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| ▶NPLMD | |
| ▶Nadjmat | |
| CActionWithInputMatrix | |
| CAdjacencyMatrixBase | |
| CAdjacencyMatrixVessel | |
| CAlignedMatrixBase | |
| CClusterAnalysisBase | |
| CClusterDiameter | Provides the keyword CLUSTER_DIAMETER |
| CClusterDistribution | Provides the keyword CLUSTER_DISTRIBUTION |
| CClusteringBase | |
| CClusterProperties | Provides the keyword CLUSTER_PROPERTIES |
| CClusterSize | Provides the keyword CLUSTER_NATOMS |
| CClusterWithSurface | Provides the keyword CLUSTER_WITHSURFACE |
| CContactAlignedMatrix | Provides the keyword ALIGNED_MATRIX |
| CContactMatrix | Provides the keyword CONTACT_MATRIX |
| CDFSClustering | Provides the keyword DFSCLUSTERING |
| CDumpGraph | Provides the keyword DUMPGRAPH |
| CHBondMatrix | Provides the keyword HBOND_MATRIX |
| CMatrixColumnSums | Provides the keyword COLUMNSUMS |
| CMatrixRowSums | Provides the keyword ROWSUMS |
| COutputCluster | Provides the keyword OUTPUT_CLUSTER |
| CSMACMatrix | Provides the keyword SMAC_MATRIX |
| CSprint | Provides the keyword SPRINT |
| CTopologyMatrix | Provides the keyword TOPOLOGY_MATRIX |
| ▶Nanalysis | |
| CAnalysisBase | This is the abstract base class to use for implementing new methods for analyzing the trajectory |
| CAverage | Provides the keyword AVERAGE |
| CAverageVessel | |
| CCommittor | Provides the keyword COMMITTOR |
| CDataCollectionObject | |
| CEuclideanDissimilarityMatrix | Provides the keyword EUCLIDEAN_DISSIMILARITIES |
| CFarthestPointSampling | Provides the keyword LANDMARK_SELECT_FPS |
| CHistogram | Provides the keyword HISTOGRAM |
| CLandmarkSelectionBase | |
| CLandmarkStaged | Provides the keyword LANDMARK_SELECT_STAGED |
| COutputColvarFile | Provides the keyword OUTPUT_ANALYSIS_DATA_TO_COLVAR |
| COutputPDBFile | Provides the keyword OUTPUT_ANALYSIS_DATA_TO_PDB |
| CPrintDissimilarityMatrix | Provides the keyword PRINT_DISSIMILARITY_MATRIX |
| CReadAnalysisFrames | Provides the keyword COLLECT_FRAMES |
| CReadDissimilarityMatrix | Provides the keyword READ_DISSIMILARITY_MATRIX |
| CReselectLandmarks | Provides the keyword RESELECT_LANDMARKS |
| CSelectRandomFrames | Provides the keyword LANDMARK_SELECT_RANDOM |
| CSelectWithStride | Provides the keyword LANDMARK_SELECT_STRIDE |
| CWhamHistogram | Provides the keyword WHAM_HISTOGRAM |
| CWhamWeights | Provides the keyword WHAM_WEIGHTS |
| ▶Nannfunc | |
| CANN | Provides the keyword ANN |
| ▶Nbias | |
| CABMD | Provides the keyword ABMD |
| CBias | This is the abstract base class to use for implementing new simulation biases, within it there is information as to how to go about implementing a new bias |
| CBiasValue | Provides the keyword BIASVALUE |
| CExtendedLagrangian | Provides the keyword EXTENDED_LAGRANGIAN |
| CExternal | Provides the keyword EXTERNAL |
| CLWalls | Provides the keyword LOWER_WALLS |
| CMaxEnt | Provides the keyword MAXENT |
| ▶CMetaD | Provides the keyword METAD |
| CGaussian | |
| CTemperingSpecs | |
| CMovingRestraint | Provides the keyword MOVINGRESTRAINT |
| ▶CPBMetaD | Provides the keyword PBMETAD |
| CGaussian | |
| CRestraint | Provides the keyword RESTRAINT |
| CReweightBase | |
| CReweightBias | Provides the keyword REWEIGHT_BIAS |
| CReweightMetad | Provides the keyword REWEIGHT_METAD |
| CReweightTemperaturePressure | Provides the keyword REWEIGHT_TEMP_PRESS |
| CReweightWham | Provides the keyword REWEIGHT_WHAM |
| CUWalls | Provides the keyword UPPER_WALLS |
| ▶Ncltools | |
| CCLToolSumHills | |
| CCompletion | |
| CDriver | |
| CGenExample | |
| CGenTemplate | |
| CInfo | |
| Ckt | |
| CManual | |
| CPdbRenumber | |
| CPesMD | |
| CSimpleMD | |
| ▶Ncolvar | |
| CAngle | Provides the keyword ANGLE |
| CCell | Provides the keyword CELL |
| CColvarFake | Provides the keyword FAKE |
| CConstant | Provides the keyword CONSTANT |
