org.xmlcml.cml
Class AtomImpl

java.lang.Object
  |
  +--org.apache.xerces.dom.NodeImpl
        |
        +--org.apache.xerces.dom.ChildNode
              |
              +--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.AbstractAtomImpl
                                                        |
                                                        +--org.xmlcml.cml.AtomImpl

public class AtomImpl

extends AbstractAtomImpl

implements Atom

See Also:

Serialized Form

Field Summary

protected double	atomParity
protected java.util.Vector	atomRefVector Vector of Objects than refer to this Atom
protected java.lang.String	elementType
protected int	formalCharge
protected int	hybridization
protected int	hydrogenCount
protected double	isotope
protected java.util.Vector	ligandVector
protected Molecule	molecule Atom know which molecule it belongs to.
protected int	nonHydrogenCount
protected double	occupancy
protected java.lang.String	residueID
protected java.lang.String	residueType
protected Real2	xy2
protected Point3	xyz3
protected Point3	xyzFract

Fields inherited from class org.xmlcml.cml.AbstractAtomImpl

count

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.AbstractAtom

ATOM_BUILTIN_COUNT, ATOM_FLOATVAL_COUNT, ATOM_FLOATVAL_END, ATOM_FLOATVAL_START, ATOM_ID, ATOM_INTEGERVAL_COUNT, ATOM_INTEGERVAL_END, ATOM_INTEGERVAL_START, ATOM_PARITY_FLOAT, ATOM_PARITY_INT, ATOM_STRINGVAL_COUNT, ATOM_STRINGVAL_END, ATOM_STRINGVAL_START, ELEMENT_TYPE, FORMAL_CHARGE_FLOAT, FORMAL_CHARGE_INT, HYDROGEN_COUNT_FLOAT, HYDROGEN_COUNT_INT, ISOTOPE_FLOAT, ISOTOPE_INT, NON_HYDROGEN_COUNT_FLOAT, NON_HYDROGEN_COUNT_INT, OCCUPANCY, RESIDUE_ID, RESIDUE_TYPE, SMILESATOMS, SP, SP2, SP3, spTypeStrings, valences, X2, X3, XFRACT, Y2, Y3, YFRACT, Z3, ZFRACT

Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

NONUNIQUE, UNIQUE

Fields inherited from interface org.xmlcml.cml.HasCount

COUNT

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	AtomImpl()
	AtomImpl(org.w3c.dom.Document document)
	AtomImpl(org.w3c.dom.Element element)
	AtomImpl(Molecule molecule, java.lang.String id) create in molecule context - must have unique id.

Method Summary

void	addLigand(Atom ligand) add a ligand to atom, but do not create a bond.
Bond	createBondToLigand(Atom ligand) add ligand.
void	debug(java.io.Writer w) output debug info to Writer
java.lang.String	generateId(int serial) give each atom an ID.
double	getAtomParity()
java.util.Vector	getAtomRefVector() finds all references to this atom, e.g.
java.lang.String	getElementType() get elementType from builtin child
int	getFormalCharge()
int	getHybridization()
int	getHydrogenCount()
java.lang.String	getId() if ID attribute is missing, returns atomId biltin child value and sets ID attribute to this value
double	getIsotope()
Atom	getLigand(int i) convenience method to get element of ligand vector
int	getLigandCount() get ligand count
java.util.Vector	getLigandVector() get vector of ligands
Molecule	getMolecule() an atom may be associated with one Molecule (or none)
int	getNonHydrogenCount()
double	getOccupancy()
java.lang.String	getResidueID()
java.lang.String	getResidueType()
Real2	getXY2()
Point3	getXYZ3()
Point3	getXYZFract()
void	plusXY2(Real2 r) increase XY2 coordinate; if atom.xy2 is null, sets coordinate to r
void	plusXYZ3(Point3 p) increase XYZ3 coordinate; if atom.xyz3 is null, sets coordinate to r
void	plusXYZFract(Point3 p) increase XYZFract coordinate; if atom.xyzFract is null, sets coordinate to p
void	processDOM() carries out class-specific processing for subclasses of PMRElement.
void	setAtomParity(double parity)
void	setElementType(java.lang.String elementType)
void	setFormalCharge(int formalCharge)
void	setHybridization(int hybridization)
void	setHydrogenCount(int hydrogenCount)
void	setIsotope(double isotope)
protected void	setMolecule(Molecule molecule)
void	setNonHydrogenCount(int nonHydrogenCount)
void	setOccupancy(double occupancy)
protected void	setRef(HasAtomRefs har) add a reference to this Atom
void	setResidueID(java.lang.String residueID)
void	setResidueType(java.lang.String residueType)
void	setXY2(double x2, double y2)
void	setXY2(Real2 xy2)
void	setXYZ3(double x3, double y3, double z3)
void	setXYZ3(Point3 xyz3)
void	setXYZFract(double x3, double y3, double z3)
void	setXYZFract(Point3 xyzFract)
java.lang.String	toString()
void	transform(Transform2 t2) transforms 2D coordinates of atom
void	updateDOM()

