase (PLMD::gridtools)    Position (PLMD::colvar)   
AlphaRMSD (PLMD::secondarystructure)    GridSearch (PLMD::gridtools)    PRE (PLMD::isdb)   
AltMin (PLMD::vesselbase)    GridToXYZ (PLMD::gridtools)    Print (PLMD::generic)   
AnalysisBase (PLMD::analysis)    GridVessel (PLMD::gridtools)    PrintDissimilarityMatrix (PLMD::analysis)   
Angle (PLMD)    Group (PLMD::generic)    ProbWeight (PLMD)   
Angle (PLMD::colvar)    Gyration (PLMD::colvar)    ProjectionOnAxis (PLMD::colvar)   
Angles (PLMD::multicolvar)   
  h  
ProjectNonLandmarkPoints (PLMD::dimred)   
annfunc::ANN (PLMD)    PropertyMap (PLMD::colvar)   
ANN (PLMD::function::annfunc)    Stopwatch::Handler (PLMD)    PropertyMap (PLMD::mapping)   
AntibetaRMSD (PLMD::secondarystructure)    Subprocess::Handler (PLMD)    Puckering (PLMD::colvar)   
ArgumentOnlyDistance (PLMD)    HBondMatrix (PLMD::adjmat)   
  q  
AsmJitRuntimePtr (PLMD::lepton)    HBPammHydrogens (PLMD::pamm)   
Exception::Assertion (PLMD)    HBPammMatrix (PLMD::pamm)    Q3 (PLMD::crystallization)   
AtomNumber (PLMD)    HBPammObject (PLMD::pamm)    Q4 (PLMD::crystallization)   
Atoms (PLMD)    Highest (PLMD::vesselbase)    Q6 (PLMD::crystallization)   
AtomValuePack (PLMD::multicolvar)    Histogram (PLMD::vesselbase)   
  r  
Average (PLMD::analysis)    Histogram (PLMD::analysis)   
AverageOnGrid (PLMD::gridtools)    HistogramBead (PLMD)    Random (PLMD)   
AverageVessel (PLMD::analysis)    HistogramOnGrid (PLMD::gridtools)    Random_Acceleration_MD (PLMD::maze)   
AveragingVessel (PLMD::vesselbase)   
  i  
Random_Walk (PLMD::maze)   
  b  
RandomExchanges (PLMD::generic)   
IFile (PLMD)    RDC (PLMD::isdb)   
BasisFunctions (PLMD::ves)    PathMSDBase::ImagePath (PLMD::colvar)    Read (PLMD::generic)   
Between (PLMD::vesselbase)    PathMSDBase::imgOrderByDist (PLMD::colvar)    ReadAnalysisFrames (PLMD::analysis)   
BF_Chebyshev (PLMD::ves)    PathMSDBase::imgOrderBySimilarity (PLMD::colvar)    ReadDissimilarityMatrix (PLMD::analysis)   
BF_Combined (PLMD::ves)    Include (PLMD::generic)    ReferenceArguments (PLMD)   
BF_Cosine (PLMD::ves)    Info (PLMD::cltools)    ReferenceAtoms (PLMD)   
BF_Custom (PLMD::ves)    InPlaneDistances (PLMD::multicolvar)    ReferenceConfiguration (PLMD)   
BF_Fourier (PLMD::ves)    IntegrateGrid (PLMD::gridtools)    ReferenceConfigurationOptions (PLMD)   
BF_Legendre (PLMD::ves)    IntermolecularDRMSD (PLMD)    ReferenceValuePack (PLMD)   
BF_Powers (PLMD::ves)    InterMolecularTorsions (PLMD::crystallization)    Communicator::Request (PLMD)   
BF_Sine (PLMD::ves)    InterpolateGrid (PLMD::gridtools)    Rescale (PLMD::isdb)   
Bias (PLMD::bias)    IntramolecularDRMSD (PLMD)    ReselectLandmarks (PLMD::analysis)   
BiasRepresentation (PLMD)    Plumed::Invalid (PLMD)    ResetCell (PLMD::generic)   
BiasValue (PLMD::bias)   
  j  
Restart (PLMD::setup)   
BiasWeight (PLMD)    Restraint (PLMD::bias)   
BondOrientation (PLMD::crystallization)    JCoupling (PLMD::isdb)    ReweightBase (PLMD::bias)   
Brent1DRootSearch (PLMD)   
