Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

BALL
__private
Constants
Exception
GeneralException
IndexUnderflow
SizeUnderflow
IndexOverflow
InvalidArgument
InvalidRange
InvalidSize
OutOfRange
InvalidFormat
IllegalSelfOperation
NullPointer
InvalidIterator
IncompatibleIterators
NotImplemented
IllegalTreeOperation
OutOfMemory
BufferOverflow
DivisionByZero
OutOfGrid
FileNotFound
IllegalPosition
ParseError
Precondition
Postcondition
InvalidOption	Exception to be thrown if an invalid option is given
TooManyErrors	Exception to be thrown if too many errors occur, e.g. in ForceField
TooManyBonds	Exception to be thrown if too many bonds for one atom
CUDAError
NoBufferAvailable
FormatUnsupported
NotInitialized
GlobalExceptionHandler
MatrixHasWrongDimension
VectorHasWrongDimension
MatrixNotRegular
MatrixNotQuadratic
MatrixIsSingular
SingularIterator
Uninitialized
GRAPH
UndoEliminateOperation
IllegalStateException
UnconnectedGraphException
GraphTraits
EditableEdgeCopier
EditableVertexCopier
PostOrderFolding
Maths
MolmecSupport
PDB
RecordTypeFormat
Residue
RecordUNKNOWN
RecordANISOU
RecordATOM
RecordAUTHOR
RecordCAVEAT
RecordCISPEP
RecordCOMPND
RecordCONECT
RecordCON06
RecordCON061
RecordCON062
RecordCON063
RecordCON064
RecordCRYST1
UnitCell
RecordDBREF
EndingDatabaseSegment
EndingSequence
InitialDatabaseSegment
InitialSequence
RecordEND
RecordENDMDL
RecordEXPDTA
RecordFORMUL
RecordFTNOTE
RecordHEADER
RecordHELIX
RecordHET
RecordHETATM
RecordHETNAM
RecordHETSYN
RecordHYDBND
HydrogenAtom
HydrogenPartnerAtom
RecordJRNL
RecordKEYWDS
RecordLINK
LinkPartner
RecordMASTER
RecordMODEL
RecordMODRES
RecordMTRIX1
RecordMTRIX2
RecordMTRIX3
RecordOBSLTE
RecordORIGX1
RecordORIGX2
RecordORIGX3
RecordREMARK
RecordREVDAT
RecordSCALE1
RecordSCALE2
RecordSCALE3
RecordSEQADV
RecordSEQRES
RecordSHEET
RecordSIGATM
RecordSIGUIJ
RecordSITE
RecordSLTBRG
PartnerAtom
RecordSOURCE
RecordSPRSDE
RecordSSBOND
RecordTER
RecordTITLE
RecordTURN
RecordTVECT
BookKeeping
Structure
AtomEntry
ConectAtomList
NCSMatrix
UnitCellInfo
AdditionalAtomInfo
Peptides
AminoAcidDescriptor
PeptideBuilder
NameConverter	This class provides conversion of atom names between naming schemata
Default	Default values for options
Option	Option names
QSAR
Exception
InvalidActivityID
PropertyError
SingularMatrixError
InconsistentUsage
KernelParameterError
WrongDataType
NoPCAVariance
ModelParameterError
TooManyPLSComponents
WrongFileFormat
FeatureSelectionParameterError
ConfigurationReadingError
ALLModel
AutomaticModelCreator
BayesModel
ClassificationModel
ClassificationValidation
InputConfiguration
InputPartitioningConfiguration
ModelConfiguration
FeatureSelectionConfiguration
ValidationConfiguration
PredictionConfiguration
ConfigIO
FeatureSelection
FitModel
GPModel
Kernel
KernelModel
KNNModel
KPCRModel
KPLSModel
LatentVariableModel
LDAModel
LibsvmModel
svm_model
LinearModel
LogitModel
MLRModel
Model
ModelFactory
NBModel
NonLinearModel
OPLSModel
PCRModel
PLSModel
QSARData
RegistryEntry
Registry
RegressionModel
RegressionValidation
BackupData
RRModel
SNBModel
Statistics
SVMModel
SVRModel
Validation
RTTI
SimpleDownloaderHelper
HelperThread
DLThread
UPThread
BasicHelper
DLArrayHelper
DLHelper
QFtpHackThread
QFtpHackHelper
SysInfo
VIEW
ColorExtension2
MultiColorExtension
ColorHSV
ColorMap
ColorRGBA
ColorUnit
NotInHexFormat
