| Home >> All >> org >> xmlcml >> [ cml Javadoc ] |
Page 1 2
• org.xmlcml.cml: Javadoc index of package org.xmlcml.cml.
Package Samples:
• org.xmlcml.cml.topology: CoreCML index
• org.xmlcml.cml.metadata
• org.xmlcml.cml.mvc
• org.xmlcml.cml.normalise
• org.xmlcml.cml.query
• org.xmlcml.cml.style
• org.xmlcml.cml.subset
• org.xmlcml.cmlimpl.jumbo3
• org.xmlcml.cmlimpl.metadata
Classes:
• AbstractBase: 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 ...
• 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 ...
• CMLLink: a link to an object - usually from org.xmlcml.cml - but could be anything uses XLink semantics where possible. CMLLink will normally refer to a locator. At present only a subset of Xlink is appropriate for chemical objects The link may mave a type associated which can be dereferenced to an object of that type. The link can have a count acting as a multiplier for the targeted Object. It will not normally create additional objects, and is more likely to be used like: <link type="molecule" href="#water" count="10"/> could occure in Sodium Sulfate (Na2SO4.10H20) License: This document may be freely ...
• CMLList: list is a generic container which has no predetermined children or attributes and use the DOM emthods to access them <list title="amide"> <link href="#c1/> <link href="#n1/> <link href="#o1/> </list> License: This document may be freely copied but not modified in any way without the permission of the author. For full license information CMLDocument all children and attributes are accessed using DOM methods
• CMLFormula: CORE Interface DTD Class Semantics being developed. Will certainly manage element counts, recursive. Although not defined in the DTD, the data model corresponds to: <formula> <formula> <string builtin="elementType" count="2">Na <string builtin="elementType">S <string builtin="elementType" count="4">O </formula> <formula count="10"> <string builtin="elementType" count="2">H <string builtin="elementType">O </formula> </formula> which corresponds to Na2SO4.10H2O. The counts can be non-integer.
• CMLMolecule: CORE Interface 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.
• StyleableMolecule: 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.
• 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.
• AbstractAtom: Base class for atomic information . Declares various static variables. Not directly used License: This document may be freely copied but not modified in any way without the permission of the author. For full license information CMLDocument
• CMLAtomParity: CORE Interface DTD Class interface supporting atom-based parity . It requires 3 or 4 atomRefs to define the parity. At present the values are doubles and only the sign is important (the values could be computed as chiral volumes)
• CML: a general top-level container. This is useful for indicating that there is an "island" of CML in a multinamespace document, e.g. <cml> <molecule> </molecule> <molecule> </molecule> </cml> It is never essential, and there are no semanmtics or meaningful Java code (yet).
• 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
• AttributeAtomRefs: some Objects (e.g. CMLBond, CMLAngle) have references to Atoms. If an CMLAtom is changed or deleted it may affect these Objects. The AttributeAtomRefs identifies these Objects and allows access to the Atoms
• CMLCrystal: CORE Interface DTD Class Supports a crystallographic unit cell (parameters and spacegroup). Provision for symmetry is limited
• CMLAtomArray: DTD Class this interface is only used if AtomArrays are stored as such in the DOM . It may become obsolete since atomArray is only a syntactic container
• CMLAngle: CORE Interface DTD Class supports angle element in CML DTD. Methods are all in constructors and superclasses.
• CMLDocument: CORE Interface DTD Class The interface for any CML Document objects. There are NO CoreCML Methods.
• AttributeSize: the size attribute is optional and gives the numebr of elements in an array. It is subservient to the actual array length and may be used to check validity and throw an Exception
• CMLException: CORE Interface CML-Specific exceptions may be thrown by CML-DOM classes and interfaces. There is no systematised set of error messages yet
• AbstractNumericVal: 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
• 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
• RingOverlap: holds information about overlap between two rings (fused or bridged). At present propellanes will give three distinct RingOverlaps - I shall probably change this.
• RingOverlapImpl: holds information about overlap between two rings (fused or bridged). At present propellanes will give three distinct RingOverlaps - I shall probably change this.
| Home | Contact Us | Privacy Policy | Terms of Service |