Table of Contents

1. Front

2. Package base

Functions for Logging

Container Class std_vector_bool

Container Class std_vector_double

Container Class std_vector_float

Container Class std_vector_int

Container Class std_vector_string

Container Class std_vector_Vector3

Container Class std_vector_std_map_int_int

Functions for Vectors and Matrices

Class Matrix3x3

Class Vector3

3. Package framework

Class Object

Stored Properties of Class Object

Calculated Properties of Class Object

Commands of Class Object

Predicate Class IsVisible

Predicate Class IsOpen

Predicate Class IsCompositeChanged

Predicate Class HasName

Predicate Class HasDescription

Predicate Class HasNumber

Predicate Class HasNumberOfObjects

Predicate Class HasNumberOfLeafs

Predicate Class HasLabel

Predicate Class HasClassName

Class License

Stored Properties of Class License

Predicate Class HasUserName

Predicate Class HasCompanyName

Predicate Class HasKey

Predicate Class HasFeatureId

Predicate Class HasDate

Predicate Class HasHostId

Class LicensingManager

Stored Properties of Class LicensingManager

Calculated Properties of Class LicensingManager

Commands of Class LicensingManager

Predicate Class IsLicenseAccepted

Predicate Class IsResult

Predicate Class HasRequestorName

Predicate Class HasCompany

Predicate Class HasEMail

Predicate Class HasCurrentDate

Predicate Class HasCurrentFeatureId

Predicate Class HasCurrentHostId

Predicate Class HasFaultString

Container Class std_vector_Object

4. Package core

Container Class std_vector_AtomComposite

Container Class std_vector_Composite

Container Class std_vector_Bond

Container Class std_vector_Atom

Container Class std_vector_Element

Functions for Atoms

Class Amino

Stored Properties of Class Amino

Predicate Class HasSymbol

Predicate Class HasAminoName

Predicate Class HasColor

Class Aminos

Class ARGEdit

Class Array

Stored Properties of Class Array

Predicate Class IsBoundingBoxVisible

Class Atom

Stored Properties of Class Atom

Calculated Properties of Class Atom

Predicate Class IsInRing

Predicate Class IsHydrogen

Predicate Class IsOxygen

Predicate Class IsCarbon

Predicate Class IsCarbonAlpha

Predicate Class IsNitrogen

Predicate Class IsSulfur

Predicate Class IsPhosphorus

Predicate Class IsBoron

Predicate Class IsIodine

Predicate Class IsBromine

Predicate Class IsChlorine

Predicate Class IsFluorine

Predicate Class IsAromatic

Predicate Class HasRadius

Predicate Class HasExtId

Predicate Class HasTypeId

Predicate Class HasIndex

Predicate Class HasImplicitHCount

Predicate Class HasTotalHCount

Predicate Class HasValence

Predicate Class HasgetConnectivity

Predicate Class HasgetDegree

Predicate Class HasIsotope

Predicate Class HasFormalCharge

Predicate Class HasHybridization

Predicate Class HasChirality

Predicate Class HasR0

Predicate Class HasNMesh

Predicate Class HasOccupancy

Predicate Class HasPositionX

Predicate Class HasPositionY

Predicate Class HasPositionZ

Predicate Class HasAmino

Predicate Class HascountBonds

Class AtomComposite

Stored Properties of Class AtomComposite

Calculated Properties of Class AtomComposite

Commands of Class AtomComposite

Predicate Class IsNameFlag

Predicate Class IsTypeFlag

Predicate Class IsElementFlag

Predicate Class IsIdFlag

Predicate Class IsRadiusFlag

Predicate Class IsBlink

Predicate Class HasAtomCompositeStickSize

Predicate Class HasBallSize

Predicate Class HasTitle

Predicate Class HasCPKScale

Predicate Class HasSelectionRadius

Predicate Class HasSelectionName

Predicate Class HasSelectionElement

Predicate Class HasSelectionType

Predicate Class HasSelectionId

Predicate Class HasSpeed

Predicate Class HasAtomDisplayStyle

Predicate Class HasReaderAllFileFilter

Predicate Class HasNumberOfAtoms

Predicate Class HasnSelection

Class AtomComponent

Stored Properties of Class AtomComponent