ColorUnitHue
Dataset
DatasetController
RaytraceableGrid
RegularData3DController
TrajectoryController
DockResultController
VectorGridController
RaytraceableGridController
Vertex
Vertex2
AmberConfigurationDialog
AssignBondOrderConfigurationDialog
AssignBondOrderResultsDialog
AtomOverview
ApplyProcessor
OverviewProcessor
BondProperties
CharmmConfigurationDialog
ClippingDialog
ColoringSettingsDialog
CompositeProperties
ContourSurfaceDialog
DisplayProperties
DockDialog
DockProgressDialog
DockResultDialog
Compare_
DownloadElectronDensity
DownloadPDBFile
EditOperationDialog
EditSettings
EditSingleShortcut
ExportGeometryDialog
FDPBDialog
FieldLinesDialog
GeometricFitDialog
GridVisualizationDialog
LabelDialog
LightSettings
MainControlPreferences
MaterialSettings
MinimizationDialog
MMFF94ConfigurationDialog
ModelSettingsDialog
ModifyRepresentationDialog
MolecularDynamicsDialog
MolecularFileDialog
NetworkPreferences
OpenBruker1DFile
OpenBruker2DFile
OpenSavePreferences
ParsedFunctionDialog
PeptideDialog
PluginModel
PluginDialog
Preferences
PTEDialog
PubChemDialog
ParsedResult_
PythonSettings
RaytraceableContourSurfaceDialog
RunGAMESSDialog
ServerPreferences
SetCamera
SetClippingPlane
ShortcutDialog
SnapshotVisualisationDialog
StageSettings
StereoSettingsDialog
UndoManagerDialog
ButtonEvent
DeviceEvent
FakeDriver
HeadTrackingEvent
InputDeviceDriver
InputPlugin
MotionTrackingEvent
NotificationEvent
TransformationEvent6D
ClippingPlane
LogEvent	Event class used for thread safe output to logview
CompositeManager
ConnectionObject
GeometricObject
IconLoader
MainControl
Message
DatasetMessage
CompositeMessage
SceneMessage
GenericSelectionMessage
ControlSelectionMessage
NewSelectionMessage
GeometricObjectSelectionMessage
RepresentationMessage	Base class for all messages concerning a Representation
MolecularTaskMessage
ShowDisplayPropertiesMessage
CreateRepresentationMessage
DeselectControlsMessage
TransformationMessage
FinishedSimulationMessage
SyncClippingPlanesMessage
ShowHelpMessage
RegisterHelpSystemMessage
DockingFinishedMessage	Message to notify docking has finished
ModelInformation
ModularWidget
PreferencesEntry
ExtendedPreferencesObject
Representation
RepresentationManager
ServerWidget
BALLViewServer
NotCompositeObject
ShortcutRegistry
SnapshotManagerInterface
LightSource
Camera
Stage
RaytracingMaterial
MessageEvent
BALLThread
CalculateFDPBThread
UpdateRepresentationThread
SimulationThread
EnergyMinimizerThread	Thread for EnergyMinimization
MDSimulationThread	Thread for MDSimulation
DockingThread	Thread for Docking
AtomBondModelBaseProcessor
AddBackboneModel
ModelPart
AddBallAndStickModel
AddCartoonModel
ColorByGridProcessor
ColorProcessor
InterpolateColorProcessor
FieldLineCreator
ForceModel
HBondModelProcessor
LabelModel
AddLineModel
ModelProcessor
ElementColorProcessor
ResidueNumberColorProcessor
PositionColorProcessor
ChainColorProcessor
MoleculeColorProcessor
ResidueNameColorProcessor
AtomChargeColorProcessor
AtomDistanceColorProcessor
CustomColorProcessor
TemperatureFactorColorProcessor
OccupancyColorProcessor
ForceColorProcessor
SecondaryStructureColorProcessor
ResidueTypeColorProcessor
AddSurfaceModel
AddVanDerWaalsModel
InputDevPluginHandler
VIEWPlugin
Box
Disc
GridVisualisation
Label
Line
Mesh
MultiLine
Point
QuadMesh
Quadruple
SimpleBox
Sphere
Tube
TwoColoredLine
