Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 1234567]

CPLMD::Tools::_Unique_if< T >	Mimic C++14 std::make_unique
CPLMD::Tools::_Unique_if< T[]>
CPLMD::Tools::_Unique_if< T[N]>
►CPLMD::Action	Base class for all the input Actions
►CPLMD::ActionAnyorder
CPLMD::generic::Include	Provides the keyword INCLUDE
CPLMD::GenericMolInfo
►CPLMD::ActionAtomistic
►CPLMD::ActionWithVirtualAtom	Class to add a single virtual atom to the system
CPLMD::multicolvar::CenterOfMultiColvar	Provides the keyword CENTER_OF_MULTICOLVAR
CPLMD::vatom::Center	Provides the keyword CENTER
CPLMD::vatom::FixedAtom	Provides the keyword FIXEDATOM
CPLMD::vatom::Ghost	Provides the keyword GHOST
►CPLMD::analysis::AnalysisBase
CPLMD::analysis::EuclideanDissimilarityMatrix	Provides the keyword EUCLIDEAN_DISSIMILARITIES
►CPLMD::analysis::LandmarkSelectionBase
CPLMD::analysis::FarthestPointSampling	Provides the keyword LANDMARK_SELECT_FPS
CPLMD::analysis::LandmarkStaged	Provides the keyword LANDMARK_SELECT_STAGED
CPLMD::analysis::ReselectLandmarks	Provides the keyword RESELECT_LANDMARKS
CPLMD::analysis::SelectRandomFrames	Provides the keyword LANDMARK_SELECT_RANDOM
CPLMD::analysis::SelectWithStride	Provides the keyword LANDMARK_SELECT_STRIDE
CPLMD::analysis::OutputColvarFile	Provides the keyword OUTPUT_ANALYSIS_DATA_TO_COLVAR
CPLMD::analysis::OutputPDBFile	Provides the keyword OUTPUT_ANALYSIS_DATA_TO_PDB
CPLMD::analysis::PrintDissimilarityMatrix	Provides the keyword PRINT_DISSIMILARITY_MATRIX
CPLMD::analysis::ReadAnalysisFrames	Provides the keyword COLLECT_FRAMES
CPLMD::analysis::ReadDissimilarityMatrix	Provides the keyword READ_DISSIMILARITY_MATRIX
►CPLMD::dimred::DimensionalityReductionBase
CPLMD::dimred::ClassicalMultiDimensionalScaling	Provides the keyword CLASSICAL_MDS
CPLMD::dimred::PCA	Provides the keyword PCA
►CPLMD::dimred::SketchMapBase
CPLMD::dimred::SketchMapConjGrad	Provides the keyword SKETCHMAP_CONJGRAD
CPLMD::dimred::SketchMapPointwise	Provides the keyword SKETCHMAP_POINTWISE
CPLMD::dimred::SketchMapRead	Provides the keyword SKETCHMAP_READ
CPLMD::dimred::SketchMapSmacof	Provides the keyword SKETCHMAP_SMACOF
CPLMD::dimred::SmacofMDS	Provides the keyword SMACOF_MDS
CPLMD::dimred::OutputPCAProjection	Provides the keyword OUTPUT_PCA_PROJECTION
CPLMD::dimred::ProjectNonLandmarkPoints	Provides the keyword PROJECT_ALL_ANALYSIS_DATA
►CPLMD::Colvar
CPLMD::colvar::Angle	Provides the keyword ANGLE
CPLMD::colvar::Cell	Provides the keyword CELL
CPLMD::colvar::ColvarFake	Provides the keyword FAKE
CPLMD::colvar::Constant	Provides the keyword CONSTANT
CPLMD::colvar::ContactMap	Provides the keyword CONTACTMAP
►CPLMD::colvar::CoordinationBase
CPLMD::colvar::Coordination	Provides the keyword COORDINATION
CPLMD::colvar::DHEnergy	Provides the keyword DHENERGY
CPLMD::colvar::GHBFIX	Provides the keyword GHBFIX
CPLMD::colvar::Dimer	Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER
CPLMD::colvar::Dipole	Provides the keyword DIPOLE
CPLMD::colvar::Distance	Provides the keyword DISTANCE
CPLMD::colvar::DRMSD	Provides the keyword DRMSD
CPLMD::colvar::EEFSolv	Provides the keyword EEFSOLV
CPLMD::colvar::Energy	Provides the keyword ENERGY
CPLMD::colvar::ERMSD	Provides the keyword ERMSD
CPLMD::colvar::ExtraCV	Provides the keyword EXTRACV
CPLMD::colvar::Gyration	Provides the keyword GYRATION
CPLMD::colvar::MultiRMSD	Provides the keyword MULTI_RMSD
►CPLMD::colvar::PathMSDBase
CPLMD::colvar::PathMSD	Provides the keyword PATHMSD
CPLMD::colvar::PropertyMap	Provides the keyword PROPERTYMAP
CPLMD::colvar::PCARMSD	Provides the keyword PCARMSD
CPLMD::colvar::Position	Provides the keyword POSITION
CPLMD::colvar::ProjectionOnAxis	Provides the keyword PROJECTION_ON_AXIS
CPLMD::colvar::Puckering	Provides the keyword PUCKERING
CPLMD::colvar::RMSD	Provides the keyword RMSD
CPLMD::colvar::Template	Provides the keyword TEMPLATE
CPLMD::colvar::Torsion	Provides the keyword TORSION
CPLMD::colvar::Volume	Provides the keyword VOLUME
CPLMD::funnel::FUNNEL_PS	Provides the keyword FUNNEL_PS
CPLMD::isdb::FretEfficiency	Provides the keyword FRET
CPLMD::maze::Loss	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS
►CPLMD::maze::Optimizer	Base class for implementing optimizers for ligand unbinding
CPLMD::maze::Memetic	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__m_e_m_e_t_i_c__s_a_m_p_l_i_n_g.html"> "MAZE_MEMETIC_SAMPLING
CPLMD::maze::Random_Acceleration_MD	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__a_c_c_e_l_e_r_a_t_i_o_n__m_d.html"> "MAZE_RANDOM_ACCELERATION_MD
