org.xmlcml.cml
Class BondImpl

java.lang.Object
  |
  +--org.apache.xerces.dom.NodeImpl
        |
        +--org.apache.xerces.dom.ChildNode
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              +--org.apache.xerces.dom.ChildAndParentNode
                    |
                    +--org.apache.xerces.dom.ElementImpl
                          |
                          +--uk.co.demon.ursus.dom.AbstractElementImpl
                                |
                                +--uk.co.demon.ursus.dom.PMRElementImpl
                                      |
                                      +--org.xmlcml.cml.CMLBaseImpl
                                            |
                                            +--org.xmlcml.cml.AbstractBuiltinContainerImpl
                                                  |
                                                  +--org.xmlcml.cml.AbstractBondImpl
                                                        |
                                                        +--org.xmlcml.cml.BondImpl

public class BondImpl

extends AbstractBondImpl

implements Bond

See Also:

Serialized Form

Field Summary

protected Atom[]	atomRefs
protected double	length
protected Molecule	molecule
protected java.lang.String	order
protected java.lang.String	stereo

Fields inherited from class org.xmlcml.cml.AbstractBondImpl

atomRefVector

Fields inherited from class org.xmlcml.cml.AbstractBuiltinContainerImpl

builtinValues, nonBuiltinTable

Fields inherited from class org.xmlcml.cml.CMLBaseImpl

conventionName, conventionTable, dictRef, id, title, validity

Fields inherited from class uk.co.demon.ursus.dom.PMRElementImpl

CLASSNAME, processFlag

Fields inherited from class uk.co.demon.ursus.dom.AbstractElementImpl

CLASSNAME

Fields inherited from class org.apache.xerces.dom.ElementImpl

attributes, name

Fields inherited from class org.apache.xerces.dom.ChildAndParentNode

changes, firstChild, nodeListIndex, nodeListLength, nodeListNode, ownerDocument

Fields inherited from class org.apache.xerces.dom.ChildNode

nextSibling, previousSibling

Fields inherited from class org.apache.xerces.dom.NodeImpl

ELEMENT_DEFINITION_NODE, FIRSTCHILD, flags, IGNORABLEWS, MUTATION_AGGREGATE, MUTATION_ALL, MUTATION_LOCAL, MUTATION_NONE, MUTATIONEVENTS, OWNED, ownerNode, READONLY, SETVALUE, SPECIFIED, SYNCCHILDREN, SYNCDATA

Fields inherited from interface org.xmlcml.cml.AbstractBond

AROMATIC, ATOMREF, ATOMREFS, BOND_BUILTIN_COUNT, BOND_FLOATVAL_COUNT, BOND_FLOATVAL_END, BOND_FLOATVAL_START, BOND_INTEGERVAL_COUNT, BOND_INTEGERVAL_END, BOND_INTEGERVAL_START, BOND_STRINGVAL_COUNT, BOND_STRINGVAL_END, BOND_STRINGVAL_START, bondOrders, bondTypeStrings, DECREASE, DEFAULTXY2LENGTH, DEFAULTXYZ3LENGTH, DELETE, DOUBLE, HATCH, INCREASE, LENGTH, NOSTEREO, ORDER, OVERRUN, SINGLE, STEREO, TRIPLE, WEDGE, ZERO

Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

NONUNIQUE, UNIQUE

Fields inherited from interface org.xmlcml.cml.CMLBase

ANGLE, ATOM, ATOMARRAY, BOND, BONDARRAY, BUILTIN, CML, CRYSTAL, ELECTRON, ELEMENT_COUNT, ELEMENT_NAMES, EXECUTE, FEATURE, FLOAT, FLOAT_TYPE, FLOATARRAY, FLOATMATRIX, FORMULA, INTEGER, INTEGER_TYPE, INTEGERARRAY, LINK, LIST, MOLECULE, PACKAGE_NAME, REACTION, SEQUENCE, STRING, STRING_TYPE, STRINGARRAY, TORSION, UNK, UNK_ELEM, UNKNOWN

