|
| FindContourSurface (PLMD::gridtools) | Path (PLMD::mapping) |
| FindSphericalContour (PLMD::gridtools) | PathBase (PLMD::mapping) |
| ABMD (PLMD::bias) | fio_iovec (PLMD::molfile) | PathMSD (PLMD::colvar) |
| Action (PLMD) | FitToTemplate (PLMD::generic) | PathMSDBase (PLMD::colvar) |
| ActionAnyorder (PLMD) | FixedAtom (PLMD::vatom) | PathReparameterization (PLMD::mapping) |
| ActionAtomistic (PLMD) | FlexibleBin (PLMD) | PathTools (PLMD::mapping) |
| ActionOptions (PLMD) | Flush (PLMD::generic) | Pbc (PLMD) |
| ActionPilot (PLMD) | ForwardDecl (PLMD) | PBMetaD (PLMD::bias) |
| ActionRegister (PLMD) | FourierTransform (PLMD::gridtools) | PCA (PLMD::dimred) |
| ActionSet (PLMD) | FretEfficiency (PLMD::isdb) | PCARMSD (PLMD::colvar) |
| ActionSetup (PLMD) | FuncPathMSD (PLMD::function) | PCAVars (PLMD::mapping) |
| ActionShortcut (PLMD) | FuncSumHills (PLMD::function) | PDB (PLMD) |
| ActionVolume (PLMD::multicolvar) | Function (PLMD::function) | PdbRenumber (PLMD::cltools) |
| ActionWithArguments (PLMD) | FunctionVessel (PLMD::vesselbase) | PesMD (PLMD::cltools) |
| ActionWithAveraging (PLMD::vesselbase) |
| Piecewise (PLMD::function) |
| ActionWithGrid (PLMD::gridtools) | PIV (PLMD::piv) |
| ActionWithInputGrid (PLMD::gridtools) | MetaD::Gaussian (PLMD::bias) | plumed |
| ActionWithInputMatrix (PLMD::adjmat) | PBMetaD::Gaussian (PLMD::bias) | Plumed (PLMD) |
| ActionWithInputVessel (PLMD::vesselbase) | GenTemplate (PLMD::cltools) | Plumed (PLMD::generic) |
| ActionWithIntegral (PLMD::gridtools) | Ghost (PLMD::vatom) | PlumedMain::plumed_error_handler (PLMD) |
| ActionWithValue (PLMD) | Gradient (PLMD::crystallization) | plumed_function_holder |
| ActionWithVessel (PLMD::vesselbase) | GradientVessel (PLMD::crystallization) | plumed_nothrow_handler |
| ActionWithVirtualAtom (PLMD) | GREX (PLMD) | plumed_plumedmain_function_holder |
| AdaptivePath (PLMD::mapping) | Grid (PLMD) | plumed_symbol_table_type |
| AdjacencyMatrixBase (PLMD::adjmat) | GridIntegrationWeights (PLMD::ves) | PlumedHandle (PLMD) |
| AdjacencyMatrixVessel (PLMD::adjmat) | GridLinearInterpolation (PLMD::ves) | PlumedMain (PLMD) |
| AlignedMatrixBase (PLMD::adjmat) | GridPrintingBase (PLMD::gridtools) | PlumedMainInitializer (PLMD) |
| AlphaBeta (PLMD::multicolvar) | GridSearch (PLMD::gridtools) | PolymerAngles (PLMD::crystallization) |
| AlphaRMSD (PLMD::secondarystructure) | GridToXYZ (PLMD::gridtools) | Position (PLMD::colvar) |
| AltMin (PLMD::vesselbase) | GridVessel (PLMD::gridtools) | PRE (PLMD::isdb) |
| AnalysisBase (PLMD::analysis) | Group (PLMD::generic) | Print (PLMD::generic) |
| Angle (PLMD::colvar) | Gyration (PLMD::colvar) | PrintDissimilarityMatrix (PLMD::analysis) |
| Angle (PLMD) |
| ProbWeight (PLMD) |
| Angles (PLMD::multicolvar) | ProjectNonLandmarkPoints (PLMD::dimred) |
| AntibetaRMSD (PLMD::secondarystructure) | Stopwatch::Handler (PLMD) | PropertyMap (PLMD::mapping) |
| ArgumentOnlyDistance (PLMD) | HBondMatrix (PLMD::adjmat) | PropertyMap (PLMD::colvar) |