| CContactMap | Provides the keyword CONTACTMAP |
| CCoordination | Provides the keyword COORDINATION |
| CCoordinationBase | |
| CDHEnergy | Provides the keyword DHENERGY |
| CDimer | Provides the keyword <a href="../../user-doc/html/_"_d_i_m_e_r.html"> "DIMER |
| CDipole | Provides the keyword DIPOLE |
| CDistance | Provides the keyword DISTANCE |
| CDRMSD | Provides the keyword DRMSD |
| CEEFSolv | Provides the keyword EEFSOLV |
| CEnergy | Provides the keyword ENERGY |
| CERMSD | Provides the keyword ERMSD |
| CExtraCV | Provides the keyword EXTRACV |
| CGHBFIX | Provides the keyword GHBFIX |
| CGyration | Provides the keyword GYRATION |
| CMultiRMSD | Provides the keyword MULTI_RMSD |
| CPathMSD | Provides the keyword PATHMSD |
| ▶CPathMSDBase | |
| CImagePath | This class is a general container for path stuff |
| CimgOrderByDist | |
| CimgOrderBySimilarity | |
| CPCARMSD | Provides the keyword PCARMSD |
| CPosition | Provides the keyword POSITION |
| CProjectionOnAxis | Provides the keyword PROJECTION_ON_AXIS |
| CPropertyMap | Provides the keyword PROPERTYMAP |
| CPuckering | Provides the keyword PUCKERING |
| CRMSD | Provides the keyword RMSD |
| CTemplate | Provides the keyword TEMPLATE |
| CTorsion | Provides the keyword TORSION |
| CVolume | Provides the keyword VOLUME |
| ▶Ncrystallization | |
| CBondOrientation | Provides the keyword BOND_DIRECTIONS |
| CCubicHarmonicBase | |
| CEnvironmentSimilarity | Provides the keyword ENVIRONMENTSIMILARITY |
| CFccubic | Provides the keyword FCCUBIC |
| CGradient | Provides the keyword GRADIENT |
| CGradientVessel | |
| CInterMolecularTorsions | Provides the keyword INTERMOLECULARTORSIONS |
| CLOCAL_Q3 | Provides the keyword LOCAL_Q3 |
| CLOCAL_Q4 | Provides the keyword LOCAL_Q4 |
| CLOCAL_Q6 | Provides the keyword LOCAL_Q6 |
| CLocalSteinhardt | |
| CMoleculeOrientation | Provides the keyword MOLECULES |
| CMoleculePlane | Provides the keyword PLANES |
| COrientationSphere | |
| CPolymerAngles | Provides the keyword POLYMER_ANGLES |
| CQ3 | Provides the keyword Q3 |
| CQ4 | Provides the keyword Q4 |
| CQ6 | Provides the keyword Q6 |
| CSimpleCubic | Provides the keyword SIMPLECUBIC |
| CSMAC | Provides the keyword SMAC |
| CSteinhardt | |
| CTetrahedral | Provides the keyword TETRAHEDRAL |
| CVectorMean | |
| CVectorMultiColvar | |
| CVectorSum | |
| ▶Ndimred | |
| CClassicalMultiDimensionalScaling | Provides the keyword CLASSICAL_MDS |
| CDimensionalityReductionBase | |
| COutputPCAProjection | Provides the keyword OUTPUT_PCA_PROJECTION |
| CPCA | Provides the keyword PCA |
| CProjectNonLandmarkPoints | Provides the keyword PROJECT_ALL_ANALYSIS_DATA |
| CSketchMap | Provides the keyword SKETCH_MAP |
| CSketchMapBase | |
| CSketchMapConjGrad | Provides the keyword SKETCHMAP_CONJGRAD |
| CSketchMapPointwise | Provides the keyword SKETCHMAP_POINTWISE |
| CSketchMapRead | Provides the keyword SKETCHMAP_READ |
| CSketchMapSmacof | Provides the keyword SKETCHMAP_SMACOF |
| CSMACOF | |
| CSmacofMDS | Provides the keyword SMACOF_MDS |
| ▶Ndrr | |
| ▶NUIestimator | |
| Cn_matrix | |
| Cn_vector | |
| CUIestimator | |
| CDynamicReferenceRestraining | Provides the keyword <a href="../../user-doc/html/_"_d_r_r.html"> "DRR |
| ▶Neds | |
| CEDS | Provides the keyword EDS |
| ▶Nfisst | |
| CFISST | Provides the keyword FISST |
| ▶Nfunction | |
| ▶Nannfunc | |
| CANN | |
| CCombine | Provides the keyword COMBINE |
| CCustom | Provides the keyword CUSTOM |
| CEnsemble | Provides the keyword ENSEMBLE |
| CFilesHandler | |
| ▶CFuncPathGeneral | 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 |
| Cpairordering | |
| ▶CFuncPathMSD | Provides the keyword FUNCPATHMSD |
| Cordering | |
| Cpairordering | |
| CFuncSumHills | Provides the keyword FUNCSUMHILLS |