CPLMD::maze::Random_Walk	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__r_a_n_d_o_m__w_a_l_k.html"> "MAZE_RANDOM_WALK
CPLMD::maze::Simulated_Annealing	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_i_m_u_l_a_t_e_d__a_n_n_e_a_l_i_n_g.html"> "MAZE_SIMULATED_ANNEALING
CPLMD::maze::Steered_MD	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__s_t_e_e_r_e_d__m_d.html"> "MAZE_STEERED_MD
CPLMD::piv::PIV	Provides the keyword PIV
CPLMD::s2cm::S2ContactModel	Provides the keyword S2CM
CPLMD::sasa::SASA_HASEL	Provides the keyword SASA_HASEL
CPLMD::sasa::SASA_LCPO	Provides the keyword SASA_LCPO
CPLMD::generic::DumpAtoms	Provides the keyword DUMPATOMS
CPLMD::generic::DumpMassCharge	Provides the keyword DUMPMASSCHARGE
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Group	Provides the keyword GROUP
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::ResetCell	Provides the keyword RESET_CELL
CPLMD::generic::WholeMolecules	Provides the keyword WHOLEMOLECULES
CPLMD::generic::WrapAround	Provides the keyword WRAPAROUND
CPLMD::GenericMolInfo
CPLMD::isdb::EMMI	Provides the keyword EMMI
►CPLMD::isdb::MetainferenceBase
CPLMD::isdb::CS2Backbone	Provides the keyword CS2BACKBONE
CPLMD::isdb::JCoupling	Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING
CPLMD::isdb::NOE	Provides the keyword NOE
CPLMD::isdb::PRE	Provides the keyword PRE
CPLMD::isdb::RDC	Provides the keyword RDC
CPLMD::isdb::SAXS	Provides the keyword SAXS
►CPLMD::mapping::Mapping
CPLMD::mapping::AdaptivePath	Provides the keyword ADAPTIVE_PATH
►CPLMD::mapping::PathBase
CPLMD::mapping::Path	Provides the keyword PATH
CPLMD::mapping::PropertyMap	Provides the keyword GPROPERTYMAP
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
►CPLMD::multicolvar::MultiColvarBase
►CPLMD::adjmat::ActionWithInputMatrix
►CPLMD::adjmat::ClusteringBase
CPLMD::adjmat::ClusterWithSurface	Provides the keyword CLUSTER_WITHSURFACE
CPLMD::adjmat::DFSClustering	Provides the keyword DFSCLUSTERING
CPLMD::adjmat::MatrixColumnSums	Provides the keyword COLUMNSUMS
CPLMD::adjmat::MatrixRowSums	Provides the keyword ROWSUMS
CPLMD::adjmat::Sprint	Provides the keyword SPRINT
►CPLMD::adjmat::AdjacencyMatrixBase
►CPLMD::adjmat::AlignedMatrixBase
CPLMD::adjmat::ContactAlignedMatrix	Provides the keyword ALIGNED_MATRIX
CPLMD::adjmat::SMACMatrix	Provides the keyword SMAC_MATRIX
CPLMD::adjmat::ContactMatrix	Provides the keyword CONTACT_MATRIX
CPLMD::adjmat::HBondMatrix	Provides the keyword HBOND_MATRIX
CPLMD::adjmat::TopologyMatrix	Provides the keyword TOPOLOGY_MATRIX
CPLMD::pamm::HBPammMatrix	Provides the keyword HBPAMM_MATRIX
►CPLMD::adjmat::ClusterAnalysisBase
CPLMD::adjmat::ClusterDiameter	Provides the keyword CLUSTER_DIAMETER
CPLMD::adjmat::ClusterDistribution	Provides the keyword CLUSTER_DISTRIBUTION
CPLMD::adjmat::ClusterProperties	Provides the keyword CLUSTER_PROPERTIES
CPLMD::adjmat::ClusterSize	Provides the keyword CLUSTER_NATOMS
►CPLMD::crystallization::CubicHarmonicBase
CPLMD::crystallization::Fccubic	Provides the keyword FCCUBIC
CPLMD::crystallization::SimpleCubic	Provides the keyword SIMPLECUBIC
CPLMD::crystallization::Tetrahedral	Provides the keyword TETRAHEDRAL
CPLMD::crystallization::EnvironmentSimilarity	Provides the keyword ENVIRONMENTSIMILARITY
CPLMD::crystallization::InterMolecularTorsions	Provides the keyword INTERMOLECULARTORSIONS
►CPLMD::crystallization::OrientationSphere
CPLMD::crystallization::LocalSteinhardt< T >
CPLMD::crystallization::PolymerAngles	Provides the keyword POLYMER_ANGLES
CPLMD::crystallization::SMAC	Provides the keyword SMAC
►CPLMD::crystallization::VectorMultiColvar
CPLMD::crystallization::BondOrientation	Provides the keyword BOND_DIRECTIONS
CPLMD::crystallization::MoleculeOrientation	Provides the keyword MOLECULES
CPLMD::crystallization::MoleculePlane	Provides the keyword PLANES
►CPLMD::crystallization::Steinhardt
CPLMD::crystallization::Q3	Provides the keyword Q3
CPLMD::crystallization::Q4	Provides the keyword Q4
CPLMD::crystallization::Q6	Provides the keyword Q6
CPLMD::multicolvar::AlphaBeta	Provides the keyword ALPHABETA
CPLMD::multicolvar::Angles	Provides the keyword ANGLES
CPLMD::multicolvar::Bridge	Provides the keyword BRIDGE
►CPLMD::multicolvar::BridgedMultiColvarFunction
►CPLMD::multicolvar::MultiColvarFilter
CPLMD::multicolvar::FilterBetween	Provides the keyword MFILTER_BETWEEN
CPLMD::multicolvar::FilterLess	Provides the keyword MFILTER_LESS
