|
| FindContourSurface (PLMD::gridtools) | OpenMP (PLMD) |
| FindSphericalContour (PLMD::gridtools) | OptimalAlignment (PLMD) |
| ABMD (PLMD::bias) | fio_iovec (PLMD::molfile) | OptimalRMSD (PLMD) |
| Action (PLMD) | FitToTemplate (PLMD::generic) | FuncPathMSD::ordering (PLMD::function) |
| ActionAtomistic (PLMD) | FixedAtom (PLMD::vatom) | OrderingVessel (PLMD::vesselbase) |
| ActionOptions (PLMD) | FlexibleBin (PLMD) | OrientationSphere (PLMD::crystallization) |
| ActionPilot (PLMD) | Flush (PLMD::generic) | OutputCluster (PLMD::adjmat) |
| ActionRegister (PLMD) | FourierTransform (PLMD::gridtools) |
|
| ActionSet (PLMD) | CS2Backbone::Fragment (PLMD::colvar) |
| ActionSetup (PLMD) | FretEfficiency (PLMD::colvar) | FuncPathMSD::pairordering (PLMD::function) |
| ActionVolume (PLMD::multicolvar) | FuncPathMSD (PLMD::function) | ParabetaRMSD (PLMD::secondarystructure) |
| ActionWithArguments (PLMD) | FuncSumHills (PLMD::function) | Path (PLMD::mapping) |
| ActionWithAveraging (PLMD::vesselbase) | Function (PLMD::function) | PathBase (PLMD::mapping) |
| ActionWithGrid (PLMD::gridtools) | FunctionVessel (PLMD::vesselbase) | PathMSD (PLMD::colvar) |
| ActionWithInputGrid (PLMD::gridtools) |
| PathMSDBase (PLMD::colvar) |
| ActionWithInputMatrix (PLMD::adjmat) | Pbc (PLMD) |
| ActionWithInputVessel (PLMD::vesselbase) | MetaD::Gaussian (PLMD::bias) | PBMetaD (PLMD::bias) |
| ActionWithValue (PLMD) | PBMetaD::Gaussian (PLMD::bias) | PCA (PLMD::analysis) |
| ActionWithVessel (PLMD::vesselbase) | GenTemplate (PLMD::cltools) | PCARMSD (PLMD::colvar) |
| ActionWithVirtualAtom (PLMD) | Ghost (PLMD::vatom) | PCAVars (PLMD::mapping) |
| AdjacencyMatrixBase (PLMD::adjmat) | Gradient (PLMD::crystallization) | PDB (PLMD) |
| AdjacencyMatrixVessel (PLMD::adjmat) | GradientVessel (PLMD::crystallization) | Piecewise (PLMD::function) |
| AlignedMatrixBase (PLMD::adjmat) | GREX (PLMD) | plumed |
| AlphaBeta (PLMD::multicolvar) | Grid (PLMD) | Plumed (PLMD) |
| AlphaRMSD (PLMD::secondarystructure) | GridPrintingBase (PLMD::gridtools) | plumed_function_holder |
| AltMin (PLMD::vesselbase) | GridVessel (PLMD::gridtools) | plumed_plumedmain_function_holder |
| Analysis (PLMD::analysis) | Group (PLMD::generic) | PlumedMain (PLMD) |
| AnalysisWithLandmarks (PLMD::analysis) | Gyration (PLMD::colvar) | PlumedMainInitializer (PLMD) |
| Angle (PLMD) |
| PointWiseMapping (PLMD) |
| Angle (PLMD::colvar) | Position (PLMD::colvar) |
| Angles (PLMD::multicolvar) | HBondMatrix (PLMD::adjmat) | PRE (PLMD::colvar) |
| AntibetaRMSD (PLMD::secondarystructure) | Highest (PLMD::vesselbase) | Print (PLMD::generic) |
| ArgumentOnlyDistance (PLMD) | Histogram (PLMD::analysis) | ProbWeight (PLMD) |
| AtomNumber (PLMD) | Histogram (PLMD::vesselbase) | PropertyMap (PLMD::mapping) |
| Atoms (PLMD) | HistogramBead (PLMD) | PropertyMap (PLMD::colvar) |
| AtomValuePack (PLMD::multicolvar) | HistogramOnGrid (PLMD::gridtools) | Puckering (PLMD::colvar) |