| CFunction | This is the abstract base class to use for implementing new CV function, within it there is information as to how to go about implementing a new function |
| CLocalEnsemble | Provides the keyword LOCALENSEMBLE |
| CMatheval | |
| CPiecewise | Provides the keyword PIECEWISE |
| CSort | Provides the keyword SORT |
| CStats | Provides the keyword STATS |
| CTarget | Provides the keyword TARGET |
| ▶Nfunnel | |
| CFunnel | Provides the keyword FUNNEL |
| CFUNNEL_PS | Provides the keyword FUNNEL_PS |
| ▶Ngeneric | |
| CDebug | Provides the keyword DEBUG |
| CDumpAtoms | Provides the keyword DUMPATOMS |
| CDumpDerivatives | Provides the keyword DUMPDERIVATIVES |
| CDumpForces | Provides the keyword DUMPFORCES |
| CDumpMassCharge | Provides the keyword DUMPMASSCHARGE |
| CDumpProjections | Provides the keyword DUMPPROJECTIONS |
| CEffectiveEnergyDrift | Provides the keyword EFFECTIVE_ENERGY_DRIFT |
| CEndPlumed | Provides the keyword ENDPLUMED |
| CFitToTemplate | Provides the keyword FIT_TO_TEMPLATE |
| CFlush | Provides the keyword FLUSH |
| CGroup | Provides the keyword GROUP |
| CInclude | Provides the keyword INCLUDE |
| CMolInfo | Provides the keyword MOLINFO |
| CPlumed | Provides the keyword PLUMED |
| CPrint | Provides the keyword PRINT |
| CRandomExchanges | Provides the keyword RANDOM_EXCHANGES |
| CRead | Provides the keyword READ |
| CResetCell | Provides the keyword RESET_CELL |
| CTime | Provides the keyword TIME |
| CUpdateIf | Provides the keyword UPDATE_IF |
| CWholeMolecules | Provides the keyword WHOLEMOLECULES |
| CWrapAround | Provides the keyword WRAPAROUND |
| ▶Ngridtools | |
| CActionWithGrid | |
| CActionWithInputGrid | |
| CActionWithIntegral | |
| CAverageOnGrid | |
| CContourFindingBase | |
| CConvertToFES | Provides the keyword CONVERT_TO_FES |
| CDumpCube | Provides the keyword DUMPCUBE |
| CDumpGrid | Provides the keyword DUMPGRID |
| CFindContour | Provides the keyword FIND_CONTOUR |
| CFindContourSurface | Provides the keyword FIND_CONTOUR_SURFACE |
| CFindSphericalContour | Provides the keyword FIND_SPHERICAL_CONTOUR |
| CFourierTransform | Provides the keyword FOURIER_TRANSFORM |
| CGridPrintingBase | |
| CGridSearch | |
| CGridToXYZ | Provides the keyword GRID_TO_XYZ |
| CGridVessel | |
| CHistogramOnGrid | |
| CIntegrateGrid | Provides the keyword INTEGRATE_GRID |
| CInterpolateGrid | Provides the keyword INTERPOLATE_GRID |
| ▶Nisdb | |
| CCaliber | Provides the keyword CALIBER |
| ▶CCS2Backbone | Provides the keyword CS2BACKBONE |
| CChemicalShift | |
| CRingInfo | |
| CCS2BackboneDB | |
| CEMMI | Provides the keyword EMMI |
| CFretEfficiency | Provides the keyword FRET |
| CJCoupling | Provides the keyword <a href="../../user-doc/html/_"_j_c_o_u_p_l_i_n_g.html"> "JCOUPLING |
| CMetainference | Provides the keyword METAINFERENCE |
| CMetainferenceBase | This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is information as to how to go about implementing a new Metainference action |
| CNOE | Provides the keyword NOE |
| CPRE | Provides the keyword PRE |
| CRDC | Provides the keyword RDC |
| CRescale | Provides the keyword RESCALE |
| CSAXS | Provides the keyword SAXS |
| CSelect | Provides the keyword SELECT |
| CSelector | Provides the keyword SELECTOR |
| ▶Nlepton | |
| CAsmJitRuntimePtr | |
| CCompiledExpression | A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate it many times as quickly as possible |
| CCustomFunction | This class is the interface for defining your own function that may be included in expressions |
| CException | This class is used for all exceptions thrown by lepton |
| CExpressionProgram | An ExpressionProgram is a linear sequence of Operations for evaluating an expression |
| CExpressionTreeNode | This class represents a node in the abstract syntax tree representation of an expression |