Calculated Properties of Class AtomComponent

Predicate Class HasRed

Predicate Class HasGreen

Predicate Class HasBlue

Predicate Class HasAnnotationMode

Predicate Class HasColorMode

Predicate Class HasCharge

Class BandStructureCalculation

Class Bond

Stored Properties of Class Bond

Predicate Class HasStickSize

Predicate Class HasOrder

Class Chain

Stored Properties of Class Chain

Commands of Class Chain

Predicate Class HasProteinDisplayStyle

Predicate Class HasProteinColorMode

Predicate Class HasProteinAnnotationMode

Class Composite

Stored Properties of Class Composite

Calculated Properties of Class Composite

Commands of Class Composite

Predicate Class HascreateSmilesString

Predicate Class HascountAtoms

Predicate Class HascountBonds

Predicate Class HasHelixRadius

Predicate Class HasFrom

Predicate Class HasTo

Class DNARNA

Class Element

Stored Properties of Class Element

Predicate Class HasElementSymbol

Predicate Class HasElementName

Predicate Class HasConfiguration

Predicate Class HasElementColor

Predicate Class HasZ

Predicate Class HasRow

Predicate Class HasColumn

Predicate Class HasMaxBond

Predicate Class HasCovRadius

Predicate Class HasVDWRadius

Predicate Class HasBSRadius

Predicate Class HasMass

Class Elements

Stored Properties of Class Elements

Class Fragment

Class Frame

Class Group

Commands of Class Group

Class Molecule

Class MolecularEnsemble

Class Nucleotide

Class ObjectComposite

Class PredicateGraph

Class PredicateGraphEdit

Class Protein

Class Residue

Stored Properties of Class Residue

Predicate Class HasSecondaryStructureType

Class Selectable

Stored Properties of Class Selectable

Commands of Class Selectable

Predicate Class IsSelected

Class StaticAtom

Stored Properties of Class StaticAtom

Class System

Class UnknownAmino

Class UnknownElement

Functions for creating Graphs

Functions for creating PredicateGraphs

Functions for Graphs and PredicateGraphs

Function to get Aminos

Function to get Elements

Class Graph

Class GraphEdit

5. Package processor

Class AddHydrogensProcessor

Class AssignBondOrderProcessor

Class AssignIndexProcessor

Class AssignInRingProcessor

Class AssignRadiusProcessor

Class AssignTypeProcessor

Class BaseProcessor

Class BuildBondsProcessor

Class BuildCompositesProcessor

Class BuildRingsProcessor

Class MCSProcessor

Class RMSDeviationProcessor

Class RotationProcessor

Class TranslationProcessor

6. Package predicate

Class MatchPredicate

Class RMSDeviationPredicate

Class SmartsPredicate

Class SmilesPredicate

7. Package io

Function for creating a System from a file

Function for creating a System from a SMILES string

Function for creating a PredicateGraph

Class FileTypeToDescription

Class FileIORegistry

Class StructureReaderRegistry

Class WriterRegistry

Class ExtToFileType

Function for creating a ExtToFileType

Function for creating a FileTypeToDescription

Function for creating a StructureReaderRegistry

Function for creating a WriterRegistry

8. Package component

Class Application

Stored Properties of Class Application

Calculated Properties of Class Application

Commands of Class Application

Predicate Class IsCheckBonds

Predicate Class IsBuildBonds

Predicate Class IsAssignTypes

Predicate Class IsVisibleBonds

Predicate Class IsNotifing

Predicate Class Ischeck

Predicate Class IsLicenseAccepted

Predicate Class IsexistFile

Predicate Class IsemptyClipboard

Predicate Class HasReaderAllFileFilter

Predicate Class HasPreamble

Predicate Class HasWriterAllFileFilter

Predicate Class HasRNADNADisplayStyle

Predicate Class HasAtomDisplayStyle

Predicate Class HasProteinDisplayStyle

Predicate Class HasAnnotationMode

Predicate Class HasN

Predicate Class HasApplicationName

Predicate Class HasVersion

Predicate Class HasBuildNumber

Predicate Class HasFileName

Predicate Class Hasdownload