TwoColoredTube
BufferedRenderer
GLDisplayList
DisplayListRedeclaration
NestedDisplayList
NoDisplayListAvailable
GLOffscreenTarget
GLRenderer
WrongModes
GLRenderWindow
ChannelFormat
PixelFormat
POVRenderer
POVRendererClippingPlane
Renderer
RenderSetup
Resolution
FrameBufferFormat
FrameBuffer
RenderTarget
RenderWindow
STLRenderer
TilingRenderer
MeshBuffer
VRMLRenderer
CanvasWidget
PixmapItem
ColorButton
ColorTable
DatasetControl
DockingController
DockWidget
EditableScene
EditOperation
EditFunctions
FileObserver
TreeWidget
GenericControl
GeometricControl
GridColorWidget
MyTextBrowser
HelpViewer
ComboBoxDelegate
HotkeyTable
DragLogView
LogView
MolecularControl
MyTreeWidgetItem
MolecularStructure
PropEditorWidget
BoolEditorWidget
IntEditorWidget
UIntEditorWidget
FloatEditorWidget
DoubleEditorWidget
StringEditorWidget
PropDeleteWidget
PDBInfoEditorWidget
EditorPDBInfoDialog
PropertyEditor
PythonHighlighter
PythonValidator
RunPythonThread
Hotkey
PyWidget
MyLineEdit
MyTextEdit
RegularData1DWidget
DockableRegularData1DWidget
RegularData2DWidget
DockableRegularData2DWidget
Scene
AnimationThread
SDWidget
Default	Default values for options
Option	Option names
ShortcutTableView
ShortcutTableModel
TestFramework
MyEventThread
MyMouseEvent
TextEditorWidget
LineNumbers
DemoTutorialDialog
GlobalInitializer
Limits
Limits< float >
Limits< double >
Limits< bool >
Limits< char >
Limits< signed char >
Limits< unsigned char >
Limits< short >
Limits< unsigned short >
Limits< int >
Limits< unsigned int >
Limits< long >
Limits< unsigned long >
LogStreamBuf
LoglineStruct
StreamStruct
LogStreamNotifier
LogStream
AutoDeletable
UnaryFunctor
BinaryFunctor
BaseIterator
ConstBidirectionalIterator
BidirectionalIterator	Mutable bidirectional iterator
Client
InvalidClient
NoPersistentObject
Comparator
Composite
AncestorIteratorTraits
ChildCompositeIteratorTraits
CompositeIteratorTraits
Embeddable
EnumeratorIndex
IncompatibleIndex
Enumerator
IteratorTraits_
Factory
ConstForwardIterator
ForwardIterator
MolecularInformation
MoleculeObjectCreator
Object
ObjectCreator
PersistenceManager
PersistentObject
UnaryPredicate
BinaryPredicate
PreferencesObject
Processor
UnaryProcessor
BinaryProcessor
NamedProperty
PropertyManager
ConstRandomAccessIterator
RandomAccessIterator
Selectable
TextPersistenceManager
PreciseTime
TimeStamp
Visitor
XDRPersistenceManager
Bit
IllegalOperation
BitVector
TContour
TContourLine
TContourSurface
Cube
MolecularGraph
TreeWidthImplementation
FillInHeuristic
GeneralLowerBoundAlgorithm	Generic lower bound algorithm on graphs
GreedyX
MinorMinWidthCriterion
MinorMinWidthReducer
QuickBB
QuickBBState
TreeDecompositionBuilder
TreeWidth
BagContentWriter
ComponentFilter_
HashGrid3
BoxIteratorTraits
HashGridBox3
BoxIteratorTraits
DataIteratorTraits
HashMap	HashMap class based on the STL map (containing serveral convenience functions)
IllegalKey	HashMap illegal key exception
HashSet
IllegalKey
IteratorTraits
Node
List
Options
Quadruple
TRegularData1D
BlockValueType	The block data type for reading and writing binary data
TRegularData2D
BlockValueType	The block data type for reading and writing binary data
IndexType	The index type used to refer to a specific element in the grid (x-, and y-index)
TRegularData3D
BlockValueType	The block data type for reading and writing binary data
