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org.xmlcml.cml
Class MoleculeImpl

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.MoleculeImpl
public class MoleculeImpl
extends CMLBaseImpl
implements Molecule

Molecule is the basic container for Atoms, Bonds, Electrons Angles, Torsion, Sequences, Features, Crystal and other objects. Molecules may contain other Molecules. When objects such as AtomArray are set or added they are deep-copied, to avoid unpleasant surprises later. In general Atom, AtomArray, Bond, BondArray should not be shared between different molecules. A molecule has only one set of Atoms and Bonds - if a molecule is created with AtomArray and an Atom is subsequently added, the components are effectively merged.

See Also:
Serialized Form

Field Summary
protected  java.util.Vector angleVector
           
protected  AtomArray atomArray
           
protected  java.util.Hashtable atomIdTable
           
protected  java.util.Vector atomVector
           
protected  BondArray bondArray
           
protected  java.util.Hashtable bondHashTable
           
protected  java.util.Hashtable bondIdTable
           
protected  java.util.Vector bondVector
           
protected  double count
           
protected  Crystal crystal
           
protected  java.util.Vector electronVector
           
protected  java.util.Vector featureVector
           
protected  java.util.Vector moleculeVector
           
protected  java.util.Vector sequenceVector
           
protected  java.util.Vector torsionVector
           
 
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.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 org.xmlcml.cml.HasCount
COUNT
 
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
 
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
protected MoleculeImpl()
           
  MoleculeImpl(org.w3c.dom.Document document)
          new Molecule in context
  MoleculeImpl(org.w3c.dom.Element element)
          replace existing tree nodes by a Molecule
 
Method Summary
 void addAngle(Angle angle)
          adds the Angle to the Angle content of the Molecule.
 void addAtom(Atom atom)
          adds the Atom to the Atom content of the Molecule.
 void addBond(Bond bond)
          adds the Bond to the Bond content of the Molecule.
 void addElectron(Electron electron)
          Adds a Electron to the Molecule content.
 void addFeature(Feature feature)
          Adds a Feature to the Molecule content.
 void addMolecule(Molecule molecule)
          Adds a Molecule to the Molecule content.
 void addSequence(Sequence sequence)
          Adds a Sequence to the Molecule content.
 void addTorsion(Torsion torsion)
          adds the Torsion to the Torsion content of the Molecule.
 void debug(java.io.Writer w)
          output debug info to Writer
 void deleteAngle(Angle angle)
          deletes the Angle from the Angle content of the Molecule.
 void deleteAtom(Atom atom)
          deletes the Atom from the Atom content of the Molecule.
 void deleteAtom(org.w3c.dom.Element executeChild)
          deletes Atoms, bonds, etc.
 void deleteAtomWithId(java.lang.String id)
          as above but finds atom by id
 void deleteBond(Bond bond)
          deletes the Bond from the Bond content of the Molecule.
 void deleteElectron(Electron electron)
          Deletes a Electron from the Molecule content.
 void deleteFeature(Feature feature)
          Deletes a Feature from the Molecule content.
protected  void deleteHasAtomRefs(HasAtomRefs har)
           
 void deleteMolecule(Molecule molecule)
          Deletes a Molecule from the Molecule content.
 void deleteSequence(Sequence sequence)
          Deletes a Sequence from the Molecule content.
 void deleteTorsion(Torsion torsion)
          deletes the Torsion from the Torsion content of the Molecule.
 java.util.Vector getAngleVector()
          extracts ALL the Angles as a Vector
 AtomArray getAtomArray()
          packs current Atoms into an AtomArray
 Atom getAtomById(java.lang.String id)
           
 int getAtomCount()
           
 java.util.Hashtable getAtomIdTable()
           
 java.util.Vector getAtomVector()
          extracts ALL the Atoms as a Vector
 Bond getBond(Atom atom1, Atom atom2)
          get a bond from the atoms - order is irrelevant
 BondArray getBondArray()
          extracts ALL the bonds in a single BondArray.
 int getBondCount()
           
 java.util.Vector getBondVector()
          extracts ALL the Bonds as a Vector
 double getCount()
           
 Crystal getCrystal()
          extracts Crystal if present
 java.util.Vector getElectronVector()
          extracts ALL the Electrons as a Vector
 Feature getFeature()
          extracts the FIRST Feature if any present
 java.util.Vector getFeatureVector()
          extracts ALL the Features as a Vector
 java.util.Vector getMoleculeVector()
          extracts ALL the Molecules as a Vector
 Sequence getSequence()
          extracts the FIRST Sequence if any present
 java.util.Vector getSequenceVector()
          extracts ALL the Sequences as a Vector
 java.util.Vector getTorsionVector()
          extracts ALL the Torsions as a Vector
 void output(org.w3c.dom.Element executeChild)
           
 void processDOM()
          carries out class-specific processing for subclasses of PMRElement.
 void run(Execute execute)
          run an <execute> child
 void setCount(double count)
           
 void setCrystal(Crystal crystal)
          replaces Crystal information; if null, deletes any existing Crystal
 void updateDOM()
          when the DOM is built from legacy the tree may be delayed.
 void updateDOMHasCount()
           