| COperation | An Operation represents a single step in the evaluation of an expression, such as a function, an operator, or a constant value |
| CParsedExpression | This class represents the result of parsing an expression |
| CParser | This class provides the main interface for parsing expressions |
| CParseToken | |
| CPlaceholderFunction | This class is an implementation of CustomFunction that does no computation |
| ▶Nlogmfd | |
| CLogMFD | Class for LogMFD parameters, variables and subroutines |
| ▶Nmanyrestraints | |
| CLWalls | Provides the keyword LWALLS |
| CManyRestraintsBase | |
| CUWalls | Provides the keyword UWALLS |
| ▶Nmapping | |
| CAdaptivePath | Provides the keyword ADAPTIVE_PATH |
| CMapping | |
| CPath | Provides the keyword PATH |
| CPathBase | |
| CPathReparameterization | This class can be used to make a set of reference configurations equidistant |
| CPathTools | |
| CPCAVars | Provides the keyword PCAVARS |
| CPropertyMap | Provides the keyword GPROPERTYMAP |
| CSpathVessel | |
| CTrigonometricPathVessel | |
| CZpathVessel | |
| ▶Nmaze | |
| CLoss | Provides the keyword <a href="../../user-doc/html/_"_m_a_z_e__l_o_s_s.html"> "MAZE_LOSS |
| CMember | Defines the encoding for a ligand conformation |
| CMemetic | 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 |
| COptimizer | Base class for implementing optimizers for ligand unbinding |
| COptimizerBias | 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 |
| CRandom_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 |
| CRandom_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 |
| Crnd | Mersenne Twister sampler for random variables |
| CSimulated_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 |
| CSteered_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 |
| ▶Ctls | Helper functions |
| Cdelete_ptr | |
| ▶Nmolfile | |
| Cfio_iovec | |
| Cmd_atom | |
| Cmd_box | |
| Cmd_file | |
| Cmd_header | |
| Cmd_ts | |
| Cmolfile_atom_t | Per-atom attributes and information |
| Cmolfile_graphics_t | Individual graphics object/element data |
| Cmolfile_metadata_t | File level comments, origin information, and annotations |
| Cmolfile_plugin_t | Main file reader API |
| Cmolfile_qm_basis_t | Data for QM basis set |
| Cmolfile_qm_hessian_t | Data from QM Hessian/normal mode runs |
| Cmolfile_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 |
| Cmolfile_qm_sysinfo_t | QM run info |
| Cmolfile_qm_t | QM related information that is timestep independent |
| Cmolfile_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 |
| Cmolfile_qm_timestep_t | QM per trajectory timestep info Note that each timestep can contain multiple wavefunctions |
| Cmolfile_qm_wavefunction_t | QM wavefunction |
| Cmolfile_timestep_metadata | |
| Cmolfile_timestep_t | |
| Cmolfile_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 |
| Cmolfile_volumetric_t | Metadata for volumetric datasets, read initially and used for subsequent memory allocations and file loading |
| Ctrx_hdr | |
| Cvmdplugin_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 |
| ▶Nmulticolvar | |
| CActionVolume | This is the abstract base class to use for implementing a new way of defining a particular region of the simulation box |
| CAlphaBeta | Provides the keyword ALPHABETA |
| CAngles | Provides the keyword ANGLES |
| CAtomValuePack | |
| CBridge | Provides the keyword BRIDGE |
| CBridgedMultiColvarFunction | |
| CCatomPack | |
| CCenterOfMultiColvar | Provides the keyword CENTER_OF_MULTICOLVAR |
| CCoordinationNumbers | Provides the keyword COORDINATIONNUMBER |
| CDensity | Provides the keyword DENSITY |
| CDihedralCorrelation | Provides the keyword DIHCOR |
| CDistanceFromContour | Provides the keyword DISTANCE_FROM_CONTOUR |
| CDistances | Provides the keyword DISTANCES |
| CDumpMultiColvar | Provides the keyword DUMPMULTICOLVAR |
| CFilterBetween | Provides the keyword MFILTER_BETWEEN |