IndexType	The index type used to refer to a specific element in the grid (x-, y-, and z-index)
RegularExpression
String
Substring
InvalidSubstring
UnboundSubstring
StringHashMap
Triple
ComposedEnergyProcessor
EnergyProcessor
AmiraMeshFile
AntechamberFile
Bruker1DFile
Bruker2DFile
CCP4File
CIFFile
Datablock
Datacontent
Item
SaveFrame
State
DCDFile
DSN6File
GAMESSDatFile
block
State
GAMESSLogFile
State
GenericMolFile
HINFile
INIFile
IteratorTraits_	Interface for the LineIterator
Section
JCAMPFile
JCAMPValue
KCFFile
LineBasedFile
MOL2File
AtomStruct
BondStruct
CommentStruct
MoleculeStruct
SetStruct	A class used for storing TRIPOS sets
SubstructureStruct
MOLFile
AtomStruct
BondStruct
CountsStruct
Property
MolFileFactory
NMRStarFile	This class provides methods for reading and assigning chemical shifts
BALLToBMRBMapper
EntryInformation
MolecularSystem
ChemicalUnit
RelatedDB
MonomericPolymer
HomologDB	Database with homolog entries
NMRAtomData
NMRAtomDataSet
NMRSpectrometer
Sample
Component
SampleCondition
ShiftReferenceElement
ShiftReferenceSet
Parameters
ParameterSection
PDBFile
Default
Option
PDBInfo
PDBRecords
PubChemDownloader	Downloads PubChem entries
ResourceEntry
IteratorTraits_
ResourceFile
SCWRLRotamerFile	Reads Dunbrack/SCWRL rotamer library files
SDFile
TrajectoryFile
TrajectoryFileFactory
TRRFile
TRRHeader
XYZFile
Atom
BondIteratorTraits
AtomContainer
AtomContainerIteratorTraits
AtomIteratorTraits
Bond
NotBound
Chain
ChainIteratorTraits
Expression
ExpressionParser
State
SyntaxTree
ExpressionPredicate
ExpressionTree
Fragment
FragmentIteratorTraits
CompositeIteratorTraits
Molecule
MoleculeIteratorTraits
NucleicAcid
NucleicAcidIteratorTraits
Nucleotide
NucleotideIteratorTraits
PDBAtom
PDBAtomIteratorTraits
KernelPredicate	Kernel predicate class
Protein
ProteinIteratorTraits
Element
PTE_
SymbolToElement
Residue
ResidueIteratorTraits
SecondaryStructure
SecondaryStructureIteratorTraits
Selector
TruePredicate
FalsePredicate
SelectedPredicate
AtomNamePredicate
AtomTypePredicate
ElementPredicate
ResiduePredicate
ResidueIDPredicate
ProteinPredicate
ChainPredicate
SecondaryStructurePredicate
SolventPredicate
MoleculePredicate
BackBonePredicate
NucleicAcidPredicate
NucleotidePredicate
InRingPredicate
NumberOfBondsPredicate
SingleBondsPredicate
DoubleBondsPredicate
TripleBondsPredicate
AromaticBondsPredicate
ConnectedToPredicate
CTPNode
greater_
SpHybridizedPredicate
Sp2HybridizedPredicate
Sp3HybridizedPredicate
ChargePredicate
AxialPredicate
Conformation4C1Predicate
RingFinder
SMARTSPredicate
System
TAngle
TBox3
TCircle3
CubicSpline1D
CubicSpline2D
TFFT1D
TFFT2D
TFFT3D
DoubleTraits
FloatTraits
LongDoubleTraits
ConstantFunction
MutableConstant
Addition
Subtraction
Product
Division
Reciprocal
SquareFunction
CubicFunction
MutablePower
BaseFilterIterator
ConstBidirectionalFilterIterator
BidirectionalFilterIterator	Mutable bidirectional iterator
Matrix
ColumnIteratorTraits
DiagonalIteratorTraits
EigenSolver
ElementColumnIteratorTraits
ElementRowIteratorTraits
ConstForwardFilterIterator
ForwardFilterIterator
Vector
MatrixInverter
StandardTraits
UpperTriangularTraits
LowerTriangularTraits
SymmetricTraits
ConstRandomAccessFilterIterator
RandomAccessFilterIterator
ConstReverseIterator
ReverseIterator
RowIteratorTraits
SVDSolver
VectorIteratorTraits
TLine3
TMatrix4x4	Default Type
NumericalIntegrator