| AsmJitRuntimePtr (PLMD::lepton) | HBPammHydrogens (PLMD::pamm) | Puckering (PLMD::colvar) |
| Exception::Assertion (PLMD) | HBPammMatrix (PLMD::pamm) |
|
| AtomNumber (PLMD) | HBPammObject (PLMD::pamm) |
| Atoms (PLMD) | Highest (PLMD::vesselbase) | Q3 (PLMD::crystallization) |
| AtomValuePack (PLMD::multicolvar) | Histogram (PLMD::vesselbase) | Q4 (PLMD::crystallization) |
| Average (PLMD::analysis) | Histogram (PLMD::analysis) | Q6 (PLMD::crystallization) |
| AverageOnGrid (PLMD::gridtools) | HistogramBead (PLMD) |
|
| AverageVessel (PLMD::analysis) | HistogramOnGrid (PLMD::gridtools) |
| AveragingVessel (PLMD::vesselbase) |
| Random (PLMD) |
|
| 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) |
| Restart (PLMD::setup) |
| BiasWeight (PLMD) | Restraint (PLMD::bias) |
| BondOrientation (PLMD::crystallization) | JCoupling (PLMD::isdb) | ReweightBase (PLMD::bias) |
| Brent1DRootSearch (PLMD) |
| ReweightBias (PLMD::bias) |
| Bridge (PLMD::multicolvar) | ReweightMetad (PLMD::bias) |
| BridgedMultiColvarFunction (PLMD::multicolvar) | KernelFunctions (PLMD) | ReweightTemperature (PLMD::bias) |
| BridgeVessel (PLMD::vesselbase) | Keywords::KeyType (PLMD) | ReweightWham (PLMD::bias) |
|
| Keywords (PLMD) | CS2Backbone::RingInfo (PLMD::isdb) |
| kt (PLMD::cltools) | RMSD (PLMD) |
| Caliber (PLMD::isdb) |
| RMSD (PLMD::colvar) |
| CatomPack (PLMD::multicolvar) | RMSDBase (PLMD) |
| Cell (PLMD::colvar) | LandmarkSelectionBase (PLMD::analysis) | RMSDCoreData (PLMD) |
| Center (PLMD::vatom) | LandmarkStaged (PLMD::analysis) | RootFindingBase (PLMD) |
| CenterOfMultiColvar (PLMD::multicolvar) | LatticeReduction (PLMD) | MatrixSquareBracketsAccess::Row (PLMD) |
| CS2Backbone::ChemicalShift (PLMD::isdb) | Plumed::LeptonException (PLMD) |
|
| Citations (PLMD) | LessThan (PLMD::vesselbase) |
| ClassicalMultiDimensionalScaling (PLMD::dimred) | LinearBasisSetExpansion (PLMD::ves) | SAXS (PLMD::isdb) |
| CLTool (PLMD) | LinkCells (PLMD) | SecondaryStructureRMSD (PLMD::secondarystructure) |
| CLToolMain (PLMD) | Load (PLMD::setup) | Select (PLMD::isdb) |
| CLToolOptions (PLMD) | LOCAL_Q3 (PLMD::crystallization) | Selector (PLMD::isdb) |
| CLToolRegister (PLMD) | LOCAL_Q4 (PLMD::crystallization) | SelectRandomFrames (PLMD::analysis) |
| CLToolSumHills (PLMD::cltools) | LOCAL_Q6 (PLMD::crystallization) | SelectWithStride (PLMD::analysis) |
| ClusterAnalysisBase (PLMD::adjmat) | LocalAverage (PLMD::multicolvar) | SetupMolInfo (PLMD) |
| ClusterDiameter (PLMD::adjmat) | LocalEnsemble (PLMD::function) | ShortcutVessel (PLMD::vesselbase) |
| ClusterDistribution (PLMD::adjmat) | LocalSteinhardt (PLMD::crystallization) | SimpleCubic (PLMD::crystallization) |
| ClusteringBase (PLMD::adjmat) | Exception::Location (PLMD) | SimpleMD (PLMD::cltools) |
| ClusterProperties (PLMD::adjmat) | Log (PLMD) | SimpleRMSD (PLMD) |
| ClusterSize (PLMD::adjmat) | LogMFD (PLMD::logmfd) | SingleDomainRMSD (PLMD) |
| ClusterWithSurface (PLMD::adjmat) | LoopUnroller (PLMD) | SketchMap (PLMD::dimred) |