| CFilterLess | Provides the keyword MFILTER_LESS |
| CFilterMore | Provides the keyword MFILTER_MORE |
| CInPlaneDistances | Provides the keyword INPLANEDISTANCES |
| CLocalAverage | Provides the keyword LOCAL_AVERAGE |
| CMultiColvarBase | |
| CMultiColvarCombine | Provides the keyword MCOLV_COMBINE |
| CMultiColvarDensity | Provides the keyword MULTICOLVARDENS |
| CMultiColvarFilter | This is the abstract base class to use for implementing a new way of filtering collective variable values to see whether or not they are within a certain range |
| CMultiColvarProduct | Provides the keyword MCOLV_PRODUCT |
| CNumberOfLinks | Provides the keyword NLINKS |
| CTorsions | Provides the keyword TORSIONS |
| CVolumeAround | Provides the keyword AROUND |
| CVolumeCavity | Provides the keyword CAVITY |
| CVolumeGradientBase | |
| CVolumeInCylinder | Provides the keyword INCYLINDER |
| CVolumeInEnvelope | Provides the keyword INENVELOPE |
| CVolumeInSphere | Provides the keyword INSPHERE |
| CVolumeTetrapore | Provides the keyword TETRAHEDRALPORE |
| CXAngles | Provides the keyword XANGLES |
| CXDistances | Provides the keyword XDISTANCES |
| CXYDistances | Provides the keyword XYDISTANCES |
| CXYTorsion | Provides the keyword XYTORSIONS |
| ▶Nopes | |
| Cconvergence | |
| CECVcustom | Provides the keyword ECV_CUSTOM |
| CECVlinear | Provides the keyword ECV_LINEAR |
| CECVmultiCanonical | Provides the keyword ECV_MULTITHERMAL |
| CECVmultiThermalBaric | Provides the keyword ECV_MULTITHERMAL_MULTIBARIC |
| CECVumbrellasFile | Provides the keyword ECV_UMBRELLAS_FILE |
| CECVumbrellasLine | Provides the keyword ECV_UMBRELLAS_LINE |
| CExpansionCVs | |
| Cexploration | |
| COPESexpanded | Provides the keyword OPES_EXPANDED |
| ▶COPESmetad | |
| Ckernel | |
| COPESmetad_c | Provides the keyword OPES_METAD |
| COPESmetad_e | Provides the keyword OPES_METAD_EXPLORE |
| ▶Npamm | |
| CHBPammHydrogens | Provides the keyword HBPAMM_SH |
| CHBPammMatrix | Provides the keyword HBPAMM_MATRIX |
| CHBPammObject | |
| CPAMM | Provides the keyword PAMM |
| CPammObject | |
| ▶Npiv | |
| CPIV | Provides the keyword PIV |
| ▶Ns2cm | |
| CS2ContactModel | Provides the keyword S2CM |
| ▶Nsasa | |
| CSASA_HASEL | Provides the keyword SASA_HASEL |
| CSASA_LCPO | Provides the keyword SASA_LCPO |
| ▶Nsecondarystructure | |
| CAlphaRMSD | Provides the keyword ALPHARMSD |
| CAntibetaRMSD | Provides the keyword ANTIBETARMSD |
| CParabetaRMSD | Provides the keyword PARABETARMSD |
| CSecondaryStructureRMSD | Base action for calculating things like AlphRMSD, AntibetaRMSD, etc |
| ▶Nsetup | |
| CLoad | Provides the keyword LOAD |
| CRestart | Provides the keyword RESTART |
| CUnits | Provides the keyword UNITS |
| ▶Nvatom | |
| CCenter | Provides the keyword CENTER |
| CFixedAtom | Provides the keyword FIXEDATOM |
| CGhost | Provides the keyword GHOST |
| ▶Nves | |
| CBasisFunctions | |
| CBF_Chebyshev | Provides the keyword BF_CHEBYSHEV |
| CBF_Combined | Provides the keyword BF_COMBINED |
| CBF_Cosine | Provides the keyword BF_COSINE |
| CBF_CubicBsplines | Provides the keyword BF_CUBIC_B_SPLINES |
| CBF_Custom | Provides the keyword BF_CUSTOM |
| CBF_Fourier | Provides the keyword BF_FOURIER |
| CBF_Gaussians | Provides the keyword BF_GAUSSIANS |
| CBF_Legendre | Provides the keyword BF_LEGENDRE |
| CBF_Powers | Provides the keyword BF_POWERS |
| CBF_Sine | Provides the keyword BF_SINE |
| CBF_Wavelets | Provides the keyword BF_WAVELETS |
| CCoeffsBase | |
| CCoeffsMatrix | |
| CCoeffsVector | |
| CFermiSwitchingFunction | Small class to compute fermi switching function |
| CFesWeight | |
| CGridIntegrationWeights | |
| CGridLinearInterpolation | |
| CLinearBasisSetExpansion | |
| CMarginalWeight | |
| CMD_LinearExpansionPES | |
| COpt_Adam | Provides the keyword OPT_ADAM |