  k  
ReweightBias (PLMD::bias)   
Bridge (PLMD::multicolvar)    ReweightMetad (PLMD::bias)   
BridgedMultiColvarFunction (PLMD::multicolvar)    OPESmetad::kernel (PLMD::opes)    ReweightTemperaturePressure (PLMD::bias)   
BridgeVessel (PLMD::vesselbase)    KernelFunctions (PLMD)    ReweightWham (PLMD::bias)   
  c  
Keywords::KeyType (PLMD)    CS2Backbone::RingInfo (PLMD::isdb)   
Keywords (PLMD)    RMSD (PLMD::colvar)   
Caliber (PLMD::isdb)    kt (PLMD::cltools)    RMSD (PLMD)   
CatomPack (PLMD::multicolvar)   
  l  
RMSDBase (PLMD)   
Cell (PLMD::colvar)    RMSDCoreData (PLMD)   
Center (PLMD::vatom)    LandmarkSelectionBase (PLMD::analysis)    rnd (PLMD::maze)   
CenterOfMultiColvar (PLMD::multicolvar)    LandmarkStaged (PLMD::analysis)    RootFindingBase (PLMD)   
CS2Backbone::ChemicalShift (PLMD::isdb)    LatticeReduction (PLMD)    MatrixSquareBracketsAccess::Row (PLMD)   
Citations (PLMD)    Plumed::LeptonException (PLMD)   
  s  
ClassicalMultiDimensionalScaling (PLMD::dimred)    LessThan (PLMD::vesselbase)   
CLTool (PLMD)    LinearBasisSetExpansion (PLMD::ves)    SAXS (PLMD::isdb)   
CLToolMain (PLMD)    LinkCells (PLMD)    SecondaryStructureRMSD (PLMD::secondarystructure)   
CLToolOptions (PLMD)    Load (PLMD::setup)    Select (PLMD::isdb)   
CLToolRegister (PLMD)    LOCAL_Q3 (PLMD::crystallization)    Selector (PLMD::isdb)   
CLToolSumHills (PLMD::cltools)    LOCAL_Q4 (PLMD::crystallization)    SelectRandomFrames (PLMD::analysis)   
ClusterAnalysisBase (PLMD::adjmat)    LOCAL_Q6 (PLMD::crystallization)    SelectWithStride (PLMD::analysis)   
ClusterDiameter (PLMD::adjmat)    LocalAverage (PLMD::multicolvar)    ShortcutVessel (PLMD::vesselbase)   
ClusterDistribution (PLMD::adjmat)    LocalEnsemble (PLMD::function)    SimpleCubic (PLMD::crystallization)   
ClusteringBase (PLMD::adjmat)    LocalSteinhardt (PLMD::crystallization)    SimpleMD (PLMD::cltools)   
ClusterProperties (PLMD::adjmat)    Exception::Location (PLMD)    SimpleRMSD (PLMD)   
ClusterSize (PLMD::adjmat)    Log (PLMD)    Simulated_Annealing (PLMD::maze)   
ClusterWithSurface (PLMD::adjmat)    LogMFD (PLMD::logmfd)    SingleDomainRMSD (PLMD)   
CoeffsBase (PLMD::ves)    LoopUnroller (PLMD)    SketchMap (PLMD::dimred)   
CoeffsMatrix (PLMD::ves)    Loss (PLMD::maze)    SketchMapBase (PLMD::dimred)   
CoeffsVector (PLMD::ves)    Lowest (PLMD::vesselbase)    SketchMapConjGrad (PLMD::dimred)   
Colvar (PLMD)    LWalls (PLMD::manyrestraints)    SketchMapPointwise (PLMD::dimred)   
ColvarFake (PLMD::colvar)    LWalls (PLMD::bias)    SketchMapRead (PLMD::dimred)   
Combine (PLMD::function)   
  m  
SketchMapSmacof (PLMD::dimred)   
Committor (PLMD::analysis)    SMAC (PLMD::crystallization)   
Communicator (PLMD)    MahalanobisDistance (PLMD)    SMACMatrix (PLMD::adjmat)   
CompiledExpression (PLMD::lepton)    Manual (PLMD::cltools)    SMACOF (PLMD::dimred)   
Completion (PLMD::cltools)    ManyRestraintsBase (PLMD::manyrestraints)    SmacofMDS (PLMD::dimred)   