| Average (PLMD::analysis) |
|
|
| AverageOnGrid (PLMD::gridtools) |
| AverageVessel (PLMD::analysis) | IFile (PLMD) | Q3 (PLMD::crystallization) |
| AveragingVessel (PLMD::vesselbase) | PathMSDBase::ImagePath (PLMD::colvar) | Q4 (PLMD::crystallization) |
|
| PathMSDBase::imgOrderByDist (PLMD::colvar) | Q6 (PLMD::crystallization) |
| PathMSDBase::imgOrderBySimilarity (PLMD::colvar) |
|
| Between (PLMD::vesselbase) | Include (PLMD::generic) |
| Bias (PLMD::bias) | Info (PLMD::cltools) | Random (PLMD) |
| BiasRepresentation (PLMD) | InPlaneDistances (PLMD::multicolvar) | RandomExchanges (PLMD::generic) |
| BiasValue (PLMD::bias) | IntermolecularDRMSD (PLMD) | RDC (PLMD::colvar) |
| BiasWeight (PLMD) | InterMolecularTorsions (PLMD::crystallization) | Read (PLMD::generic) |
| Brent1DRootSearch (PLMD) | InterpolateBicubic (PLMD) | ReferenceArguments (PLMD) |
| Bridge (PLMD::multicolvar) | InterpolateCubic (PLMD) | ReferenceAtoms (PLMD) |
| BridgedMultiColvarFunction (PLMD::multicolvar) | InterpolateGrid (PLMD::gridtools) | ReferenceConfiguration (PLMD) |
| BridgeVessel (PLMD::vesselbase) | IntramolecularDRMSD (PLMD) | ReferenceConfigurationOptions (PLMD) |
|
|
| ReferenceValuePack (PLMD) |
| Communicator::Request (PLMD) |
| CatomPack (PLMD::multicolvar) | JCoupling (PLMD::colvar) | ResetCell (PLMD::generic) |
| Cell (PLMD::colvar) |
| Restart (PLMD::setup) |
| Center (PLMD::vatom) | Restraint (PLMD::bias) |
| CenterOfMultiColvar (PLMD::multicolvar) | Kearsley (PLMD) | ReweightBase (PLMD::bias) |
| CInterpolation (PLMD) | KernelFunctions (PLMD) | ReweightBias (PLMD::bias) |
| Citations (PLMD) | Keywords::KeyType (PLMD) | ReweightMetad (PLMD::bias) |
| ClassicalMultiDimensionalScaling (PLMD::analysis) | Keywords (PLMD) | ReweightTemperature (PLMD::bias) |
| ClassicalScaling (PLMD::analysis) | kt (PLMD::cltools) | CS2Backbone::RingInfo (PLMD::colvar) |
| CLTool (PLMD) |
| RMSD (PLMD) |
| CLToolMain (PLMD) | RMSD (PLMD::colvar) |
| CLToolOptions (PLMD) | LandmarkRegister (PLMD::analysis) | RMSDBase (PLMD) |
| CLToolRegister (PLMD) | LandmarkSelectionBase (PLMD::analysis) | RMSDCoreData (PLMD) |
| CLToolSumHills (PLMD::cltools) | LandmarkSelectionOptions (PLMD::analysis) | RootFindingBase (PLMD) |
| ClusterAnalysisBase (PLMD::adjmat) | LatticeReduction (PLMD) | MatrixSquareBracketsAccess::Row (PLMD) |
| ClusterDiameter (PLMD::adjmat) | LessThan (PLMD::vesselbase) |
|
| ClusterDistribution (PLMD::adjmat) | LinkCells (PLMD) |
| ClusteringBase (PLMD::adjmat) | Load (PLMD::setup) | SecondaryStructureRMSD (PLMD::secondarystructure) |
| ClusterProperties (PLMD::adjmat) | LOCAL_Q3 (PLMD::crystallization) | SetupMolInfo (PLMD) |
| ClusterSize (PLMD::adjmat) | LOCAL_Q4 (PLMD::crystallization) | ShortcutVessel (PLMD::vesselbase) |
| ClusterWithSurface (PLMD::adjmat) | LOCAL_Q6 (PLMD::crystallization) | SimpleCubic (PLMD::crystallization) |
| Colvar (PLMD) | LocalAverage (PLMD::multicolvar) | SimpleMD (PLMD::cltools) |