 
Methods inherited from class org.xmlcml.cml.CMLBaseImpl
addValidity, convertToSubclass, getConventionName, getDictRef, getId, getSubClassedElement, getTitle, getValidity, 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, toString
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

atomVector

protected java.util.Vector atomVector

bondVector

protected java.util.Vector bondVector

electronVector

protected java.util.Vector electronVector

moleculeVector

protected java.util.Vector moleculeVector

angleVector

protected java.util.Vector angleVector

torsionVector

protected java.util.Vector torsionVector

crystal

protected Crystal crystal

sequenceVector

protected java.util.Vector sequenceVector

featureVector

protected java.util.Vector featureVector

atomArray

protected AtomArray atomArray

bondArray

protected BondArray bondArray

atomIdTable

protected java.util.Hashtable atomIdTable

bondIdTable

protected java.util.Hashtable bondIdTable

bondHashTable

protected java.util.Hashtable bondHashTable

count

protected double count
Constructor Detail

MoleculeImpl

protected MoleculeImpl()

MoleculeImpl

public MoleculeImpl(org.w3c.dom.Element element)
replace existing tree nodes by a Molecule

MoleculeImpl

public MoleculeImpl(org.w3c.dom.Document document)
new Molecule in context
Method Detail

run

public void run(Execute execute)
         throws java.lang.Exception
run an <execute> child
Specified by:
run in interface Molecule

deleteAtom

public void deleteAtom(org.w3c.dom.Element executeChild)
                throws CMLException
deletes Atoms, bonds, etc. controlled from XML execute script

output

public void output(org.w3c.dom.Element executeChild)
            throws java.lang.Exception

getAtomArray

public AtomArray getAtomArray()
packs current Atoms into an AtomArray
Specified by:
getAtomArray in interface Molecule
Returns:
AtomArray the atoms; empty AtomArray if none

addAtom

public void addAtom(Atom atom)
             throws CMLException
adds the Atom to the Atom content of the Molecule. The atom is shallow-copied
Specified by:
addAtom in interface Molecule

deleteAtom

public void deleteAtom(Atom atom)
                throws CMLException
deletes the Atom from the Atom content of the Molecule. If atom does not exist, or is in a different Molecule or is null, no action. Also deletes all HasAtomRefs (Bonds, Angles...) that refer to atom. NOTE: This does NOT check the validity of the Molecule after deletion.
Specified by:
deleteAtom in interface Molecule
Tags copied from interface: Molecule
Parameters:
Atom - atom to be deleted
Throws:
CMLException - atom does not belong to this molecule

deleteHasAtomRefs

protected void deleteHasAtomRefs(HasAtomRefs har)
                          throws CMLException

deleteAtomWithId

public void deleteAtomWithId(java.lang.String id)
                      throws CMLException
as above but finds atom by id

getAtomVector

public java.util.Vector getAtomVector()
extracts ALL the Atoms as a Vector
Specified by:
getAtomVector in interface Molecule
Returns:
Vector empty Vector if no atoms

getAtomIdTable

public java.util.Hashtable getAtomIdTable()
Specified by:
getAtomIdTable in interface Molecule

getAtomById

public Atom getAtomById(java.lang.String id)
Specified by:
getAtomById in interface Molecule

getAtomCount

public int getAtomCount()
Specified by:
getAtomCount in interface Molecule

getBondArray

public BondArray getBondArray()
extracts ALL the bonds in a single BondArray.
Specified by:
getBondArray in interface Molecule
Returns:
BondArray the bonds; empty BondArray if none

getBond

public Bond getBond(Atom atom1,
                    Atom atom2)
Description copied from interface: Molecule
get a bond from the atoms - order is irrelevant
Specified by:
getBond in interface Molecule
Tags copied from interface: Molecule
Parameters:
Atom - atom1 first atom
Atom - atom2 other atom

addBond

public void addBond(Bond bond)
             throws CMLException
adds the Bond to the Bond content of the Molecule. The bond is shallow-copied
Specified by:
addBond in interface Molecule

deleteBond

public void deleteBond(Bond bond)
                throws CMLException
deletes the Bond from the Bond content of the Molecule. If bond does not exist, or is in a different Molecule or is null, no action.
Specified by:
deleteBond in interface Molecule
Tags copied from interface: Molecule
Throws:
CMLException - bond does not belong to this Molecule

getBondVector

public java.util.Vector getBondVector()
extracts ALL the Bonds as a Vector
Specified by:
getBondVector in interface Molecule
Returns:
Vector empty Vector if no bonds

