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• org.xmlcml.cmlimpl: Javadoc index of package org.xmlcml.cmlimpl.
Package Samples:
• org.xmlcml.cmlimpl.jumbo3
• org.xmlcml.cmlimpl.metadata
• org.xmlcml.cmlimpl.normalise
• org.xmlcml.cmlimpl.query
• org.xmlcml.cmlimpl.stereo
• org.xmlcml.cmlimpl.style
• org.xmlcml.cmlimpl.subset
• org.xmlcml.cmlimpl.topology
Classes:
• CMLBaseImpl: The base class for all elementObjects mentioned in the CML DTD. Any CML element may have attributes: title id dictRef convention and convenience get/set methods are provided for all, through the interfaces AttributeTitle, AttributeId and AttributeConvention. An element (FOO) subclassed from a AbstractBase may be constructed in the following ways: FOO(). Creates a new empty element with null values of the attributes. Required for newInstance(), but use carefully since it has no tagName and no document associated with it. FOO(String tagName, Document document). Creates an empty element with null ...
• JUMBOBaseImpl: The base class for all elementObjects mentioned in the CML DTD. Any CML element may have attributes: title id dictRef convention and convenience get/set methods are provided for all, through the interfaces AttributeTitle, AttributeId and AttributeConvention. An element (FOO) subclassed from a AbstractBase may be constructed in the following ways: FOO(). Creates a new empty element with null values of the attributes. Required for newInstance(), but use carefully since it has no tagName and no document associated with it. FOO(String tagName, Document document). Creates an empty element with null ...
• MoleculeImpl: CMLMolecule is the basic container for Atoms, Bonds, Electrons Angles, CMLTorsion, Sequences, Features, CMLCrystal and other objects. Molecules may contain other Molecules. When objects such as CMLAtomArray are set or added they are deep-copied, to avoid unpleasant surprises later. In general CMLAtom, CMLAtomArray, CMLBond, CMLBondArray should not be shared between different molecules. A molecule has only one set of Atoms and Bonds - if a molecule is created with CMLAtomArray and an CMLAtom is subsequently added, the components are effectively merged.
• JUMBOMoleculeImpl: CMLMolecule is the basic container for Atoms, Bonds, Electrons Angles, CMLTorsion, Sequences, Features, CMLCrystal and other objects. Molecules may contain other Molecules. When objects such as CMLAtomArray are set or added they are deep-copied, to avoid unpleasant surprises later. In general CMLAtom, CMLAtomArray, CMLBond, CMLBondArray should not be shared between different molecules. A molecule has only one set of Atoms and Bonds - if a molecule is created with CMLAtomArray and an CMLAtom is subsequently added, the components are effectively merged.
• AtomSetImpl: a set of atoms. Counts number of times an atom has been added (e.g. for bonds). An AtomSet may have coordinates associated with it which may or may not be related to the molecule. This should make calcuation of fragment geometries easier and therefore assembly less painful
• NumericValImpl: supports a number (either Float or Integer). Supports CMLUnits. Does not support max and min or values since double and int are used rather than Double and Integer
• RingOverlapImpl: holds information about overlap between two rings (fused or bridged). At present propellanes will give three distinct RingOverlaps - I shall probably change this.
• RingNucleusImpl: a nucleus of rings (e.g. androstane but not biphenyl (which would be 2 separate RingNucleus)). Contains information about which rings overlap.
• TreeStyleImpl: holds all style information for nodes in a tree; some of these may be dynamically generated from content or context
• UnitsImpl: supports scientific units. At present only holds names of units, without lookup, but will develop
• TopologyImpl: Topology adapts a SpanningTree to have increased function for connection table analysis
• SubstituentListImpl: a list of substituents (Chains, RingNucleus)- usually on an CMLAtom in a Ring(Nucleus)
• IsotopeImpl: supports isotopic information on a per-atom basis - being developed
• SymbolImpl: a placeholder for the need to hold symbolic values (e.g. for Parity
• AtomStyleImpl: holds all style information for a CMLAtom or all Atoms
• DefaultMoleculeViewerPanel: default panel simply announces it doesn't do anything!
• ArrayDelegate: a delegate class to manage splitting of arrays, etc.
• CMLDocumentImpl: The base class for any CML Document objects
• JUMBODocumentImpl: The base class for any CML Document objects
• JUMBOMoleculeFactory: manufacture CMLMolecules of an appropriate subclass
• BondStyleImpl: holds all style information for a bond or all bonds
• STElementImpl: Node for Spanning tree, holds pointer to CMLAtom.
• AbstractMoleculeViewerPanel: panel in which 2- or 3-D strucures can be viewed
• DocumentFactoryImpl: manufacture CMLBonds of an appropriate subclass
• JUMBOAtomFactory: manufacture CMLAtoms of an appropriate subclass
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