CPLMD::multicolvar::FilterMore	Provides the keyword MFILTER_MORE
►CPLMD::multicolvar::VolumeGradientBase
CPLMD::crystallization::Gradient	Provides the keyword GRADIENT
►CPLMD::multicolvar::ActionVolume
CPLMD::multicolvar::VolumeAround	Provides the keyword AROUND
CPLMD::multicolvar::VolumeCavity	Provides the keyword CAVITY
CPLMD::multicolvar::VolumeInCylinder	Provides the keyword INCYLINDER
CPLMD::multicolvar::VolumeInEnvelope	Provides the keyword INENVELOPE
CPLMD::multicolvar::VolumeInSphere	Provides the keyword INSPHERE
CPLMD::multicolvar::VolumeTetrapore	Provides the keyword TETRAHEDRALPORE
CPLMD::multicolvar::CoordinationNumbers	Provides the keyword COORDINATIONNUMBER
CPLMD::multicolvar::Density	Provides the keyword DENSITY
CPLMD::multicolvar::DihedralCorrelation	Provides the keyword DIHCOR
CPLMD::multicolvar::DistanceFromContour	Provides the keyword DISTANCE_FROM_CONTOUR
CPLMD::multicolvar::Distances	Provides the keyword DISTANCES
CPLMD::multicolvar::InPlaneDistances	Provides the keyword INPLANEDISTANCES
CPLMD::multicolvar::LocalAverage	Provides the keyword LOCAL_AVERAGE
CPLMD::multicolvar::MultiColvarCombine	Provides the keyword MCOLV_COMBINE
CPLMD::multicolvar::MultiColvarProduct	Provides the keyword MCOLV_PRODUCT
CPLMD::multicolvar::NumberOfLinks	Provides the keyword NLINKS
CPLMD::multicolvar::Torsions	Provides the keyword TORSIONS
CPLMD::multicolvar::XAngles	Provides the keyword XANGLES
CPLMD::multicolvar::XDistances	Provides the keyword XDISTANCES
CPLMD::multicolvar::XYDistances	Provides the keyword XYDISTANCES
CPLMD::multicolvar::XYTorsion	Provides the keyword XYTORSIONS
CPLMD::pamm::HBPammHydrogens	Provides the keyword HBPAMM_SH
CPLMD::pamm::PAMM	Provides the keyword PAMM
►CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::secondarystructure::AlphaRMSD	Provides the keyword ALPHARMSD
CPLMD::secondarystructure::AntibetaRMSD	Provides the keyword ANTIBETARMSD
CPLMD::secondarystructure::ParabetaRMSD	Provides the keyword PARABETARMSD
►CPLMD::vesselbase::ActionWithAveraging
CPLMD::analysis::Average	Provides the keyword AVERAGE
►CPLMD::gridtools::ActionWithGrid
CPLMD::analysis::Histogram	Provides the keyword HISTOGRAM
►CPLMD::gridtools::ActionWithInputGrid
►CPLMD::gridtools::ActionWithIntegral
CPLMD::gridtools::IntegrateGrid	Provides the keyword INTEGRATE_GRID
►CPLMD::gridtools::ContourFindingBase
CPLMD::gridtools::FindContour	Provides the keyword FIND_CONTOUR
CPLMD::gridtools::FindContourSurface	Provides the keyword FIND_CONTOUR_SURFACE
CPLMD::gridtools::FindSphericalContour	Provides the keyword FIND_SPHERICAL_CONTOUR
CPLMD::gridtools::ConvertToFES	Provides the keyword CONVERT_TO_FES
CPLMD::gridtools::FourierTransform	Provides the keyword FOURIER_TRANSFORM
CPLMD::gridtools::InterpolateGrid	Provides the keyword INTERPOLATE_GRID
CPLMD::multicolvar::MultiColvarDensity	Provides the keyword MULTICOLVARDENS
►CPLMD::ActionPilot
CPLMD::adjmat::DumpGraph	Provides the keyword DUMPGRAPH
CPLMD::adjmat::OutputCluster	Provides the keyword OUTPUT_CLUSTER
CPLMD::analysis::AnalysisBase
CPLMD::analysis::Committor	Provides the keyword COMMITTOR
►CPLMD::bias::Bias
CPLMD::bias::ABMD	Provides the keyword ABMD
CPLMD::bias::BiasValue	Provides the keyword BIASVALUE
CPLMD::bias::ExtendedLagrangian	Provides the keyword EXTENDED_LAGRANGIAN
CPLMD::bias::External	Provides the keyword EXTERNAL
CPLMD::bias::LWalls	Provides the keyword LOWER_WALLS
CPLMD::bias::MaxEnt	Provides the keyword MAXENT
CPLMD::bias::MetaD	Provides the keyword METAD
CPLMD::bias::MovingRestraint	Provides the keyword MOVINGRESTRAINT
CPLMD::bias::PBMetaD	Provides the keyword PBMETAD
CPLMD::bias::Restraint	Provides the keyword RESTRAINT
CPLMD::bias::UWalls	Provides the keyword UPPER_WALLS
CPLMD::eds::EDS	Provides the keyword <a href="../../user-doc/html/_"_e_d_s.html"> "EDS
CPLMD::fisst::FISST	Provides the keyword FISST
CPLMD::funnel::Funnel	Provides the keyword FUNNEL
CPLMD::isdb::Caliber	Provides the keyword CALIBER
CPLMD::isdb::Metainference	Provides the keyword METAINFERENCE
CPLMD::isdb::Rescale	Provides the keyword RESCALE
CPLMD::logmfd::LogMFD	Class for LogMFD parameters, variables and subroutines
CPLMD::maze::OptimizerBias	Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__o_p_t_i_m_i_z_e_r__b_i_a_s.html"> "MAZE_OPTIMIZER_BIAS
CPLMD::opes::OPESexpanded	Provides the keyword OPES_EXPANDED
CPLMD::opes::OPESmetad< mode >
►CPLMD::ves::VesBias