| ColvarFake (PLMD::colvar) | LocalEnsemble (PLMD::function) | SimpleRMSD (PLMD) |
| COM (PLMD::vatom) | LocalSteinhardt (PLMD::crystallization) | SingleDomainRMSD (PLMD) |
| Combine (PLMD::function) | Log (PLMD) | SMAC (PLMD::crystallization) |
| Committor (PLMD::analysis) | LoopUnroller (PLMD) | SMACMatrix (PLMD::adjmat) |
| Communicator (PLMD) | Lowest (PLMD::vesselbase) | Sort (PLMD::function) |
| MatrixSquareBracketsAccess::Const_row (PLMD) | LWalls (PLMD::bias) | SparseGrid (PLMD) |
| Constant (PLMD::colvar) |
| SpathVessel (PLMD::mapping) |
| Communicator::ConstData (PLMD) | Sprint (PLMD::adjmat) |
| ContactAlignedMatrix (PLMD::adjmat) | MahalanobisDistance (PLMD) | Stats (PLMD::function) |
| ContactMap (PLMD::colvar) | Manual (PLMD::cltools) | Communicator::Status (PLMD) |
| ContactMatrix (PLMD::adjmat) | ManyRestraintsBase (PLMD::manyrestraints) | Steinhardt (PLMD::crystallization) |
| ContourFindingBase (PLMD::gridtools) | Mapping (PLMD::mapping) | Stopwatch (PLMD) |
| ConvertToFES (PLMD::gridtools) | Matheval (PLMD::function) | StoreDataVessel (PLMD::vesselbase) |
| Coordination (PLMD::colvar) | Matrix (PLMD) | Sum (PLMD::vesselbase) |
| CoordinationBase (PLMD::colvar) | MatrixColumnSums (PLMD::adjmat) | SwitchingFunction (PLMD) |
| CoordinationNumbers (PLMD::multicolvar) | MatrixRowSums (PLMD::adjmat) |
|
| CopyAllFrames (PLMD::analysis) | MatrixSquareBracketsAccess (PLMD) |
| CS2Backbone (PLMD::colvar) | Max (PLMD::vesselbase) | Target (PLMD::function) |
| CS2BackboneDB (PLMD::colvar) | md_atom (PLMD::molfile) | TargetDist (PLMD) |
| CubicHarmonicBase (PLMD::crystallization) | md_box (PLMD::molfile) | Template (PLMD::colvar) |
|
| md_file (PLMD::molfile) | TensorChecks (PLMD) |
| md_header (PLMD::molfile) | TensorGeneric (PLMD) |
| Communicator::Data (PLMD) | md_ts (PLMD::molfile) | Tetrahedral (PLMD::crystallization) |
| Debug (PLMD::generic) | MDAtomsBase (PLMD) | Stopwatch::Time (PLMD) |
| Density (PLMD::multicolvar) | MDAtomsTyped (PLMD) | Time (PLMD::generic) |
| DFSClustering (PLMD::adjmat) | Mean (PLMD::vesselbase) | Tools (PLMD) |
| DHEnergy (PLMD::colvar) | MetaD (PLMD::bias) | Torsion (PLMD::colvar) |
| DihedralCorrelation (PLMD::multicolvar) | Metainference (PLMD::bias) | Torsion (PLMD) |
| Dipole (PLMD::colvar) | MetricRegister (PLMD) | Torsions (PLMD::multicolvar) |
| Direction (PLMD) | Min (PLMD::vesselbase) | trx_hdr (PLMD::molfile) |
| Distance (PLMD::colvar) | Minimise1DBrent (PLMD) |
|
| DistanceFromContour (PLMD::multicolvar) | MinimiseBase (PLMD) |
| Distances (PLMD::multicolvar) | MolDataClass (PLMD) | Units (PLMD::setup) |
| DLLoader (PLMD) | MoleculeOrientation (PLMD::crystallization) | Units (PLMD) |
| Atoms::DomainDecomposition (PLMD) | MoleculePlane (PLMD::crystallization) | UpdateIf (PLMD::generic) |
| DotProductDistance (PLMD) | molfile_atom_t (PLMD::molfile) | UWalls (PLMD::manyrestraints) |
| Driver (PLMD::cltools) | molfile_graphics_t (PLMD::molfile) | UWalls (PLMD::bias) |