Fields inherited from interface uk.co.demon.ursus.dom.PMRElement

CLASSNAME, LOCAL, QUALIFIED, UNIVERSAL

Fields inherited from interface org.xmlcml.cml.HasTitle

TITLE

Fields inherited from interface org.xmlcml.cml.HasDictRef

DICTREF

Fields inherited from interface org.xmlcml.cml.HasId

ID

Fields inherited from interface org.xmlcml.cml.HasConvention

CONVENTION

Fields inherited from interface uk.co.demon.ursus.dom.PMRNode

ATTRIBUTES, CONTENT, ELEMENTNAME, IDLIST, NESTED, NESTEDATTS, PACKAGENAME, PRETTY, SPLITFILES, STYLE, TAGGED, UNTAGGED, WHITESPACE, XMLCONTENT

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Constructor Summary

BondImpl()

BondImpl(Atom atom1, Atom atom2)
new Bond formed from atoms, in context but no other info Atoms must belong to the same non-null Molecule

BondImpl(org.w3c.dom.Document document)
new BondImpl in context

BondImpl(org.w3c.dom.Element element)

Method Summary

protected static java.lang.String	atomHash(Atom atom1, Atom atom2)
boolean	contains(Atom atom) true if bond contains this atom
void	debug(java.io.Writer w) output debug info to Writer
Atom	getAtom(int i)
double	getBondLength()
Molecule	getMolecule() every Bond should be associated with one molecule
java.lang.String	getOrder()
Atom	getOtherAtom(Atom atom) returns other atom in a 2-atom bond else null
java.lang.String	getStereo()
StringVal	getStringVal(int i)
java.lang.String	hashKey()
void	processAtomRefs(Molecule molecule) give each atom an ID.
void	processDOM() carries out class-specific processing for subclasses of PMRElement.
void	setBondLength(double length)
protected void	setMolecule(Molecule molecule) every Bond should be associated with one molecule
void	setOrder(java.lang.String order)
void	setStereo(java.lang.String stereo)
void	setStringVal(int i, StringVal stringVal)
java.lang.String	toString()
void	updateDOM()

Methods inherited from class org.xmlcml.cml.AbstractBondImpl

addAtomRef, deleteAtomRef, getAtomRef, getAtomRefVector, getBuiltinCount, getBuiltinFloatValCount, getBuiltinFloatValNames, getBuiltinIntegerValCount, getBuiltinIntegerValNames, getBuiltinNames, getBuiltinStringValCount, getBuiltinStringValNames, getValidity, showBuiltinNames

Methods inherited from class org.xmlcml.cml.AbstractBuiltinContainerImpl

addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinVal, getNonBuiltinVal, setBuiltinVal, setNonBuiltinVal

Methods inherited from class org.xmlcml.cml.CMLBaseImpl

addValidity, convertToSubclass, getConventionName, getDictRef, getId, getSubClassedElement, getTitle, help, isValid, main, setConventionName, setDictRef, setId, setTitle, showElementNames, test1, updateDOMHasConvention, updateDOMHasConvention, updateDOMHasCount, updateDOMHasDictRef, updateDOMHasDictRef, updateDOMHasId, updateDOMHasId, updateDOMHasTitle, updateDOMHasTitle, updateDOMHasUnits

Methods inherited from class uk.co.demon.ursus.dom.PMRElementImpl

appendTo, initialise, processDescendants, setProcessFlag

Methods inherited from class uk.co.demon.ursus.dom.AbstractElementImpl

setTagName

Methods inherited from class org.apache.xerces.dom.ElementImpl

cloneNode, getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getAttributes, getElementsByTagName, getElementsByTagNameNS, getNodeName, getNodeType, getTagName, hasAttribute, hasAttributeNS, normalize, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS, setReadOnly, setupDefaultAttributes, synchronizeData