| CoeffsBase (PLMD::ves) | Lowest (PLMD::vesselbase) | SketchMapBase (PLMD::dimred) |
| CoeffsMatrix (PLMD::ves) | LWalls (PLMD::bias) | SketchMapConjGrad (PLMD::dimred) |
| CoeffsVector (PLMD::ves) | LWalls (PLMD::manyrestraints) | SketchMapPointwise (PLMD::dimred) |
| Colvar (PLMD) |
| SketchMapRead (PLMD::dimred) |
| ColvarFake (PLMD::colvar) | SketchMapSmacof (PLMD::dimred) |
| Combine (PLMD::function) | MahalanobisDistance (PLMD) | SMAC (PLMD::crystallization) |
| Committor (PLMD::analysis) | Manual (PLMD::cltools) | SMACMatrix (PLMD::adjmat) |
| Communicator (PLMD) | ManyRestraintsBase (PLMD::manyrestraints) | SMACOF (PLMD::dimred) |
| CompiledExpression (PLMD::lepton) | Mapping (PLMD::mapping) | SmacofMDS (PLMD::dimred) |
| Completion (PLMD::cltools) | MarginalWeight (PLMD::ves) | Sort (PLMD::function) |
| ConjugateGradient (PLMD) | Matheval (PLMD::function) | SparseGrid (PLMD) |
| MatrixSquareBracketsAccess::Const_row (PLMD) | Matrix (PLMD) | SpathVessel (PLMD::mapping) |
| Constant (PLMD::colvar) | MatrixColumnSums (PLMD::adjmat) | Sprint (PLMD::adjmat) |
| Communicator::ConstData (PLMD) | MatrixRowSums (PLMD::adjmat) | Stats (PLMD::function) |
| ContactAlignedMatrix (PLMD::adjmat) | MatrixSquareBracketsAccess (PLMD) | Communicator::Status (PLMD) |
| ContactMap (PLMD::colvar) | Max (PLMD::vesselbase) | Steinhardt (PLMD::crystallization) |
| ContactMatrix (PLMD::adjmat) | MaxEnt (PLMD::bias) | Stopwatch (PLMD) |
| ContourFindingBase (PLMD::gridtools) | md_atom (PLMD::molfile) | StoreDataVessel (PLMD::vesselbase) |
| ConvertToFES (PLMD::gridtools) | md_box (PLMD::molfile) | Sum (PLMD::vesselbase) |
| Coordination (PLMD::colvar) | md_file (PLMD::molfile) | SwitchingFunction (PLMD) |
| CoordinationBase (PLMD::colvar) | md_header (PLMD::molfile) |
|
| CoordinationNumbers (PLMD::multicolvar) | MD_LinearExpansionPES (PLMD::ves) |
| CS2Backbone (PLMD::isdb) | md_ts (PLMD::molfile) | Target (PLMD::function) |
| CS2BackboneDB (PLMD::isdb) | MDAtomsBase (PLMD) | TargetDist (PLMD) |
| CubicHarmonicBase (PLMD::crystallization) | MDAtomsTyped (PLMD) | TargetDistModifer (PLMD::ves) |
| Custom (PLMD::function) | Mean (PLMD::vesselbase) | TargetDistribution (PLMD::ves) |
| CustomFunction (PLMD::lepton) | MetaD (PLMD::bias) | TD_Chi (PLMD::ves) |
|
| Metainference (PLMD::isdb) | TD_ChiSquared (PLMD::ves) |
| MetainferenceBase (PLMD::isdb) | TD_Custom (PLMD::ves) |
| Communicator::Data (PLMD) | MetricRegister (PLMD) | TD_Exponential (PLMD::ves) |
| DataCollectionObject (PLMD::analysis) | Min (PLMD::vesselbase) | TD_ExponentiallyModifiedGaussian (PLMD::ves) |
| DataFetchingObject (PLMD) | Minimise1DBrent (PLMD) | TD_Gaussian (PLMD::ves) |
| DataFetchingObjectTyped (PLMD) | MinimiseBase (PLMD) | TD_GeneralizedExtremeValue (PLMD::ves) |
| Debug (PLMD::generic) | MolDataClass (PLMD) | TD_GeneralizedNormal (PLMD::ves) |
| Density (PLMD::multicolvar) | MoleculeOrientation (PLMD::crystallization) | TD_Grid (PLMD::ves) |
| DFSClustering (PLMD::adjmat) | MoleculePlane (PLMD::crystallization) | TD_LinearCombination (PLMD::ves) |