| DRMSD (PLMD) | molfile_metadata_t (PLMD::molfile) |
|
| DRMSD (PLMD::colvar) | molfile_plugin_t (PLMD::molfile) |
| DumpAtoms (PLMD::generic) | molfile_qm_basis_t (PLMD::molfile) | Value (PLMD) |
| DumpCube (PLMD::gridtools) | molfile_qm_hessian_t (PLMD::molfile) | ValueVessel (PLMD::vesselbase) |
| DumpDerivatives (PLMD::generic) | molfile_qm_metadata_t (PLMD::molfile) | VectorChecks (PLMD) |
| DumpForces (PLMD::generic) | molfile_qm_sysinfo_t (PLMD::molfile) | VectorGeneric (PLMD) |
| DumpGrid (PLMD::gridtools) | molfile_qm_t (PLMD::molfile) | VectorMean (PLMD::crystallization) |
| DumpMassCharge (PLMD::generic) | molfile_qm_timestep_metadata (PLMD::molfile) | VectorMultiColvar (PLMD::crystallization) |
| DumpMultiColvar (PLMD::multicolvar) | molfile_qm_timestep_t (PLMD::molfile) | VectorSum (PLMD::crystallization) |
| DumpProjections (PLMD::generic) | molfile_qm_wavefunction_t (PLMD::molfile) | Vessel (PLMD::vesselbase) |
| DynamicList (PLMD) | molfile_timestep_metadata (PLMD::molfile) | VesselOptions (PLMD::vesselbase) |
|
| molfile_timestep_t (PLMD::molfile) | VesselRegister (PLMD::vesselbase) |
| molfile_volumetric_t (PLMD::molfile) | vmdplugin_t (PLMD::molfile) |
| EffectiveEnergyDrift (PLMD::generic) | MolInfo (PLMD::setup) | Volume (PLMD::colvar) |
| Energy (PLMD::colvar) | Moments (PLMD::vesselbase) | VolumeAround (PLMD::multicolvar) |
| Ensemble (PLMD::function) | MoreThan (PLMD::vesselbase) | VolumeCavity (PLMD::multicolvar) |
| ERMSD (PLMD::colvar) | MovingRestraint (PLMD::bias) | VolumeGradientBase (PLMD::multicolvar) |
| ERMSD (PLMD) | MPI_Comm (PLMD) | VolumeInCylinder (PLMD::multicolvar) |
| EuclideanDistance (PLMD) | MPI_Datatype (PLMD) | VolumeInSphere (PLMD::multicolvar) |
| Exception (PLMD) | MPI_Request (PLMD) | VolumeTetrapore (PLMD::multicolvar) |
| ExchangePatterns (PLMD) | MPI_Status (PLMD) |
|
| ExtendedLagrangian (PLMD::bias) | MultiColvar (PLMD::multicolvar) |
| External (PLMD::bias) | MultiColvarBase (PLMD::multicolvar) | Stopwatch::Watch (PLMD) |
|
| MultiColvarDensity (PLMD::multicolvar) | WeightBase (PLMD) |
| MultiColvarFilter (PLMD::multicolvar) | WholeMolecules (PLMD::generic) |
| F1dim (PLMD) | MultiColvarFunction (PLMD::multicolvar) | WithCmd (PLMD) |
| FakeFrame (PLMD) | MultiDomainRMSD (PLMD) | WrapAround (PLMD::generic) |
| Fccubic (PLMD::crystallization) | MultiReferenceBase (PLMD) |
|
| IFile::Field (PLMD) | MultiRMSD (PLMD::colvar) |
| OFile::Field (PLMD) | MultiValue (PLMD) | XDistances (PLMD::multicolvar) |
| FileBase::FieldBase (PLMD) |
| XYDistances (PLMD::multicolvar) |
| FileBase (PLMD) |
|
| FilesHandler (PLMD::function) | NeighborList (PLMD) |
| FilterBetween (PLMD::multicolvar) | NOE (PLMD::colvar) | ZpathVessel (PLMD::mapping) |
| FilterLess (PLMD::multicolvar) | NormalizedEuclideanDistance (PLMD) | |
| FilterMore (PLMD::multicolvar) | NumberOfLinks (PLMD::multicolvar) | |
| FindContour (PLMD::gridtools) |
| |
| |
| OFile (PLMD) | |
| | |
1.8.14