Predicate Class HasnModel

Class AtomDisplayStyle

Stored Properties of Class AtomDisplayStyle

Predicate Class IsDisplayBondOrder

Predicate Class HasStickSize

Predicate Class HasBallSize

Predicate Class HasCPKScale

Predicate Class HasColorMode

Class Basis

Class ComponentInterface

Class Component

Class Data

Calculated Properties of Class Data

Predicate Class HasReaderAllFileFilter

Class Model

Stored Properties of Class Model

Calculated Properties of Class Model

Commands of Class Model

Predicate Class IsCameraInitialized

Predicate Class IsVisibleBonds

Predicate Class IsemptySelection

Predicate Class HasRadians

Predicate Class HasnSelection

Class Monitors

Stored Properties of Class Monitors

Predicate Class HasCurrentTarget

Class GroupOfAtoms

Stored Properties of Class GroupOfAtoms

Commands of Class GroupOfAtoms

Predicate Class IsColorLegend

Predicate Class IsDisableAcceleration

Predicate Class IsAddAndUpdateHydrogens

Predicate Class IsAutomaticallyCleanMolecules

Predicate Class IsCleanSelectedAtoms

Predicate Class IsDepthCue

Predicate Class IsFastRender

Predicate Class IsUsePDBSecondary

Predicate Class IsPerceiveAromaticity

Predicate Class IsDisplayUnitCell

Predicate Class IsCreateAnimation

Predicate Class IsConvertTo3D

Predicate Class IsAddHydrogens

Predicate Class IsUseAtomChargesFromFile

Predicate Class IsStereo

Predicate Class IsHeadLight

Predicate Class IsLight1

Predicate Class IsLight2

Predicate Class IsIncludeIntermolecularForces

Predicate Class IsPerceiveAndUpdateAromaticity

Predicate Class HasPositiveColorRed

Predicate Class HasPositiveColorGreen

Predicate Class HasPositiveColorBlue

Predicate Class HasNeutralColorRed

Predicate Class HasNeutralColorGreen

Predicate Class HasNeutralColorBlue

Predicate Class HasNegativeColorRed

Predicate Class HasNegativeColorGreen

Predicate Class HasNegativeColorBlue

Predicate Class HasLighting1ColorRed

Predicate Class HasLighting1ColorGreen

Predicate Class HasLighting1ColorBlue

Predicate Class HasLighting2ColorRed

Predicate Class HasLighting2ColorGreen

Predicate Class HasLighting2ColorBlue

Predicate Class HasBackgroundColorRed

Predicate Class HasBackgroundColorGreen

Predicate Class HasBackgroundColorBlue

Predicate Class HasLighting1DirectionX

Predicate Class HasLighting1DirectionY

Predicate Class HasLighting1DirectionZ

Predicate Class HasLighting2DirectionX

Predicate Class HasLighting2DirectionY

Predicate Class HasLighting2DirectionZ

Predicate Class HasStereoOffset

Predicate Class HasPerspectiveAngle

Predicate Class HasLineWidth

Predicate Class HasGraphicsQuality

Predicate Class HasPrintQuality

Predicate Class HasPickTolerance

Predicate Class HasViewSize

Predicate Class HasRotateMode

Predicate Class HasSelectMode

Predicate Class HasProjectionMode

Predicate Class HasEyesMode

Class Groups

Stored Properties of Class Groups

Commands of Class Groups

Class Simulation

Stored Properties of Class Simulation

Commands of Class Simulation

Predicate Class HasDistance

Predicate Class HasIter

Predicate Class HasEpsilon

Predicate Class HasNMax

Predicate Class HasStatus

Class SpaceGroup

Stored Properties of Class SpaceGroup

Calculated Properties of Class SpaceGroup

Predicate Class HasA

Predicate Class HasB

Predicate Class HasC

Predicate Class HasAlpha

Predicate Class HasBeta

Predicate Class HasGamma

Predicate Class HasSpaceGroupName

Predicate Class HasSpaceGroupNumber

Predicate Class HasGenerator

Predicate Class HasSpaceGroupId

Predicate Class HasCrystalFamilyName

Predicate Class HasCrystalSystemName

Predicate Class HasSpaceGroupString

Predicate Class HasPointGroupString

Predicate Class HasBravaisSystemNumber

Predicate Class HasBravaisLatticeNumber

Predicate Class HasV

Class Selection

Stored Properties of Class Selection

Commands of Class Selection

Class Parameter