Methods inherited from class org.xmlcml.cml.AbstractAtomImpl

getBuiltinCount, getBuiltinFloatValCount, getBuiltinFloatValNames, getBuiltinIntegerValCount, getBuiltinIntegerValNames, getBuiltinNames, getBuiltinStringValCount, getBuiltinStringValNames, getCount, getValidity, setCount, showBuiltinNames, updateDOMHasCount

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, 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

ligandVector

protected java.util.Vector ligandVector

molecule

protected Molecule molecule

Atom know which molecule it belongs to. This MUST correspond to the parent element. The programmer must maintain this

atomRefVector

protected java.util.Vector atomRefVector

Vector of Objects than refer to this Atom

xy2

protected Real2 xy2

xyz3

protected Point3 xyz3

xyzFract

protected Point3 xyzFract

elementType

protected java.lang.String elementType

occupancy

protected double occupancy

isotope

protected double isotope

formalCharge

protected int formalCharge

hydrogenCount

protected int hydrogenCount

nonHydrogenCount

protected int nonHydrogenCount

atomParity

protected double atomParity

residueType

protected java.lang.String residueType

residueID

protected java.lang.String residueID

hybridization

protected int hybridization

Constructor Detail

AtomImpl

protected AtomImpl()

AtomImpl

public AtomImpl(Molecule molecule,
                java.lang.String id)
         throws CMLException

create in molecule context - must have unique id. calls addAtom

AtomImpl

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

AtomImpl

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

Method Detail

getMolecule

public Molecule getMolecule()

Description copied from interface: Atom

an atom may be associated with one Molecule (or none)

Specified by:

getMolecule in interface Atom

setMolecule

protected void setMolecule(Molecule molecule)

getAtomRefVector

public java.util.Vector getAtomRefVector()

finds all references to this atom, e.g. from Bonds, Angles, Torsions, who must register this information

Specified by:

getAtomRefVector in interface Atom

setRef

protected void setRef(HasAtomRefs har)

add a reference to this Atom

Parameters:

HasAtomRefs - har bond, angle, etc. which references this atom

getXY2

public Real2 getXY2()

Specified by:

getXY2 in interface Atom

getXYZ3

public Point3 getXYZ3()

Specified by:

getXYZ3 in interface Atom

getXYZFract

public Point3 getXYZFract()

Specified by:

getXYZFract in interface Atom

setXY2

public void setXY2(double x2,
                   double y2)

Specified by:

setXY2 in interface Atom

setXY2

public void setXY2(Real2 xy2)

Specified by:

setXY2 in interface Atom

setXYZ3

public void setXYZ3(double x3,
                    double y3,
                    double z3)

Specified by:

setXYZ3 in interface Atom

setXYZ3

public void setXYZ3(Point3 xyz3)

Specified by:

setXYZ3 in interface Atom

setXYZFract

public void setXYZFract(double x3,
                        double y3,
                        double z3)

Specified by:

setXYZFract in interface Atom

setXYZFract

public void setXYZFract(Point3 xyzFract)

Specified by:

setXYZFract in interface Atom

getOccupancy

public double getOccupancy()
                    throws CMLException

Specified by:

getOccupancy in interface Atom

setOccupancy

public void setOccupancy(double occupancy)