getBondCount

public int getBondCount()
Specified by:
getBondCount in interface Molecule

addAngle

public void addAngle(Angle angle)
adds the Angle to the Angle content of the Molecule. The angle is shallow-copied
Specified by:
addAngle in interface Molecule

deleteAngle

public void deleteAngle(Angle angle)
deletes the Angle from the Angle content of the Molecule. If angle does not exist, or is in a different Molecule or is null, no action.
Specified by:
deleteAngle in interface Molecule

getAngleVector

public java.util.Vector getAngleVector()
extracts ALL the Angles as a Vector
Specified by:
getAngleVector in interface Molecule
Returns:
Vector empty Vector if no angles

addTorsion

public void addTorsion(Torsion torsion)
adds the Torsion to the Torsion content of the Molecule. The torsion is shallow-copied
Specified by:
addTorsion in interface Molecule

deleteTorsion

public void deleteTorsion(Torsion torsion)
deletes the Torsion from the Torsion content of the Molecule. If torsion does not exist, or is in a different Molecule or is null, no action.
Specified by:
deleteTorsion in interface Molecule

getTorsionVector

public java.util.Vector getTorsionVector()
extracts ALL the Torsions as a Vector
Specified by:
getTorsionVector in interface Molecule
Returns:
Vector empty Vector if no torsions

getCrystal

public Crystal getCrystal()
extracts Crystal if present
Specified by:
getCrystal in interface Molecule
Returns:
Crystal. null if none

setCrystal

public void setCrystal(Crystal crystal)
replaces Crystal information; if null, deletes any existing Crystal
Specified by:
setCrystal in interface Molecule
Parameters:
Crystal - the crystallographic information

getSequence

public Sequence getSequence()
extracts the FIRST Sequence if any present
Specified by:
getSequence in interface Molecule
Returns:
Sequence. null if none

addSequence

public void addSequence(Sequence sequence)
Adds a Sequence to the Molecule content.
Specified by:
addSequence in interface Molecule
Parameters:
Sequence - the sequence to be added. null is ignored

deleteSequence

public void deleteSequence(Sequence sequence)
Deletes a Sequence from the Molecule content.
Specified by:
deleteSequence in interface Molecule
Parameters:
Sequence - the sequence to be deleted. null is ignored

getSequenceVector

public java.util.Vector getSequenceVector()
extracts ALL the Sequences as a Vector
Specified by:
getSequenceVector in interface Molecule
Returns:
Vector empty Vector if no Sequences

getFeature

public Feature getFeature()
extracts the FIRST Feature if any present
Specified by:
getFeature in interface Molecule
Returns:
Feature. null if none

addFeature

public void addFeature(Feature feature)
Adds a Feature to the Molecule content.
Specified by:
addFeature in interface Molecule
Parameters:
Feature - the feature to be added. null is ignored

deleteFeature

public void deleteFeature(Feature feature)
Deletes a Feature from the Molecule content.
Specified by:
deleteFeature in interface Molecule
Parameters:
Feature - the feature to be deleted. null is ignored

getFeatureVector

public java.util.Vector getFeatureVector()
extracts ALL the Features as a Vector
Specified by:
getFeatureVector in interface Molecule
Returns:
Vector empty Vector if no Features

addElectron

public void addElectron(Electron electron)
Adds a Electron to the Molecule content.
Specified by:
addElectron in interface Molecule
Parameters:
Electron - the electron to be added. null is ignored

deleteElectron

public void deleteElectron(Electron electron)
Deletes a Electron from the Molecule content.
Specified by:
deleteElectron in interface Molecule
Parameters:
Electron - the electron to be deleted. null is ignored

getElectronVector

public java.util.Vector getElectronVector()
extracts ALL the Electrons as a Vector
Specified by:
getElectronVector in interface Molecule
Returns:
Vector empty Vector if no Electrons

addMolecule

public void addMolecule(Molecule molecule)
Adds a Molecule to the Molecule content.
Specified by:
addMolecule in interface Molecule
Parameters:
Molecule - the molecule to be added. null is ignored

deleteMolecule

public void deleteMolecule(Molecule molecule)
Deletes a Molecule from the Molecule content.
Specified by:
deleteMolecule in interface Molecule
Parameters:
Molecule - the molecule to be deleted. null is ignored

getMoleculeVector

public java.util.Vector getMoleculeVector()
extracts ALL the Molecules as a Vector
Specified by:
getMoleculeVector in interface Molecule
Returns:
Vector empty Vector if no Molecules

setCount

public void setCount(double count)
Specified by:
setCount in interface Molecule

getCount

public double getCount()
Specified by:
getCount in interface Molecule

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

updateDOMHasCount

public void updateDOMHasCount()

updateDOM

public void updateDOM()
               throws CMLException
when the DOM is built from legacy the tree may be delayed. This should be called after legacy has been read in - will recursively call its children to update them. Forces complete rebuild
Overrides:
updateDOM in class CMLBaseImpl

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
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