ParsedFunction
PiecewiseFunction
PiecewisePolynomial
TPlane3
TQuaternion
RandomNumberGenerator
RombergIntegrator
TSimpleBox3
TSphere3
TSurface
Triangle
TVector2
TVector3
TVector4
AmberFF
Default
Option
AmberBend
AmberNonBonded
AmberStretch
AmberTorsion
SingleAmberTorsion
GAFFCESParser
APSMatcher
APSTerm
CESelementConnectionPredicate
CESelementPredicate
CESPredicate
CESwildcardsConnectionPredicate
CESwildcardsPredicate
State
TruePredicate
GAFFTypeProcessor
Default
Option
TypeDefinition	Nested class definitions
CharmmFF
Default
Option
CharmmBend
CharmmImproperTorsion
CharmmNonBonded
CharmmStretch
CharmmTorsion
SingleCharmmTorsion
AssignBaseProcessor	Only used for deriving interface
AssignTypeProcessor
AssignTypeNameProcessor
AtomVector
BendComponent
ChargeRuleProcessor
ForceField
ForceFieldComponent
Gradient
PeriodicBoundary
Default	Default values
Option
RadiusRuleProcessor
RuleEvaluator
RuleProcessor
SnapShot
SnapShotManager
Default	Local class for handling default values for the options
Option	Local class for handling options
StretchComponent
TypenameRuleProcessor
TypeRuleProcessor
CanonicalMD
AuxFactors	Helper class containing auxiliary factors
MicroCanonicalMD
AuxFactors
MolecularDynamics
Default
Option
ConjugateGradientMinimizer
Default
Option
EnergyMinimizer
Default
Option
LineSearch
ShiftedLVMMMinimizer
Default
Option
SteepestDescentMinimizer
StrangLBFGSMinimizer
Default
Option
MMFF94
Default
Option
MMFF94NonBonded
NonBondedPairData
MMFF94OutOfPlaneBend
OutOfPlaneBend
MMFF94ParametersBase
MMFF94AtomTypeEquivalences
MMFF94AtomType	Class to store the values of an atom type from MMFFPROP.PAR
MMFF94AtomTypes
MMFF94StretchParameters
BondData
EmpiricalBondData
MMFF94BendParameters
MMFF94StretchBendParameters
MMFF94TorsionParameters
MMFF94PlaneParameters
MMFF94VDWParameters
VDWEntry
MMFF94ESParameters
MMFF94AtomTyper
AromaticType
MMFF94ChargeProcessor
MMFF94StretchBend
Bend	See MMFFANG.PAR
Stretch
StretchBend
MMFF94Torsion
Torsion	See MMFFTOR.PAR
AtomTypes
CharmmEEF1
Data
Values
CosineTorsion
Data
SingleData
SingleValues
Values
ForceFieldParameters
LennardJones
Data
Values
Potential1210
Data
Values
QuadraticAngleBend
Data
Values
QuadraticBondStretch
Data
Values
QuadraticImproperTorsion
Data
Values
ResidueTorsions
Data
Templates
AnisotropyShiftProcessor
ClearShiftProcessor
CreateSpectrumProcessor
EFShiftProcessor
EmpiricalHSShiftProcessor
Default	Default values for options
Option	Option names
PropertiesForShift_
ShiftHyperSurface_
Experiment
SimpleExperiment1D
HaighMallionShiftProcessor
HBondShiftProcessor
JohnsonBoveyShiftProcessor
Ring
Peak
PeakList
RandomCoilShiftProcessor
ShiftModel
ShiftModel1D
ShiftModel2D
ShiftModule
Spectrum
BALLPlugin
PluginHandler
PluginManager
PyColorRGBAVector
PyCompositeList
Constant
PyDatasetVector
PyIndexList
PyInterpreter
AromaticityProcessor	This processor provides methods for detection and assignment of aromaticity
Default	Default values for options
Option	Option names
ConnectivityBase
ZagrebIndex
BalabanIndexJ
Descriptor
PartialChargeBase
TotalPositivePartialCharge
TotalNegativePartialCharge
RelPositivePartialCharge
RelNegativePartialCharge
PartialChargeProcessor
RingPerceptionProcessor
Default	Default options for the ring perception
Option	Option names
PathMessage_
TNode_
SimpleBase
MolecularWeight
NumberOfBonds