CPLMD::ves::VesLinearExpansion	Provides the keyword VES_LINEAR_EXPANSION
CPLMD::ves::VesDeltaF	Provides the keyword VES_DELTA_F
CPLMD::generic::Debug	Provides the keyword DEBUG
CPLMD::generic::DumpAtoms	Provides the keyword DUMPATOMS
CPLMD::generic::DumpDerivatives	Provides the keyword DUMPDERIVATIVES
CPLMD::generic::DumpForces	Provides the keyword DUMPFORCES
CPLMD::generic::DumpMassCharge	Provides the keyword DUMPMASSCHARGE
CPLMD::generic::DumpProjections	Provides the keyword DUMPPROJECTIONS
CPLMD::generic::EffectiveEnergyDrift	Provides the keyword EFFECTIVE_ENERGY_DRIFT
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Flush	Provides the keyword FLUSH
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::Print	Provides the keyword PRINT
CPLMD::generic::Read	Provides the keyword READ
CPLMD::generic::ResetCell	Provides the keyword RESET_CELL
CPLMD::generic::UpdateIf	Provides the keyword UPDATE_IF
CPLMD::generic::WholeMolecules	Provides the keyword WHOLEMOLECULES
CPLMD::generic::WrapAround	Provides the keyword WRAPAROUND
CPLMD::GenericMolInfo
►CPLMD::gridtools::GridPrintingBase
CPLMD::gridtools::DumpCube	Provides the keyword DUMPCUBE
CPLMD::gridtools::DumpGrid	Provides the keyword DUMPGRID
CPLMD::gridtools::GridToXYZ	Provides the keyword GRID_TO_XYZ
►CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::manyrestraints::LWalls	Provides the keyword LWALLS
CPLMD::manyrestraints::UWalls	Provides the keyword UWALLS
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
►CPLMD::ves::Optimizer
CPLMD::ves::Opt_Adam	Provides the keyword OPT_ADAM
CPLMD::ves::Opt_BachAveragedSGD	Provides the keyword OPT_AVERAGED_SGD
CPLMD::ves::Opt_Dummy	Provides the keyword OPT_DUMMY
CPLMD::ves::Opt_RobbinsMonroSGD	Provides the keyword OPT_ROBBINS_MONRO_SGD
CPLMD::vesselbase::ActionWithAveraging
►CPLMD::ActionSetup
CPLMD::setup::Load	Provides the keyword LOAD
CPLMD::setup::Restart	Provides the keyword RESTART
CPLMD::setup::Units	Provides the keyword UNITS
►CPLMD::ActionShortcut
CPLMD::analysis::WhamHistogram	Provides the keyword WHAM_HISTOGRAM
CPLMD::analysis::WhamWeights	Provides the keyword WHAM_WEIGHTS
CPLMD::dimred::SketchMap	Provides the keyword SKETCH_MAP
►CPLMD::ActionWithArguments
CPLMD::analysis::AnalysisBase
CPLMD::analysis::Committor	Provides the keyword COMMITTOR
CPLMD::bias::Bias
►CPLMD::bias::ReweightBase
CPLMD::bias::ReweightBias	Provides the keyword REWEIGHT_BIAS
CPLMD::bias::ReweightMetad	Provides the keyword REWEIGHT_METAD
CPLMD::bias::ReweightTemperaturePressure	Provides the keyword REWEIGHT_TEMP_PRESS
CPLMD::bias::ReweightWham	Provides the keyword REWEIGHT_WHAM
►CPLMD::function::Function
CPLMD::function::annfunc::ANN
CPLMD::function::Combine	Provides the keyword COMBINE
►CPLMD::function::Custom	Provides the keyword CUSTOM
CPLMD::function::Matheval
CPLMD::function::Ensemble	Provides the keyword ENSEMBLE
CPLMD::function::FuncPathGeneral	Provides the keyword <a href="../../user-doc/html/_"_f_u_n_c_p_a_t_h_g_e_n_e_r_a_l.html"> "FUNCPATHGENERAL
CPLMD::function::FuncPathMSD	Provides the keyword FUNCPATHMSD
CPLMD::function::FuncSumHills	Provides the keyword FUNCSUMHILLS
CPLMD::function::LocalEnsemble	Provides the keyword LOCALENSEMBLE
CPLMD::function::Piecewise	Provides the keyword PIECEWISE
CPLMD::function::Sort	Provides the keyword SORT
CPLMD::function::Stats	Provides the keyword STATS
CPLMD::function::Target	Provides the keyword TARGET
CPLMD::isdb::Select	Provides the keyword SELECT
CPLMD::generic::DumpDerivatives	Provides the keyword DUMPDERIVATIVES
CPLMD::generic::DumpForces	Provides the keyword DUMPFORCES
CPLMD::generic::DumpProjections	Provides the keyword DUMPPROJECTIONS
CPLMD::generic::Print	Provides the keyword PRINT
CPLMD::generic::UpdateIf	Provides the keyword UPDATE_IF
CPLMD::isdb::EMMI	Provides the keyword EMMI
CPLMD::isdb::MetainferenceBase
CPLMD::mapping::Mapping
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
►CPLMD::opes::ExpansionCVs
CPLMD::opes::ECVcustom	Provides the keyword ECV_CUSTOM
CPLMD::opes::ECVlinear	Provides the keyword ECV_LINEAR
CPLMD::opes::ECVmultiThermal	Provides the keyword ECV_MULTITHERMAL
CPLMD::opes::ECVmultiThermalBaric	Provides the keyword ECV_MULTITHERMAL_MULTIBARIC
CPLMD::opes::ECVumbrellasFile	Provides the keyword ECV_UMBRELLAS_FILE
CPLMD::opes::ECVumbrellasLine	Provides the keyword ECV_UMBRELLAS_LINE
CPLMD::vesselbase::ActionWithAveraging
►CPLMD::ActionWithValue
CPLMD::analysis::AnalysisBase
CPLMD::bias::Bias
CPLMD::bias::ReweightBase
