org.xmlcml.cml
Interface Atom

All Known Implementing Classes:

AtomImpl

public interface Atom

extends AbstractAtom

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

Method Summary

void	addLigand(Atom ligand) add ligand.
Bond	createBondToLigand(Atom ligand) add ligand.
java.lang.String	generateId(int serial) give each atom an ID.
double	getAtomParity()
java.util.Vector	getAtomRefVector() Vector of elements which refer to this atom
java.lang.String	getElementType()
int	getFormalCharge()
int	getHybridization()
int	getHydrogenCount()
double	getIsotope()
Atom	getLigand(int i) convenience method to get element of ligand vector
int	getLigandCount() get ligand count
java.util.Vector	getLigandVector()
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	setAtomParity(double parity)
void	setElementType(java.lang.String elementType)
void	setFormalCharge(int charge)
void	setHybridization(int hybridization)
void	setHydrogenCount(int hydrogenCount)
void	setIsotope(double isotope)
void	setNonHydrogenCount(int nonHydrogenCount)
void	setOccupancy(double occ)
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)
void	transform(Transform2 t) transform XY2 coordinate; if atom.xy2 is null, no op

Methods inherited from interface org.xmlcml.cml.AbstractAtom

getCount, setCount

Methods inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

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

Methods inherited from interface org.xmlcml.cml.HasCount

updateDOMHasCount

Methods inherited from interface org.xmlcml.cml.CMLBase

addValidity, debug, isValid, processDOM, updateDOM

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

appendTo, getValidity, processDescendants, setProcessFlag, setTagName

Methods inherited from interface org.xmlcml.cml.HasTitle

getTitle, setTitle, updateDOMHasTitle

Methods inherited from interface org.xmlcml.cml.HasDictRef

getDictRef, setDictRef, updateDOMHasDictRef

Methods inherited from interface org.xmlcml.cml.HasId

getId, setId, updateDOMHasId

Methods inherited from interface org.xmlcml.cml.HasConvention

getConventionName, setConventionName, updateDOMHasConvention

Methods inherited from interface org.w3c.dom.Element

getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getElementsByTagName, getElementsByTagNameNS, getTagName, hasAttribute, hasAttributeNS, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS

Method Detail

getAtomRefVector

public java.util.Vector getAtomRefVector()

Vector of elements which refer to this atom

getXY2

public Real2 getXY2()

getXYZ3

public Point3 getXYZ3()

getXYZFract

public Point3 getXYZFract()

setXY2

public void setXY2(double x2,
                   double y2)

setXY2

public void setXY2(Real2 xy2)

setXYZ3

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

setXYZ3

public void setXYZ3(Point3 xyz3)

setXYZFract

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

setXYZFract

public void setXYZFract(Point3 xyzFract)

getOccupancy

public double getOccupancy()
                    throws CMLException

setOccupancy

public void setOccupancy(double occ)

getIsotope

public double getIsotope()
                  throws CMLException

setIsotope

public void setIsotope(double isotope)

getFormalCharge

public int getFormalCharge()
                    throws CMLException

setFormalCharge

public void setFormalCharge(int charge)

getHydrogenCount

public int getHydrogenCount()
                     throws CMLException

setHydrogenCount

public void setHydrogenCount(int hydrogenCount)

getNonHydrogenCount

public int getNonHydrogenCount()
                        throws CMLException

setNonHydrogenCount

public void setNonHydrogenCount(int nonHydrogenCount)

getAtomParity

public double getAtomParity()
                     throws CMLException

setAtomParity

public void setAtomParity(double parity)

getElementType

public java.lang.String getElementType()
                                throws CMLException

setElementType

public void setElementType(java.lang.String elementType)

getHybridization

public int getHybridization()
                     throws CMLException

setHybridization

public void setHybridization(int hybridization)

getResidueType

public java.lang.String getResidueType()
                                throws CMLException

setResidueType

public void setResidueType(java.lang.String residueType)

getResidueID

public java.lang.String getResidueID()
                              throws CMLException

setResidueID

public void setResidueID(java.lang.String residueID)

generateId

public java.lang.String generateId(int serial)

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

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

Parameters:

Atom - ligand the ligand

Returns:

Bond the new bond

addLigand

public void addLigand(Atom ligand)
               throws CMLException

add ligand. If already known, ignore.

Parameters:

Atom - ligand to add

getLigandVector

public java.util.Vector getLigandVector()

getLigandCount

public int getLigandCount()

get ligand count

Returns:

int ligand count (0 or more)

getLigand

public Atom getLigand(int i)

convenience method to get element of ligand vector

getMolecule

public Molecule getMolecule()

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

plusXY2

public void plusXY2(Real2 r)

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

transform

public void transform(Transform2 t)

transform XY2 coordinate; if atom.xy2 is null, no op

plusXYZ3

public void plusXYZ3(Point3 p)

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

plusXYZFract

public void plusXYZFract(Point3 p)

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