| DHEnergy (PLMD::colvar) | molfile_atom_t (PLMD::molfile) | TD_ProductCombination (PLMD::ves) |
| DihedralCorrelation (PLMD::multicolvar) | molfile_graphics_t (PLMD::molfile) | TD_ProductDistribution (PLMD::ves) |
| DimensionalityReductionBase (PLMD::dimred) | molfile_metadata_t (PLMD::molfile) | TD_Uniform (PLMD::ves) |
| Dimer (PLMD::colvar) | molfile_plugin_t (PLMD::molfile) | TD_VonMises (PLMD::ves) |
| Dipole (PLMD::colvar) | molfile_qm_basis_t (PLMD::molfile) | TD_WellTempered (PLMD::ves) |
| Direction (PLMD) | molfile_qm_hessian_t (PLMD::molfile) | MetaD::TemperingSpecs (PLMD::bias) |
| Tools::DirectoryChanger (PLMD) | molfile_qm_metadata_t (PLMD::molfile) | Template (PLMD::colvar) |
| Distance (PLMD::colvar) | molfile_qm_sysinfo_t (PLMD::molfile) | TensorChecks (PLMD) |
| DistanceFromContour (PLMD::multicolvar) | molfile_qm_t (PLMD::molfile) | TensorGeneric (PLMD) |
| Distances (PLMD::multicolvar) | molfile_qm_timestep_metadata (PLMD::molfile) | TensorGenericAux (PLMD) |
| PlumedHandle::DlHandle (PLMD) | molfile_qm_timestep_t (PLMD::molfile) | Tetrahedral (PLMD::crystallization) |
| DLLoader (PLMD) | molfile_qm_wavefunction_t (PLMD::molfile) | Time (PLMD::generic) |
| Atoms::DomainDecomposition (PLMD) | molfile_timestep_metadata (PLMD::molfile) | Tools (PLMD) |
| DotProductDistance (PLMD) | molfile_timestep_t (PLMD::molfile) | TopologyMatrix (PLMD::adjmat) |
| Driver (PLMD::cltools) | molfile_volumetric_readwrite_t (PLMD::molfile) | Torsion (PLMD) |
| DRMSD (PLMD::colvar) | molfile_volumetric_t (PLMD::molfile) | Torsion (PLMD::colvar) |
| DRMSD (PLMD) | MolInfo (PLMD::setup) | Torsions (PLMD::multicolvar) |
| DumpAtoms (PLMD::generic) | Moments (PLMD::vesselbase) | TrigonometricPathVessel (PLMD::mapping) |
| DumpCube (PLMD::gridtools) | MoreThan (PLMD::vesselbase) | trx_hdr (PLMD::molfile) |
| DumpDerivatives (PLMD::generic) | MovingRestraint (PLMD::bias) |
|
| DumpForces (PLMD::generic) | MPI_Comm (PLMD) |
| DumpGraph (PLMD::adjmat) | MPI_Datatype (PLMD) | UIestimator (PLMD::drr::UIestimator) |
| DumpGrid (PLMD::gridtools) | MPI_Request (PLMD) | Units (PLMD::setup) |
| DumpMassCharge (PLMD::generic) | MPI_Status (PLMD) | Units (PLMD) |
| DumpMultiColvar (PLMD::multicolvar) | Multi_RMSD (PLMD::colvar) | UpdateIf (PLMD::generic) |
| DumpProjections (PLMD::generic) | MultiColvarBase (PLMD::multicolvar) | UWalls (PLMD::bias) |
| DynamicList (PLMD) | MultiColvarCombine (PLMD::multicolvar) | UWalls (PLMD::manyrestraints) |
| DynamicReferenceRestraining (PLMD::drr) | MultiColvarDensity (PLMD::multicolvar) |
|
|
| MultiColvarFilter (PLMD::multicolvar) |
| MultiColvarProduct (PLMD::multicolvar) | Value (PLMD) |
| EDS (PLMD::eds) | MultiDomainRMSD (PLMD) | ValueVessel (PLMD::vesselbase) |
| EEFSolv (PLMD::colvar) | MultiRMSD (PLMD::colvar) | VectorChecks (PLMD) |
| EffectiveEnergyDrift (PLMD::generic) | MultiValue (PLMD) | VectorGeneric (PLMD) |
| EMMI (PLMD::isdb) |
| VectorMean (PLMD::crystallization) |