CPLMD::Colvar
CPLMD::function::Function
CPLMD::generic::FitToTemplate	Provides the keyword FIT_TO_TEMPLATE
CPLMD::generic::Plumed	Provides the keyword PLUMED
CPLMD::generic::Read	Provides the keyword READ
CPLMD::generic::Time	Provides the keyword TIME
CPLMD::isdb::EMMI	Provides the keyword EMMI
CPLMD::isdb::MetainferenceBase
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::mapping::Mapping
CPLMD::mapping::PCAVars	Provides the keyword PCAVARS
CPLMD::multicolvar::MultiColvarBase
CPLMD::opes::ExpansionCVs
CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::ves::Optimizer
CPLMD::vesselbase::ActionWithAveraging
CPLMD::generic::EndPlumed	Provides the keyword ENDPLUMED
CPLMD::generic::RandomExchanges	Provides the keyword RANDOM_EXCHANGES
CPLMD::isdb::Selector	Provides the keyword SELECTOR
►CPLMD::ves::BasisFunctions
CPLMD::ves::BF_Chebyshev	Provides the keyword BF_CHEBYSHEV
CPLMD::ves::BF_Combined	Provides the keyword BF_COMBINED
CPLMD::ves::BF_Cosine	Provides the keyword BF_COSINE
CPLMD::ves::BF_CubicBsplines	Provides the keyword BF_CUBIC_B_SPLINES
CPLMD::ves::BF_Custom	Provides the keyword BF_CUSTOM
CPLMD::ves::BF_Fourier	Provides the keyword BF_FOURIER
CPLMD::ves::BF_Gaussians	Provides the keyword BF_GAUSSIANS
CPLMD::ves::BF_Legendre	Provides the keyword BF_LEGENDRE
CPLMD::ves::BF_Powers	Provides the keyword BF_POWERS
CPLMD::ves::BF_Sine	Provides the keyword BF_SINE
CPLMD::ves::BF_Wavelets	Provides the keyword BF_WAVELETS
CPLMD::ves::OutputBasisFunctions	Provides the keyword VES_OUTPUT_BASISFUNCTIONS
CPLMD::ves::OutputFesBias	Provides the keyword VES_OUTPUT_FES
CPLMD::ves::OutputTargetDistribution	Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION
►CPLMD::ves::TargetDistribution
CPLMD::ves::TD_Chi	Provides the keyword TD_CHI
CPLMD::ves::TD_ChiSquared	Provides the keyword TD_CHISQUARED
CPLMD::ves::TD_Custom	Provides the keyword TD_CUSTOM
CPLMD::ves::TD_Exponential	Provides the keyword TD_EXPONENTIAL
CPLMD::ves::TD_ExponentiallyModifiedGaussian	Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN
CPLMD::ves::TD_Gaussian	Provides the keyword TD_GAUSSIAN
CPLMD::ves::TD_GeneralizedExtremeValue	Provides the keyword TD_GENERALIZED_EXTREME_VALUE
CPLMD::ves::TD_GeneralizedNormal	Provides the keyword TD_GENERALIZED_NORMAL
CPLMD::ves::TD_Grid	Provides the keyword TD_GRID
CPLMD::ves::TD_LinearCombination	Provides the keyword TD_LINEAR_COMBINATION
CPLMD::ves::TD_Multicanonical	Provides the keyword TD_MULTICANONICAL
CPLMD::ves::TD_MultithermalMultibaric	Provides the keyword TD_MULTITHERMAL_MULTIBARIC
CPLMD::ves::TD_ProductCombination	Provides the keyword TD_PRODUCT_COMBINATION
CPLMD::ves::TD_ProductDistribution	Provides the keyword TD_PRODUCT_DISTRIBUTION
CPLMD::ves::TD_Uniform	Provides the keyword TD_UNIFORM
CPLMD::ves::TD_VonMises	Provides the keyword TD_VONMISES
CPLMD::ves::TD_WellTempered	Provides the keyword TD_WELLTEMPERED
►CPLMD::vesselbase::ActionWithInputVessel
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::multicolvar::DumpMultiColvar	Provides the keyword DUMPMULTICOLVAR
►CPLMD::vesselbase::ActionWithVessel
CPLMD::analysis::AnalysisBase
CPLMD::manyrestraints::ManyRestraintsBase
CPLMD::mapping::Mapping
CPLMD::multicolvar::MultiColvarBase
CPLMD::secondarystructure::SecondaryStructureRMSD	Base action for calculating things like AlphRMSD, AntibetaRMSD, etc
CPLMD::vesselbase::ActionWithAveraging
CPLMD::ActionOptions	This class is used to bring the relevant information to the Action constructor
CPLMD::ActionRegister	Register holding all the allowed keywords
CPLMD::Angle
CANN	Provides the keyword ANN
CPLMD::lepton::AsmJitRuntimePtr
CPLMD::Exception::Assertion	Auxiliary containing the failed assertion
CPLMD::AtomNumber
CPLMD::Atoms	Class containing atom related quantities from the MD code
CPLMD::multicolvar::AtomValuePack
CPLMD::BiasRepresentation	This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias
CPLMD::Brent1DRootSearch< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
CPLMD::multicolvar::CatomPack
CPLMD::isdb::CS2Backbone::ChemicalShift
CPLMD::Citations
►CPLMD::CLTool
CPLMD::cltools::CLToolSumHills
CPLMD::cltools::Completion
CPLMD::cltools::Driver< real >
CPLMD::cltools::GenExample
CPLMD::cltools::GenTemplate
CPLMD::cltools::Info
CPLMD::cltools::kt
CPLMD::cltools::Manual
CPLMD::cltools::PdbRenumber
CPLMD::cltools::PesMD
CPLMD::cltools::SimpleMD
CPLMD::mapping::PathTools
CPLMD::ves::MD_LinearExpansionPES
CPLMD::CLToolOptions