| COpt_BachAveragedSGD | Provides the keyword OPT_AVERAGED_SGD |
| COpt_Dummy | Provides the keyword OPT_DUMMY |
| COpt_RobbinsMonroSGD | Provides the keyword OPT_ROBBINS_MONRO_SGD |
| COptimizer | |
| COutputBasisFunctions | Provides the keyword VES_OUTPUT_BASISFUNCTIONS |
| COutputFesBias | Provides the keyword VES_OUTPUT_FES |
| COutputTargetDistribution | Provides the keyword VES_OUTPUT_TARGET_DISTRIBUTION |
| CTargetDistModifer | |
| CTargetDistribution | |
| CTD_Chi | Provides the keyword TD_CHI |
| CTD_ChiSquared | Provides the keyword TD_CHISQUARED |
| CTD_Custom | Provides the keyword TD_CUSTOM |
| CTD_Exponential | Provides the keyword TD_EXPONENTIAL |
| CTD_ExponentiallyModifiedGaussian | Provides the keyword TD_EXPONENTIALLY_MODIFIED_GAUSSIAN |
| CTD_Gaussian | Provides the keyword TD_GAUSSIAN |
| CTD_GeneralizedExtremeValue | Provides the keyword TD_GENERALIZED_EXTREME_VALUE |
| CTD_GeneralizedNormal | Provides the keyword TD_GENERALIZED_NORMAL |
| CTD_Grid | Provides the keyword TD_GRID |
| CTD_LinearCombination | Provides the keyword TD_LINEAR_COMBINATION |
| CTD_Multicanonical | Provides the keyword TD_MULTICANONICAL |
| CTD_MultithermalMultibaric | Provides the keyword TD_MULTITHERMAL_MULTIBARIC |
| CTD_ProductCombination | Provides the keyword TD_PRODUCT_COMBINATION |
| CTD_ProductDistribution | Provides the keyword TD_PRODUCT_DISTRIBUTION |
| CTD_Uniform | Provides the keyword TD_UNIFORM |
| CTD_VonMises | Provides the keyword TD_VONMISES |
| CTD_WellTempered | Provides the keyword TD_WELLTEMPERED |
| CVesBias | Abstract base class for implementing biases the extents the normal Bias.h class to include functions related to the variational approach |
| CVesDeltaF | Provides the keyword VES_DELTA_F |
| CVesLinearExpansion | Provides the keyword VES_LINEAR_EXPANSION |
| CVesTools | |
| CWaveletGrid | |
| CWellTemperedModifer | |
| ▶Nvesselbase | |
| CActionWithAveraging | This abstract base class should be used if you are writing some method that calculates an "average" from a set of trajectory frames |
| CActionWithInputVessel | |
| CActionWithVessel | This is used to create PLMD::Action objects that are computed by calculating the same function multiple times |
| CAltMin | |
| CAveragingVessel | |
| CBetween | |
| CBridgeVessel | This class allows you to calculate the vessel in one ActionWithVessel |
| CFunctionVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate functions of the form \(\prod_k H_k[ \sum_j \prod_i g_i(x) ]\) |
| CHighest | |
| CHistogram | |
| CLessThan | |
| CLowest | |
| CMax | |
| CMean | |
| CMin | |
| CMoments | |
| CMoreThan | |
| COrderingVessel | |
| CShortcutVessel | |
| CStoreDataVessel | Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to store values and derivatives for a set of scalars or vectors that are calculated by a PLMD::vesselbase::ActionWithVessel |
| CSum | |
| CValueVessel | |
| CVessel | |
| CVesselOptions | This class is used to pass the input to Vessels |
| CVesselRegister | |
| ▶Nxdrfile | |
| Ct_trnheader | |
| ▶CXDR | |
| Cxdr_ops | |
| CXDRFILE | Contents of the abstract XDRFILE data structure |
| CAction | Base class for all the input Actions |
| CActionAnyorder | Action used to create a PLMD::Action that can go both before and after ActionSetup actions |
| CActionAtomistic | Action used to create objects that access the positions of the atoms from the MD code |
| CActionOptions | This class is used to bring the relevant information to the Action constructor |
| CActionPilot | This is used to create PLMD::Action objects that are run with some set frequency |
| CActionRegister | Register holding all the allowed keywords |
| CActionSet | Std::vector containing the sequence of Action to be done |
| CActionSetup | Action used to create a PLMD::Action that do something during setup only e.g |