NumberOfSingleBonds
NumberOfDoubleBonds
NumberOfTripleBonds
NumberOfAromaticBonds
NumberOfAtoms
NumberOfBoron
NumberOfCarbon
NumberOfNitrogen
NumberOfOxygen
NumberOfFlourine
NumberOfPhosphorus
NumberOfSulfur
NumberOfChlorine
NumberOfBromine
NumberOfIodine
NumberOfHydrogen
FormalCharge
NumberOfHeavyAtoms
MeanAtomInformationContent
AtomInformationContent
NumberOfRotatableSingleBonds
RelNumberOfRotatableSingleBonds
NumberOfAromaticAtoms
NumberOfHeavyBonds
NumberOfRotatableBonds
RelNumberOfRotatableBonds
VertexAdjacency
VertexAdjacencyEquality
NumberOfHydrogenBondAcceptors
NumberOfHydrogenBondDonors
NumberOfHydrophobicAtoms
BondPolarizabilities
AtomicPolarizabilities
SizeOfSSSR
PrincipalMomentOfInertia
PrincipalMomentOfInertiaX
PrincipalMomentOfInertiaY
PrincipalMomentOfInertiaZ
SurfaceBase
PositiveVdWSurface
NegativeVdWSurface
PositivePolarVdWSurface
NegativePolarVdWSurface
HydrophobicVdWSurface
PolarVdWSurface
RelPositiveVdWSurface
RelNegativeVdWSurface
RelPositivePolarVdWSurface
RelNegativePolarVdWSurface
RelHydrophobicVdWSurface
RelPolarVdWSurface
VdWVolume
Density
VdWSurface
ScoringBaseFunction
FermiBaseFunction
LinearBaseFunction
ScoringComponent
ScoringFunction
Default
Option
ScoringTypes
AromaticRingStacking
Default
Option
BuriedPolar
Default
Option
CHPI
AromaticRing
CHGroup
Default
Option
HydrogenBond
Default
Option
Lipophilic
Default
Option
ChemScoreMetal
NonpolarSolvation
Default
Option
PolarSolvation
Default
Option
RotationalEntropyLoss
Default
Option
VanDerWaals
Default
Option
SLICKEnergy
Default
Option
SLICKScore
Default
Option
FresnoTypes
ClaverieParameter
ElectrostaticPotentialCalculator
Default
Option
GeneralizedBornModel
Default
GBParameters
Option
Pair6_12InteractionEnergyProcessor
Default
Option
Pair6_12RDFIntegrator
Default
Option
PairExpInteractionEnergyProcessor
Default
Option
PairExpRDFIntegrator
Default
Option
PCMCavFreeEnergyProcessor
Default
Option
PierottiCavFreeEnergyProcessor
Default
Option
FDPB
Boundary
ChargeDistribution
Default
DielectricSmoothing
FastAtomStruct
Option
ReissCavFreeEnergyProcessor
Default
Option
SolventAtomDescriptor
SolventDescriptor
SolventParameter
UhligCavFreeEnergyProcessor
Default
Option
AddHydrogenProcessor
AssignBondOrderProcessor	Assignment of bond orders from topology information
Algorithm
Default	Default values for options
Option	Option names
AtomBijection
AtomTyper
BindingPocketProcessor
Default
Option
Sphere_
SphereComparator_
AStarBondOrderStrategy
Default
Heuristic
Option	Option names
BondOrderAssignment	A solution to the bond order assignment problem
BondOrderAssignmentStrategy	Base class for bond order assignment algorithms
BranchAndBoundBondOrderStrategy
Default
Option	Option names
FPTBondOrderStrategy
AdditionalBagProperties_
Assignment_
BackTrackingState_
ComputingData_
Default	Default option values
DPBackTracking_
StateComparator_
DPBackTrackingCombiner_
DPConfig_
DPJoinMapComparator_
DPTable_
EdgeComparator_
FPTBondOrderAssignment_
Option	Option names
ILPBondOrderStrategy
KGreedyBondOrderStrategy
Default
Option	Option names
PartialBondOrderAssignment	A full or partial solution to the AStar-based bond order assignment problem
BuildBondsProcessor
Default	Default values for options
Option	Option names
ConnectedComponentsProcessor
ClearChargeProcessor
ClearRadiusProcessor
AssignRadiusProcessor