Methods inherited from class org.apache.xerces.dom.ChildAndParentNode

changed, changes, getChildNodes, getFirstChild, getLastChild, getLength, getOwnerDocument, hasChildNodes, insertBefore, item, removeChild, replaceChild, synchronizeChildren, synchronizeChildren

Methods inherited from class org.apache.xerces.dom.ChildNode

getNextSibling, getParentNode, getPreviousSibling

Methods inherited from class org.apache.xerces.dom.NodeImpl

addEventListener, appendChild, dispatchEvent, finalize, getLocalName, getNamespaceURI, getNodeValue, getPrefix, getReadOnly, getUserData, removeEventListener, setNodeValue, setPrefix, setUserData, supports

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

atomRefs

protected Atom[] atomRefs

molecule

protected Molecule molecule

length

protected double length

order

protected java.lang.String order

stereo

protected java.lang.String stereo

Constructor Detail

BondImpl

public BondImpl()

BondImpl

public BondImpl(org.w3c.dom.Element element)

BondImpl

public BondImpl(org.w3c.dom.Document document)

new BondImpl in context

BondImpl

public BondImpl(Atom atom1,
                Atom atom2)
         throws CMLException

new Bond formed from atoms, in context but no other info Atoms must belong to the same non-null Molecule

Method Detail

setMolecule

protected void setMolecule(Molecule molecule)

every Bond should be associated with one molecule

getMolecule

public Molecule getMolecule()

every Bond should be associated with one molecule

Specified by:

getMolecule in interface Bond

getBondLength

public double getBondLength()
                     throws CMLException

Specified by:

getBondLength in interface Bond

setBondLength

public void setBondLength(double length)

Specified by:

setBondLength in interface Bond

getOrder

public java.lang.String getOrder()
                          throws CMLException

Specified by:

getOrder in interface Bond

setOrder

public void setOrder(java.lang.String order)

Specified by:

setOrder in interface Bond

getStereo

public java.lang.String getStereo()
                           throws CMLException

Specified by:

getStereo in interface Bond

setStereo

public void setStereo(java.lang.String stereo)

Specified by:

setStereo in interface Bond

getStringVal

public StringVal getStringVal(int i)

Specified by:

getStringVal in interface Bond

setStringVal

public void setStringVal(int i,
                         StringVal stringVal)

Specified by:

setStringVal in interface Bond

getAtom

public Atom getAtom(int i)

Specified by:

getAtom in interface Bond

getOtherAtom

public Atom getOtherAtom(Atom atom)

returns other atom in a 2-atom bond else null

Specified by:

getOtherAtom in interface Bond

contains

public boolean contains(Atom atom)

true if bond contains this atom

Specified by:

contains in interface Bond

processAtomRefs

public void processAtomRefs(Molecule molecule)
                     throws CMLException

give each atom an ID. Order is: id attribute, atomId builtin child, then serial

Specified by:

processAtomRefs in interface Bond

processDOM

public void processDOM()
                throws CMLException

Description copied from interface: PMRElement

carries out class-specific processing for subclasses of PMRElement. The default for a generic PMRElement is no-op. Often creates an internal model

Overrides:

processDOM in class CMLBaseImpl

Tags copied from class: PMRElementImpl

Throws:

java.lang.Exception - these can be of many kinds and may include class-specific ones

updateDOM

public void updateDOM()
               throws CMLException

Overrides:

updateDOM in class CMLBaseImpl

atomHash

protected static java.lang.String atomHash(Atom atom1,
                                           Atom atom2)

hashKey

public java.lang.String hashKey()

Specified by:

hashKey in interface Bond

toString

public java.lang.String toString()

Overrides:

toString in class org.apache.xerces.dom.NodeImpl

debug

public void debug(java.io.Writer w)
           throws java.io.IOException

output debug info to Writer

Overrides:

debug in class CMLBaseImpl

Parameters:

Writer - w output