Specified by:

setOccupancy in interface Atom

getIsotope

public double getIsotope()
                  throws CMLException

Specified by:

getIsotope in interface Atom

setIsotope

public void setIsotope(double isotope)

Specified by:

setIsotope in interface Atom

getFormalCharge

public int getFormalCharge()
                    throws CMLException

Specified by:

getFormalCharge in interface Atom

setFormalCharge

public void setFormalCharge(int formalCharge)

Specified by:

setFormalCharge in interface Atom

getHydrogenCount

public int getHydrogenCount()
                     throws CMLException

Specified by:

getHydrogenCount in interface Atom

setHydrogenCount

public void setHydrogenCount(int hydrogenCount)

Specified by:

setHydrogenCount in interface Atom

getNonHydrogenCount

public int getNonHydrogenCount()
                        throws CMLException

Specified by:

getNonHydrogenCount in interface Atom

setNonHydrogenCount

public void setNonHydrogenCount(int nonHydrogenCount)

Specified by:

setNonHydrogenCount in interface Atom

getAtomParity

public double getAtomParity()
                     throws CMLException

Specified by:

getAtomParity in interface Atom

setAtomParity

public void setAtomParity(double parity)

Specified by:

setAtomParity in interface Atom

getElementType

public java.lang.String getElementType()
                                throws CMLException

get elementType from builtin child

Specified by:

getElementType in interface Atom

setElementType

public void setElementType(java.lang.String elementType)

Specified by:

setElementType in interface Atom

getHybridization

public int getHybridization()
                     throws CMLException

Specified by:

getHybridization in interface Atom

setHybridization

public void setHybridization(int hybridization)

Specified by:

setHybridization in interface Atom

getResidueType

public java.lang.String getResidueType()
                                throws CMLException

Specified by:

getResidueType in interface Atom

setResidueType

public void setResidueType(java.lang.String residueType)

Specified by:

setResidueType in interface Atom

getResidueID

public java.lang.String getResidueID()
                              throws CMLException

Specified by:

getResidueID in interface Atom

setResidueID

public void setResidueID(java.lang.String residueID)

Specified by:

setResidueID in interface Atom

generateId

public java.lang.String generateId(int serial)

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

Specified by:

generateId in interface Atom

getId

public java.lang.String getId()

if ID attribute is missing, returns atomId biltin child value and sets ID attribute to this value

Overrides:

getId in class CMLBaseImpl

createBondToLigand

public Bond createBondToLigand(Atom ligand)
                        throws CMLException

add ligand. If already known, ignore. Else look for bond including atom/ligand. If not present, create default bond. return Bond

Specified by:

createBondToLigand in interface Atom

Parameters:

Atom - ligand the ligand

Returns:

Bond the new bond

addLigand

public void addLigand(Atom ligand)

add a ligand to atom, but do not create a bond. If already present, no-op

Specified by:

addLigand in interface Atom

Parameters:

Atom - ligand to add

getLigandVector

public java.util.Vector getLigandVector()

get vector of ligands

Specified by:

getLigandVector in interface Atom

Returns:

Vector vector of Atoms (or null if none)

getLigandCount

public int getLigandCount()

get ligand count

Specified by:

getLigandCount in interface Atom

Returns:

int ligand count (0 or more)

getLigand

public Atom getLigand(int i)

Description copied from interface: Atom

convenience method to get element of ligand vector

Specified by:

getLigand in interface Atom

plusXY2

public void plusXY2(Real2 r)

increase XY2 coordinate; if atom.xy2 is null, sets coordinate to r

Specified by:

plusXY2 in interface Atom

transform

public void transform(Transform2 t2)

transforms 2D coordinates of atom

Specified by:

transform in interface Atom

plusXYZ3

public void plusXYZ3(Point3 p)

increase XYZ3 coordinate; if atom.xyz3 is null, sets coordinate to r

Specified by:

plusXYZ3 in interface Atom

plusXYZFract

public void plusXYZFract(Point3 p)

increase XYZFract coordinate; if atom.xyzFract is null, sets coordinate to p

Specified by:

plusXYZFract in interface Atom

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

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

updateDOM

public void updateDOM()
               throws CMLException

Overrides:

updateDOM in class AbstractAtomImpl