| EndPlumed (PLMD::generic) | VectorMultiColvar (PLMD::crystallization) |
| Energy (PLMD::colvar) | n_matrix (PLMD::drr::UIestimator) | VectorSum (PLMD::crystallization) |
| Ensemble (PLMD::function) | n_vector (PLMD::drr::UIestimator) | VesBias (PLMD::ves) |
| ERMSD (PLMD) | NeighborList (PLMD) | VesLinearExpansion (PLMD::ves) |
| ERMSD (PLMD::colvar) | NOE (PLMD::isdb) | Vessel (PLMD::vesselbase) |
| EuclideanDissimilarityMatrix (PLMD::analysis) | NormalizedEuclideanDistance (PLMD) | VesselOptions (PLMD::vesselbase) |
| EuclideanDistance (PLMD) | Plumed::NothrowHandler (PLMD) | VesselRegister (PLMD::vesselbase) |
| Exception (PLMD) | NumberOfLinks (PLMD::multicolvar) | VesTools (PLMD::ves) |
| Plumed::Exception (PLMD) |
| vmdplugin_t (PLMD::molfile) |
| Exception (PLMD::lepton) | Volume (PLMD::colvar) |
| ExceptionDebug (PLMD) | OFile (PLMD) | VolumeAround (PLMD::multicolvar) |
| Plumed::ExceptionDebug (PLMD) | OpenMP (PLMD) | VolumeCavity (PLMD::multicolvar) |
| ExceptionError (PLMD) | OpenMPVars (PLMD) | VolumeGradientBase (PLMD::multicolvar) |
| Plumed::ExceptionError (PLMD) | Operation (PLMD::lepton) | VolumeInCylinder (PLMD::multicolvar) |
| ExchangePatterns (PLMD) | Opt_BachAveragedSGD (PLMD::ves) | VolumeInEnvelope (PLMD::multicolvar) |
| ExpressionProgram (PLMD::lepton) | Opt_Dummy (PLMD::ves) | VolumeInSphere (PLMD::multicolvar) |
| ExpressionTreeNode (PLMD::lepton) | OptimalRMSD (PLMD) | VolumeTetrapore (PLMD::multicolvar) |
| ExtendedLagrangian (PLMD::bias) | Optimizer (PLMD::ves) |
|
| External (PLMD::bias) | FuncPathMSD::ordering (PLMD::function) |
| ExtraCV (PLMD::colvar) | OrderingVessel (PLMD::vesselbase) | Stopwatch::Watch (PLMD) |
|
| OrientationSphere (PLMD::crystallization) | WeightBase (PLMD) |
| OutputBasisFunctions (PLMD::ves) | WellTemperedModifer (PLMD::ves) |
| F1dim (PLMD) | OutputCluster (PLMD::adjmat) | WhamHistogram (PLMD::analysis) |
| FakeFrame (PLMD) | OutputColvarFile (PLMD::analysis) | WhamWeights (PLMD::analysis) |
| FarthestPointSampling (PLMD::analysis) | OutputFesBias (PLMD::ves) | WholeMolecules (PLMD::generic) |
| Fccubic (PLMD::crystallization) | OutputPCAProjection (PLMD::dimred) | WithCmd (PLMD) |
| FermiSwitchingFunction (PLMD::ves) | OutputPDBFile (PLMD::analysis) | WrapAround (PLMD::generic) |
| FesWeight (PLMD::ves) | OutputTargetDistribution (PLMD::ves) |
|
| IFile::Field (PLMD) |
|
| OFile::Field (PLMD) | XAngles (PLMD::multicolvar) |
| FileBase::FieldBase (PLMD) | FuncPathMSD::pairordering (PLMD::function) | XDistances (PLMD::multicolvar) |
| FileBase (PLMD) | PAMM (PLMD::pamm) | XYDistances (PLMD::multicolvar) |
| FilesHandler (PLMD::function) | PammObject (PLMD::pamm) | XYTorsion (PLMD::multicolvar) |
| FilterBetween (PLMD::multicolvar) | ParabetaRMSD (PLMD::secondarystructure) |
|
| FilterLess (PLMD::multicolvar) | ParsedExpression (PLMD::lepton) |
| FilterMore (PLMD::multicolvar) | Parser (PLMD::lepton) | ZpathVessel (PLMD::mapping) |
| FindContour (PLMD::gridtools) | ParseToken (PLMD::lepton) | |
| | |
1.8.14