ConjugateGradient (PLMD)    Mapping (PLMD::mapping)    Sort (PLMD::function)   
MatrixSquareBracketsAccess::Const_row (PLMD)    MarginalWeight (PLMD::ves)    SparseGrid (PLMD)   
Constant (PLMD::colvar)    Matheval (PLMD::function)    SpathVessel (PLMD::mapping)   
Communicator::ConstData (PLMD)    Matrix (PLMD)    Sprint (PLMD::adjmat)   
ContactAlignedMatrix (PLMD::adjmat)    MatrixColumnSums (PLMD::adjmat)    Stats (PLMD::function)   
ContactMap (PLMD::colvar)    MatrixRowSums (PLMD::adjmat)    Communicator::Status (PLMD)   
ContactMatrix (PLMD::adjmat)    MatrixSquareBracketsAccess (PLMD)    Steered_MD (PLMD::maze)   
ContourFindingBase (PLMD::gridtools)    Max (PLMD::vesselbase)    Steinhardt (PLMD::crystallization)   
ConvertToFES (PLMD::gridtools)    MaxEnt (PLMD::bias)    Stopwatch (PLMD)   
Coordination (PLMD::colvar)    md_atom (PLMD::molfile)    StoreDataVessel (PLMD::vesselbase)   
CoordinationBase (PLMD::colvar)    md_box (PLMD::molfile)    Subprocess (PLMD)   
CoordinationNumbers (PLMD::multicolvar)    md_file (PLMD::molfile)    SubprocessPid (PLMD)   
CS2Backbone (PLMD::isdb)    md_header (PLMD::molfile)    Sum (PLMD::vesselbase)   
CS2BackboneDB (PLMD::isdb)    MD_LinearExpansionPES (PLMD::ves)    SwitchingFunction (PLMD)   
CubicHarmonicBase (PLMD::crystallization)    md_ts (PLMD::molfile)   
  t  
Custom (PLMD::function)    MDAtomsBase (PLMD)   
CustomFunction (PLMD::lepton)    MDAtomsTyped (PLMD)    Target (PLMD::function)   
  d  
Mean (PLMD::vesselbase)    TargetDist (PLMD)   
Member (PLMD::maze)    TargetDistModifer (PLMD::ves)   
Communicator::Data (PLMD)    Memetic (PLMD::maze)    TargetDistribution (PLMD::ves)   
DataCollectionObject (PLMD::analysis)    MetaD (PLMD::bias)    TD_Chi (PLMD::ves)   
DataFetchingObject (PLMD)    Metainference (PLMD::isdb)    TD_ChiSquared (PLMD::ves)   
DataFetchingObjectTyped (PLMD)    MetainferenceBase (PLMD::isdb)    TD_Custom (PLMD::ves)   
Debug (PLMD::generic)    MetricRegister (PLMD)    TD_Exponential (PLMD::ves)   
tls::delete_ptr (PLMD::maze)    Min (PLMD::vesselbase)    TD_ExponentiallyModifiedGaussian (PLMD::ves)   
Density (PLMD::multicolvar)    Minimise1DBrent (PLMD)    TD_Gaussian (PLMD::ves)   
DFSClustering (PLMD::adjmat)    MinimiseBase (PLMD)    TD_GeneralizedExtremeValue (PLMD::ves)   
DHEnergy (PLMD::colvar)    MolDataClass (PLMD)    TD_GeneralizedNormal (PLMD::ves)   
DihedralCorrelation (PLMD::multicolvar)    MoleculeOrientation (PLMD::crystallization)    TD_Grid (PLMD::ves)   
DimensionalityReductionBase (PLMD::dimred)    MoleculePlane (PLMD::crystallization)    TD_LinearCombination (PLMD::ves)   
Dimer (PLMD::colvar)    molfile_atom_t (PLMD::molfile)    TD_Multicanonical (PLMD::ves)   
Dipole (PLMD::colvar)    molfile_graphics_t (PLMD::molfile)    TD_MultithermalMultibaric (PLMD::ves)   
Direction (PLMD)    molfile_metadata_t (PLMD::molfile)    TD_ProductCombination (PLMD::ves)   
Tools::DirectoryChanger (PLMD)    molfile_plugin_t (PLMD::molfile)    TD_ProductDistribution (PLMD::ves)   