| CActionShortcut | Action used to create a command that expands to multiple PLMD::Action commands when read in during input |
| CActionWithArguments | This is used to create PLMD::Action objects that take the output from some other Action as input |
| CActionWithValue | Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives |
| CActionWithVirtualAtom | Inherit from here if you are calculating the position of a virtual atom (eg a center of mass) |
| CAngle | Class to compute angles |
| CArgumentOnlyDistance | |
| CAtomNumber | Simple class to store the index of an atom |
| ▶CAtoms | Class containing atom related quantities from the MD code |
| CDomainDecomposition | |
| CBiasRepresentation | This class implements a general purpose class that aims to provide a Grid/list transparently add gaussians to a bias |
| CBiasWeight | |
| CBrent1DRootSearch | A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method |
| CCitations | Class taking care of bibliography |
| CCLTool | This 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 |
| CCLToolMain | Class providing cmd() access to command line tools |
| CCLToolOptions | |
| CCLToolRegister | Same as ActionRegister, but for CLTools |
| CColvar | This is the abstract base class to use for implementing new collective variables, within it there is information as to how to go about implementing a new CV |
| ▶CCommunicator | Class containing wrappers to MPI |
| CConstData | Const version of Communicator::Data See Communicator::Data documentation |
| CData | Structure defining a buffer for MPI |
| CRequest | Wrapper class for MPI_Request |
| CStatus | Wrapper class for MPI_Status |
| CConjugateGradient | |
| CDataFetchingObject | |
| CDataFetchingObjectTyped | |
| CDirection | |
| CDLLoader | Class taking care of dynamic loading |
| CDotProductDistance | |
| CDRMSD | |
| CDynamicList | A class for storing a list that changes which members are active as a function of time |
| CERMSD | A class that implements ERMSD calculations |
| CEuclideanDistance | |
| ▶CException | Class to deal with Plumed runtime errors |
| CAssertion | Auxiliary containing the failed assertion |
| CLocation | Auxiliary containing the location of the exception in the file |
| CExceptionDebug | Class representing a debug error (can only be thrown when using debug options) |
| CExceptionError | Class representing a generic error |
| CExceptionTypeError | Class representing a type error in the PLMD::Plumed interface |
| CExchangePatterns | |
| CF1dim | |
| CFakeFrame | |
| ▶CFileBase | Base class for dealing with files |
| CFieldBase | Internal tool |
| CFlexibleBin | |
| CForwardDecl | Utility class for forward declaration of references |
| CGenericMolInfo | |
| CGREX | |
| CGrid | |
| CGridBase | |
| CHistogramBead | A class for calculating whether or not values are within a given range using : \( \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \) |
| ▶CIFile | Class for input files |
| CField | |
| CIntermolecularDRMSD | |
| CIntramolecularDRMSD | |
| CKernelFunctions | |
| ▶CKeywords | This class holds the keywords and their documentation |
| CKeyType | This class lets me pass keyword types easily |
| CLatticeReduction | Class implementing algorithms for lattice reduction |
| CLinkCells | A class for doing link cells |
| CLog | Class containing the log stream |
| CLoopUnroller | Utiliy class for loop unrolling |
| CMahalanobisDistance | |
| CMatrix | This class stores a full matrix and allows one to do some simple matrix operations |
| ▶CMatrixSquareBracketsAccess | Utility class to add [][] access |
| CConst_row | Small utility class which just contains a pointer to the T and the row number |
| CRow | Small utility class which just contains a pointer to the T and the row number |
| CMDAtomsBase | Class containing interface to MDAtomsTyped |