AssignChargeProcessor
DNAMutator
AmberEvaluation
ConformationSet
DockingAlgorithm
DockResult
Compare_
Scoring_
EnergeticEvaluation
ForceFieldEvaluation
GeometricFit
Default
Option
Peak_
RotationAngles_
RandomEvaluation
FragmentDB
BuildBondsProcessor
Connection
NoFragmentNode
NormalizeNamesProcessor
BoundingBoxProcessor
GeometricCenterProcessor
FragmentDistanceCollector
TranslationProcessor
TransformationProcessor
GraphVertex
GraphFace
GraphTriangle
GraphEdge
HBondProcessor	Computation of hydrogen bonds from topology information
Default	Default values for options
HBond
Option	Option names
PredictionMethod	Default values for options
ResidueData
HybridisationProcessor
AtomNames_
Default	Default values for options
Elements_
Method
Option	Option names
Kekuliser
AtomInfo
Mutator
NucleotideMapping
NumericalSAS
Default
Option
PeptideCapProcessor	This processor adds ACE-N and NME-C caps to proteins
RadialDistributionFunction
RDFIntegrator
RDFParameter
RDFSection
ReconstructFragmentProcessor
SortedPosition2
SortedPosition3
ReducedSurface
RSComputer
ProbePosition
ResidueChecker
Rotamer
ResidueRotamerSet
RotamerProbabilityGreaterThan_
RingAnalyser	Methods for the analysis of the structure of ringsystems
Ring
RMSDMinimizer
IncompatibleCoordinateSets
TooFewCoordinates
RotamerLibrary	Rotamer Library Class
RSEdge
RSFace
RSVertex
SASEdge
SASFace
SASVertex
SDGenerator
AtomComparator
Default	Default values for options
Option	Option names
SecondaryStructureProcessor	Secondary structure extraction from 3D structure
SESEdge
SESFace
SESVertex
SideChainPlacementProcessor
Default	Default values for options
Method
Option	Option names
EdgeItem
TSimpleMolecularGraph
NodeItem
SmartsMatcher
RecStruct_	Wrapper class which is used as an interface in the matching code to the pool
RecStructCore_	Core structure of the recursive matching algorithm for the object pool
RecStructPool_	Class which does the pool operations of the RecStructCore_ pool
SmartsParser
SPAtom	Smarts Parser Atom class
Property	Property struct of smarts parser atom
PropertyValue	Possible types of the properties
SPBond	Bond representation of the smarts parser
SPEdge	Edge representation of the smarts parser graph
SPNode	Representation of a node in the smarts parser graph
State	Parser state (used by the parser itself)
SmilesParser
SPAtom
SPBond
State
SolventAccessibleSurface
SolventExcludedSurface
SESComputer
SESSingularityCleaner
ProbeIntersection
StructureMapper
SurfaceProcessor
Triangle
TriangleEdge
TrianglePoint
TriangulatedSAS
SASTriangulator
TriangulatedSES
SESTriangulator
TriangulatedSurface
TriangulatedSphere
Face
UCK
BinaryFileAdaptor
Directory
TransformationManager
File
CannotWrite
FileSystem
MPISupport
TMutex
TMutex< QMutex >
TMutexLocker
TReadWriteLock
TReadWriteLock< QReadWriteLock >
TReadLocker
TWriteLocker
TCPIOStream
TCPServer
TCPServerThread
Path
SimpleDownloader
Timer
CrystalGenerator
CrystalInfo
Default
Option
Mainframe
boost
Ui
MolecularGraphBase
MutexLockerType
QAbstractListModel
QAbstractTableModel
QCanvasRectangle
QCanvasView
QDialog
QDockWidget
QEvent
QGLWidget
QItemDelegate
QLineEdit
QMainWindow
QMouseEvent
QObject
QPaintDevice
QPlainTextEdit
QPushButton
QSyntaxHighlighter
QTableView
QTableWidget
QTextBrowser
QThread
QTreeWidget
QTreeWidgetItem
QValidator
QWidget
ReadLockerType
ReadWriteLockType
WriteLockerType