Distance (PLMD::colvar)    molfile_qm_basis_t (PLMD::molfile)    TD_Uniform (PLMD::ves)   
DistanceFromContour (PLMD::multicolvar)    molfile_qm_hessian_t (PLMD::molfile)    TD_VonMises (PLMD::ves)   
Distances (PLMD::multicolvar)    molfile_qm_metadata_t (PLMD::molfile)    TD_WellTempered (PLMD::ves)   
PlumedHandle::DlHandle (PLMD)    molfile_qm_sysinfo_t (PLMD::molfile)    MetaD::TemperingSpecs (PLMD::bias)   
DLLoader (PLMD)    molfile_qm_t (PLMD::molfile)    Template (PLMD::colvar)   
Atoms::DomainDecomposition (PLMD)    molfile_qm_timestep_metadata (PLMD::molfile)    TensorChecks (PLMD)   
DotProductDistance (PLMD)    molfile_qm_timestep_t (PLMD::molfile)    TensorGeneric (PLMD)   
Driver (PLMD::cltools)    molfile_qm_wavefunction_t (PLMD::molfile)    TensorGenericAux (PLMD)   
DRMSD (PLMD)    molfile_timestep_metadata (PLMD::molfile)    Tetrahedral (PLMD::crystallization)   
DRMSD (PLMD::colvar)    molfile_timestep_t (PLMD::molfile)    Time (PLMD::generic)   
DumpAtoms (PLMD::generic)    molfile_volumetric_readwrite_t (PLMD::molfile)    tls (PLMD::maze)   
DumpCube (PLMD::gridtools)    molfile_volumetric_t (PLMD::molfile)    Tools (PLMD)   
DumpDerivatives (PLMD::generic)    MolInfo (PLMD::generic)    TopologyMatrix (PLMD::adjmat)   
DumpForces (PLMD::generic)    Moments (PLMD::vesselbase)    Torsion (PLMD::colvar)   
DumpGraph (PLMD::adjmat)    MoreThan (PLMD::vesselbase)    Torsion (PLMD)   
DumpGrid (PLMD::gridtools)    MovingRestraint (PLMD::bias)    Torsions (PLMD::multicolvar)   
DumpMassCharge (PLMD::generic)    MPI_Comm (PLMD)    TrigonometricPathVessel (PLMD::mapping)   
DumpMultiColvar (PLMD::multicolvar)    MPI_Datatype (PLMD)    trx_hdr (PLMD::molfile)   
DumpProjections (PLMD::generic)    MPI_Request (PLMD)   
  u  
DynamicList (PLMD)    MPI_Status (PLMD)   
DynamicReferenceRestraining (PLMD::drr)    MultiColvarBase (PLMD::multicolvar)    UIestimator (PLMD::drr::UIestimator)   
  e  
MultiColvarCombine (PLMD::multicolvar)    Units (PLMD)   
MultiColvarDensity (PLMD::multicolvar)    Units (PLMD::setup)   
EDS (PLMD::eds)    MultiColvarFilter (PLMD::multicolvar)    UpdateIf (PLMD::generic)   
EEFSolv (PLMD::colvar)    MultiColvarProduct (PLMD::multicolvar)    UWalls (PLMD::manyrestraints)   
EffectiveEnergyDrift (PLMD::generic)    MultiDomainRMSD (PLMD)    UWalls (PLMD::bias)   
EMMI (PLMD::isdb)    MultiRMSD (PLMD::colvar)   
  v  
EndPlumed (PLMD::generic)    MultiValue (PLMD)   
Energy (PLMD::colvar)   
  n  
Value (PLMD)   
Ensemble (PLMD::function)    ValueVessel (PLMD::vesselbase)   
EnvironmentSimilarity (PLMD::crystallization)    n_matrix (PLMD::drr::UIestimator)    VectorChecks (PLMD)   
ERMSD (PLMD::colvar)    n_vector (PLMD::drr::UIestimator)    VectorGeneric (PLMD)   
ERMSD (PLMD)    NeighborList (PLMD)    VectorMean (PLMD::crystallization)   
EuclideanDissimilarityMatrix (PLMD::analysis)    NOE (PLMD::isdb)    VectorMultiColvar (PLMD::crystallization)   
EuclideanDistance (PLMD)    NormalizedEuclideanDistance (PLMD)    VectorSum (PLMD::crystallization)   