CPLMD::CLToolRegister	Same as ActionRegister, but for CLTools
►CPLMD::ves::CoeffsBase
CPLMD::ves::CoeffsMatrix
CPLMD::ves::CoeffsVector
►CPLMD::Communicator
CPLMD::Atoms::DomainDecomposition
CPLMD::lepton::CompiledExpression	A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate it many times as quickly as possible
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Const_row	Small utility class which just contains a pointer to the T and the row number
CPLMD::Communicator::ConstData	Const version of Communicator::Data See Communicator::Data documentation
CPLMD::opes::convergence
CPLMD::isdb::CS2BackboneDB
►CPLMD::lepton::CustomFunction	This class is the interface for defining your own function that may be included in expressions
CPLMD::lepton::PlaceholderFunction	This class is an implementation of CustomFunction that does no computation
CPLMD::Communicator::Data	Structure defining a buffer for MPI
CPLMD::analysis::DataCollectionObject
►CPLMD::DataFetchingObject
CPLMD::DataFetchingObjectTyped< T >
CPLMD::maze::tls::delete_ptr
CPLMD::Tools::DirectoryChanger	Tiny class that changes directory and comes back when going out of scope
CPLMD::DLLoader
CPLMD::DynamicList< T >
CPLMD::DynamicList< unsigned >
CDynamicReferenceRestraining	Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR
CPLMD::ERMSD	A class that implements ERMSD calculations
►Cstd::exception	STL class
CPLMD::Exception
►CPLMD::lepton::Exception	This class is used for all exceptions thrown by lepton
CPLMD::ExceptionDebug	Class representing a debug error (can only be thrown when using debug options)
CPLMD::ExceptionError	Class representing a generic error
CPLMD::ExceptionTypeError	Class representing a type error in the PLMD::Plumed interface
►CPLMD::Plumed::Exception	Base class used to rethrow PLUMED exceptions
CPLMD::Plumed::ExceptionDebug	Used to rethrow a PLMD::ExceptionDebug
CPLMD::Plumed::ExceptionError	Used to rethrow a PLMD::ExceptionError
CPLMD::Plumed::ExceptionTypeError	Thrown when a wrong pointer is passed to the PLUMED interface
CPLMD::Plumed::Invalid	Thrown when trying to access an invalid plumed object
CPLMD::Plumed::LeptonException	Class used to rethrow Lepton exceptions
CPLMD::ExchangePatterns
CPLMD::opes::exploration
CPLMD::lepton::ExpressionProgram	An ExpressionProgram is a linear sequence of Operations for evaluating an expression
CPLMD::lepton::ExpressionTreeNode	This class represents a node in the abstract syntax tree representation of an expression
CPLMD::F1dim< FCLASS >
CPLMD::ves::FermiSwitchingFunction
►CFieldBase
CPLMD::OFile::Field	Class identifying a single field for fielded output
►CPLMD::FileBase::FieldBase	Internal tool
CPLMD::IFile::Field
►CPLMD::FileBase	Base class for dealing with files
CPLMD::IFile
►CPLMD::OFile
CPLMD::Log	Class containing the log stream
CPLMD::function::FilesHandler
CPLMD::molfile::fio_iovec
CPLMD::FlexibleBin
CPLMD::bias::PBMetaD::Gaussian
CPLMD::bias::MetaD::Gaussian
►CPLMD::GridBase
CPLMD::Grid
CPLMD::SparseGrid
CPLMD::ves::GridIntegrationWeights
CPLMD::ves::GridLinearInterpolation
CPLMD::gridtools::GridSearch< FCLASS >
CPLMD::Stopwatch::Handler	Auxiliary class for handling exception-safe start/pause and start/stop
CPLMD::Subprocess::Handler	Class used to cont/stop a Subprocess in an exception safe manner
CPLMD::pamm::HBPammObject
CPLMD::HistogramBead
CPLMD::colvar::PathMSDBase::ImagePath	This class is a general container for path stuff
CPLMD::colvar::PathMSDBase::imgOrderByDist
CPLMD::colvar::PathMSDBase::imgOrderBySimilarity
CPLMD::opes::OPESmetad< mode >::kernel
CPLMD::KernelFunctions
CPLMD::Keywords::KeyType	This class lets me pass keyword types easily
CPLMD::Keywords	This class holds the keywords and their documentation
CPLMD::LatticeReduction	Class implementing algorithms for lattice reduction
CPLMD::ves::LinearBasisSetExpansion
CPLMD::LinkCells
CLOCAL_Q3	Provides the keyword LOCAL_Q3
CLOCAL_Q4	Provides the keyword LOCAL_Q4
CLOCAL_Q6	Provides the keyword LOCAL_Q6
CPLMD::Exception::Location	Auxiliary containing the location of the exception in the file
CPLMD::LoopUnroller< n >
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >	Utility class to add [][] access
►CPLMD::MatrixSquareBracketsAccess< Matrix< double >, double >
CPLMD::Matrix< double >
►CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::pamm::HBPammObject >, PLMD::pamm::HBPammObject >
CPLMD::Matrix< PLMD::pamm::HBPammObject >