| CMDAtomsTyped | Class containing the pointers to the MD data It is templated so that single and double precision versions coexist IT IS STILL UNDOCUMENTED |
| CMetricRegister | |
| CMinimise1DBrent | A class for doing parabolic interpolation and minimisation of 1D functions using Brent's method |
| CMinimiseBase | |
| CMolDataClass | 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 |
| CMPI_Comm | Surrogate of MPI_Comm when MPI library is not available |
| CMPI_Datatype | Surrogate of MPI_Datatype when MPI library is not available |
| CMPI_Request | Surrogate of MPI_Request when MPI library is not available |
| CMPI_Status | Surrogate of MPI_Status when MPI library is not available |
| CMultiDomainRMSD | |
| CMultiValue | |
| CNeighborList | A class that implements neighbor lists from two lists or a single list of atoms |
| CNormalizedEuclideanDistance | |
| ▶COFile | Class for output files |
| CField | Class identifying a single field for fielded output |
| COpenMP | |
| COpenMPVars | |
| COptimalRMSD | |
| CPbc | |
| CPDB | Minimalistic pdb parser |
| ▶CPlumed | C++ wrapper for plumed |
| CException | Base class used to rethrow PLUMED exceptions |
| CExceptionDebug | Used to rethrow a PLMD::ExceptionDebug |
| CExceptionError | Used to rethrow a PLMD::ExceptionError |
| CExceptionTypeError | Thrown when a wrong pointer is passed to the PLUMED interface |
| CInvalid | Thrown when trying to access an invalid plumed object |
| CLeptonException | Class used to rethrow Lepton exceptions |
| CNothrowHandler | Error handler used to rethrow exceptions |
| CSafePtr | Small class that wraps plumed_safeptr in order to make its initialization easier |
| CPlumedHandle | Tiny local class to load a PLUMED kernel |
| ▶CPlumedMain | Main plumed object |
| Cplumed_error_handler | Error handler |
| CProbWeight | |
| CRandom | |
| CReferenceArguments | In many applications (e.g |
| CReferenceAtoms | In many applications (e.g |
| CReferenceConfiguration | Abstract base class for calculating the distance from a reference configuration |
| CReferenceConfigurationOptions | |
| CReferenceValuePack | |
| CRMSD | A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame |
| CRMSDBase | |
| CRMSDCoreData | 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 |
| CRootFindingBase | |
| CSimpleRMSD | |
| CSingleDomainRMSD | |
| CSparseGrid | |
| ▶CStopwatch | |
| CHandler | Auxiliary class for handling exception-safe start/pause and start/stop |
| CWatch | Class to store a single stopwatch |
| ▶CSubprocess | Class managing a subprocess |
| CHandler | Class used to cont/stop a Subprocess in an exception safe manner |
| CSubprocessPid | Small utility class, used to avoid inclusion of unistd.h> in a header file |
| CSwitchingFunction | Small class to compure switching functions |
| CTargetDist | |
| CTensorGeneric | Class implementing fixed size matrices of doubles |
| CTensorGenericAux | Small class to contain local utilities |
| ▶CTools | Empty class which just contains several (static) tools |
| C_Unique_if | Mimic C++14 std::make_unique |
| C_Unique_if< T[]> | |
| C_Unique_if< T[N]> | |
| CDirectoryChanger | Tiny class that changes directory and comes back when going out of scope |
| CTorsion | Class to compute torsional angles |
| CTree | |
| CTypesafePtr | Class to deal with propoagation of typesafe pointers |
| CUnits | Small utility class that contains information about units |
| CValue | A class for holding the value of a function together with its derivatives |
| CVectorGeneric | Class implementing fixed size vectors of doubles |
| CWeightBase | |
| CWithCmd | Base for classes with cmd() method |
| Cplumed | Main plumed object |
| Cplumed_error | Small structure that is only defined locally to retrieve errors |
| 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 |
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