Exception (PLMD)    Plumed::NothrowHandler (PLMD)    VesBias (PLMD::ves)   
Plumed::Exception (PLMD)    NumberOfLinks (PLMD::multicolvar)    VesDeltaF (PLMD::ves)   
Exception (PLMD::lepton)   
  o  
VesLinearExpansion (PLMD::ves)   
ExceptionDebug (PLMD)    Vessel (PLMD::vesselbase)   
Plumed::ExceptionDebug (PLMD)    OFile (PLMD)    VesselOptions (PLMD::vesselbase)   
ExceptionError (PLMD)    OpenMP (PLMD)    VesselRegister (PLMD::vesselbase)   
Plumed::ExceptionError (PLMD)    OpenMPVars (PLMD)    VesTools (PLMD::ves)   
ExchangePatterns (PLMD)    Operation (PLMD::lepton)    vmdplugin_t (PLMD::molfile)   
ExpressionProgram (PLMD::lepton)    OPESmetad (PLMD::opes)    Volume (PLMD::colvar)   
ExpressionTreeNode (PLMD::lepton)    Opt_BachAveragedSGD (PLMD::ves)    VolumeAround (PLMD::multicolvar)   
ExtendedLagrangian (PLMD::bias)    Opt_Dummy (PLMD::ves)    VolumeCavity (PLMD::multicolvar)   
External (PLMD::bias)    OptimalRMSD (PLMD)    VolumeGradientBase (PLMD::multicolvar)   
ExtraCV (PLMD::colvar)    Optimizer (PLMD::ves)    VolumeInCylinder (PLMD::multicolvar)   
  f  
Optimizer (PLMD::maze)    VolumeInEnvelope (PLMD::multicolvar)   
OptimizerBias (PLMD::maze)    VolumeInSphere (PLMD::multicolvar)   
F1dim (PLMD)    FuncPathMSD::ordering (PLMD::function)    VolumeTetrapore (PLMD::multicolvar)   
FakeFrame (PLMD)    OrderingVessel (PLMD::vesselbase)   
  w  
FarthestPointSampling (PLMD::analysis)    OrientationSphere (PLMD::crystallization)   
Fccubic (PLMD::crystallization)    OutputBasisFunctions (PLMD::ves)    Stopwatch::Watch (PLMD)   
FermiSwitchingFunction (PLMD::ves)    OutputCluster (PLMD::adjmat)    WeightBase (PLMD)   
FesWeight (PLMD::ves)    OutputColvarFile (PLMD::analysis)    WellTemperedModifer (PLMD::ves)   
IFile::Field (PLMD)    OutputFesBias (PLMD::ves)    WhamHistogram (PLMD::analysis)   
OFile::Field (PLMD)    OutputPCAProjection (PLMD::dimred)    WhamWeights (PLMD::analysis)   
FileBase::FieldBase (PLMD)    OutputPDBFile (PLMD::analysis)    WholeMolecules (PLMD::generic)   
FileBase (PLMD)    OutputTargetDistribution (PLMD::ves)    WithCmd (PLMD)   
FilesHandler (PLMD::function)   
  p  
WrapAround (PLMD::generic)   
FilterBetween (PLMD::multicolvar)   
  x  
FilterLess (PLMD::multicolvar)    FuncPathGeneral::pairordering (PLMD::function)   
FilterMore (PLMD::multicolvar)    FuncPathMSD::pairordering (PLMD::function)    XAngles (PLMD::multicolvar)   
FindContour (PLMD::gridtools)    PAMM (PLMD::pamm)    XDistances (PLMD::multicolvar)   
FindContourSurface (PLMD::gridtools)    PammObject (PLMD::pamm)    XYDistances (PLMD::multicolvar)   
FindSphericalContour (PLMD::gridtools)    ParabetaRMSD (PLMD::secondarystructure)    XYTorsion (PLMD::multicolvar)   
fio_iovec (PLMD::molfile)    ParsedExpression (PLMD::lepton)   
  z  
FISST (PLMD::fisst)    Parser (PLMD::lepton)   
FitToTemplate (PLMD::generic)    ParseToken (PLMD::lepton)    ZpathVessel (PLMD::mapping)   
FixedAtom (PLMD::vatom)    Path (PLMD::mapping)   
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