►CPLMD::MatrixSquareBracketsAccess< Matrix< PLMD::SwitchingFunction >, PLMD::SwitchingFunction >
CPLMD::Matrix< PLMD::SwitchingFunction >
►CPLMD::MatrixSquareBracketsAccess< Matrix< std::pair< unsigned, unsigned > >, std::pair< unsigned, unsigned > >
CPLMD::Matrix< std::pair< unsigned, unsigned > >
►CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::KernelFunctions > >, std::vector< PLMD::KernelFunctions > >
CPLMD::Matrix< std::vector< PLMD::KernelFunctions > >
►CPLMD::MatrixSquareBracketsAccess< Matrix< std::vector< PLMD::VectorGeneric > >, std::vector< PLMD::VectorGeneric > >
CPLMD::Matrix< std::vector< PLMD::VectorGeneric > >
►CPLMD::MatrixSquareBracketsAccess< Matrix< T >, T >
CPLMD::Matrix< T >	This class stores a full matrix and allows one to do some simple matrix operations
►CPLMD::MatrixSquareBracketsAccess< Matrix< unsigned >, unsigned >
CPLMD::Matrix< unsigned >
►CPLMD::MatrixSquareBracketsAccess< TensorGeneric< n, m >, double >
CPLMD::TensorGeneric< n, m >
CPLMD::TensorGeneric< 4, 4 >
CPLMD::molfile::md_atom
CPLMD::molfile::md_box
CPLMD::molfile::md_file
CPLMD::molfile::md_header
CPLMD::molfile::md_ts
►CPLMD::MDAtomsBase	Class containing interface to MDAtomsTyped
CPLMD::MDAtomsTyped< T >	Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED
CPLMD::maze::Member	Defines the encoding for a ligand conformation
CPLMD::MetricRegister
CPLMD::Minimise1DBrent< FCLASS >	A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method
►CPLMD::MinimiseBase< FCLASS >
CPLMD::ConjugateGradient< FCLASS >
CPLMD::MolDataClass	This 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_t	Per-atom attributes and information
CPLMD::molfile::molfile_graphics_t	Individual graphics object/element data
CPLMD::molfile::molfile_metadata_t	File level comments, origin information, and annotations
CPLMD::molfile::molfile_plugin_t	Main file reader API
CPLMD::molfile::molfile_qm_basis_t	Data for QM basis set
CPLMD::molfile::molfile_qm_hessian_t	Data from QM Hessian/normal mode runs
CPLMD::molfile::molfile_qm_metadata_t	Sizes 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_t	QM run info
CPLMD::molfile::molfile_qm_t	QM related information that is timestep independent
CPLMD::molfile::molfile_qm_timestep_metadata	Sizes 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_t	QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions
CPLMD::molfile::molfile_qm_wavefunction_t	QM wavefunction
CPLMD::molfile::molfile_timestep_metadata
CPLMD::molfile::molfile_timestep_t
CPLMD::molfile::molfile_volumetric_readwrite_t	Volumetric dataset read/write structure with both flag/parameter sets and VMD-allocated pointers for fields to be used by the plugin
CPLMD::molfile::molfile_volumetric_t	Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading
CMolInfo	Provides the keyword MOLINFO
CPLMD::MPI_Comm	Surrogate of MPI_Comm when MPI library is not available
CPLMD::MPI_Datatype	Surrogate of MPI_Datatype when MPI library is not available
CPLMD::MPI_Request	Surrogate of MPI_Request when MPI library is not available
CPLMD::MPI_Status	Surrogate of MPI_Status when MPI library is not available
CPLMD::MultiValue
CPLMD::drr::UIestimator::n_matrix
CPLMD::drr::UIestimator::n_vector< T >
CPLMD::drr::UIestimator::n_vector< double >
CPLMD::drr::UIestimator::n_vector< int >
CPLMD::drr::UIestimator::n_vector< std::vector< double > >
CPLMD::NeighborList
CPLMD::Plumed::NothrowHandler	Error handler used to rethrow exceptions
CPLMD::OpenMP
CPLMD::OpenMPVars
CPLMD::lepton::Operation	An Operation represents a single step in the evaluation of an expression, such as a function, an operator, or a constant value
COPESmetad_c	Provides the keyword OPES_METAD
COPESmetad_e	Provides the keyword OPES_METAD_EXPLORE
CPLMD::function::FuncPathMSD::ordering
CPLMD::function::FuncPathMSD::pairordering
CPLMD::function::FuncPathGeneral::pairordering
CPLMD::pamm::PammObject
CPLMD::lepton::ParsedExpression	This class represents the result of parsing an expression
CPLMD::lepton::Parser	This class provides the main interface for parsing expressions
CPLMD::lepton::ParseToken
CPLMD::mapping::PathReparameterization
CPLMD::Pbc
CPLMD::PDB	Minimalistic pdb parser
Cplumed	Main plumed object
CPLMD::Plumed	C++ wrapper for plumed
Cplumed_error	Small structure that is only defined locally to retrieve errors
CPLMD::PlumedMain::plumed_error_handler	Error handler
Cplumed_function_holder
Cplumed_nothrow_handler
Cplumed_nothrow_handler_x
Cplumed_plumedmain_function_holder_x	Container for plumedmain function pointers (create, cmd and finalize)
Cplumed_safeptr	Structure holding a typesafe pointer
Cplumed_safeptr_x
Cplumed_symbol_table_type_x	Container for symbol table
CPLMD::Random
►CPLMD::ReferenceConfiguration
CPLMD::FakeFrame
►CPLMD::ReferenceArguments
►CPLMD::ArgumentOnlyDistance
CPLMD::DotProductDistance
CPLMD::EuclideanDistance
CPLMD::MahalanobisDistance
CPLMD::NormalizedEuclideanDistance
CPLMD::Direction
►CPLMD::ReferenceAtoms
CPLMD::Direction
CPLMD::MultiDomainRMSD
►CPLMD::SingleDomainRMSD
►CPLMD::DRMSD
CPLMD::IntermolecularDRMSD
CPLMD::IntramolecularDRMSD
►CPLMD::RMSDBase
CPLMD::OptimalRMSD
CPLMD::SimpleRMSD
CPLMD::ReferenceConfigurationOptions
CPLMD::ReferenceValuePack
CPLMD::Communicator::Request	Wrapper class for MPI_Request
CPLMD::isdb::CS2Backbone::RingInfo
CPLMD::RMSD
CPLMD::RMSDCoreData	This is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information
CPLMD::maze::rnd	Mersenne Twister sampler for random variables
CPLMD::RootFindingBase< FCLASS >
CPLMD::RootFindingBase< PLMD::gridtools::ContourFindingBase >
CPLMD::RootFindingBase< PLMD::multicolvar::DistanceFromContour >
CPLMD::MatrixSquareBracketsAccess< T, C, I, J >::Row	Small utility class which just contains a pointer to the T and the row number
CPLMD::Plumed::SafePtr	Small class that wraps plumed_safeptr in order to make its initialization easier
CPLMD::dimred::SMACOF
CPLMD::Communicator::Status	Wrapper class for MPI_Status
CPLMD::Stopwatch
CPLMD::Subprocess	Class managing a subprocess
CPLMD::SubprocessPid	Small utility class, used to avoid inclusion of unistd.h> in a header file
CPLMD::SwitchingFunction
CPLMD::xdrfile::t_trnheader
CPLMD::TargetDist
►CPLMD::ves::TargetDistModifer
CPLMD::ves::WellTemperedModifer
CPLMD::bias::MetaD::TemperingSpecs
CPLMD::TensorGenericAux	Small class to contain local utilities
CPLMD::maze::tls	Helper functions
CPLMD::Tools
CPLMD::Torsion
CPLMD::Tree
CPLMD::molfile::trx_hdr
CPLMD::TypesafePtr
CPLMD::drr::UIestimator::UIestimator
►Cstd::unique_ptr< T >	STL class
CPLMD::ForwardDecl< PLMD::ActionSet >
CPLMD::ForwardDecl< PLMD::Atoms >
CPLMD::ForwardDecl< PLMD::Citations >
CPLMD::ForwardDecl< PLMD::Communicator >
CPLMD::ForwardDecl< PLMD::DLLoader >
CPLMD::ForwardDecl< PLMD::ExchangePatterns >
CPLMD::ForwardDecl< PLMD::Log >
CPLMD::ForwardDecl< PLMD::Pbc >
CPLMD::ForwardDecl< PLMD::PDB >
CPLMD::ForwardDecl< PLMD::Random >
CPLMD::ForwardDecl< PLMD::Stopwatch >
CPLMD::ForwardDecl< PLMD::TypesafePtr >
CPLMD::ForwardDecl< T >	Utility class for forward declaration of references
CPLMD::Units
CPLMD::Value
►Cstd::vector< T >	STL class
CPLMD::ActionSet	Std::vector containing the sequence of Action to be done
CPLMD::VectorGeneric< n >
CPLMD::VectorGeneric< 4 >
CPLMD::VectorGeneric< 6 >
►CPLMD::vesselbase::Vessel
►CPLMD::vesselbase::AveragingVessel
CPLMD::analysis::AverageVessel
►CPLMD::gridtools::GridVessel
►CPLMD::gridtools::HistogramOnGrid
CPLMD::gridtools::AverageOnGrid
CPLMD::vesselbase::BridgeVessel
CPLMD::vesselbase::Moments
►CPLMD::vesselbase::ShortcutVessel
CPLMD::vesselbase::Histogram
►CPLMD::vesselbase::StoreDataVessel
CPLMD::adjmat::AdjacencyMatrixVessel
CPLMD::mapping::TrigonometricPathVessel
►CPLMD::vesselbase::ValueVessel
►CPLMD::vesselbase::FunctionVessel
CPLMD::crystallization::GradientVessel
CPLMD::crystallization::VectorMean
CPLMD::crystallization::VectorSum
CPLMD::mapping::SpathVessel
CPLMD::mapping::ZpathVessel
CPLMD::vesselbase::AltMin
CPLMD::vesselbase::Between
CPLMD::vesselbase::LessThan
CPLMD::vesselbase::Max
CPLMD::vesselbase::Mean
CPLMD::vesselbase::Min
CPLMD::vesselbase::MoreThan
CPLMD::vesselbase::Sum
►CPLMD::vesselbase::OrderingVessel
CPLMD::vesselbase::Highest
CPLMD::vesselbase::Lowest
CPLMD::vesselbase::VesselOptions	This class is used to pass the input to Vessels
CPLMD::vesselbase::VesselRegister
CPLMD::ves::VesTools
CPLMD::molfile::vmdplugin_t	Typedef 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::Watch	Class to store a single stopwatch
CPLMD::ves::WaveletGrid
►CPLMD::WeightBase
CPLMD::BiasWeight
CPLMD::ProbWeight
CPLMD::ves::FesWeight
CPLMD::ves::MarginalWeight
►CPLMD::WithCmd	Base for classes with cmd() method
CPLMD::CLToolMain	Class providing cmd() access to command line tools
CPLMD::GREX
CPLMD::PlumedHandle	Tiny local class to load a PLUMED kernel
CPLMD::PlumedMain	Main plumed object
CPLMD::xdrfile::XDR
CPLMD::xdrfile::XDR::xdr_ops
CPLMD::xdrfile::XDRFILE	Contents of the abstract XDRFILE data structure