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org.xmlcml.cml
Interface CMLAtom  

All Superinterfaces:

AbstractAtom, AbstractBase, AbstractBuiltinContainer, AttributeConvention, AttributeCount, AttributeDictRef, AttributeId, AttributeTitle, BuiltinContainer, org.w3c.dom.Element, org.w3c.dom.Node

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public interface CMLAtom

extends AbstractAtom

CORE Interface
DTD Class
Supports <atom> elements

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Field Summary

 

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, ATOMID_NAME, builtinFloatValNames, builtinIntegerValNames, builtinStringValNames, ELEMENT_TYPE, ELTYPE_NAME, FCHARGE_NAME, FORMAL_CHARGE_FLOAT, FORMAL_CHARGE_INT, HCOUNT_NAME, HYDROGEN_COUNT_FLOAT, HYDROGEN_COUNT_INT, ISOTOPE_FLOAT, ISOTOPE_INT, ISOTOPE_NAME, NON_HYDROGEN_COUNT_FLOAT, NON_HYDROGEN_COUNT_INT, NONH_NAME, OCC_NAME, OCCUPANCY, PARITY_NAME, RESID_NAME, RESIDUE_ID, RESIDUE_TYPE, RESTYPE_NAME, SMILESATOMS, SP, SP2, SP3, spTypeStrings, valences, X2, X2_NAME, X3, X3_NAME, XFRACT, XFRACT_NAME, Y2, Y2_NAME, Y3, Y3_NAME, YFRACT, YFRACT_NAME, Z3, Z3_NAME, ZFRACT, ZFRACT_NAME

 

Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

NONUNIQUE, STEREO_2D, STEREO_3D, STEREO_ANY, UNIQUE

 

Fields inherited from interface org.xmlcml.cml.AbstractBase

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

 

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_POSITION_CONTAINED_BY, DOCUMENT_POSITION_CONTAINS, DOCUMENT_POSITION_DISCONNECTED, DOCUMENT_POSITION_FOLLOWING, DOCUMENT_POSITION_IMPLEMENTATION_SPECIFIC, DOCUMENT_POSITION_PRECEDING, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

 

Fields inherited from interface org.xmlcml.cml.AttributeTitle

TITLE

 

Fields inherited from interface org.xmlcml.cml.AttributeDictRef

DICTREF

 

Fields inherited from interface org.xmlcml.cml.AttributeId

ID

 

Fields inherited from interface org.xmlcml.cml.AttributeConvention

CONVENTION

 

Fields inherited from interface org.xmlcml.cml.AttributeCount

COUNT

 

Method Summary
void	addLigand(CMLAtom ligand)           add ligand.
CMLAtom	cloneAtom(CMLMolecule newMolecule)           creates a new Atom - can use a Factory method internally if required.
CMLBond	createBondToLigand(CMLAtom ligand)           add ligand.
java.lang.String	generateId(int serial)           give each atom an ID.
CMLAtomParity	getAtomParity()           DOM Method [CMLCore] get AtomParity.
java.util.Vector	getAtomRefVector()           CORE Method Vector of elements which refer to this atom; possibly better located in CMLMolecule and perhaps protected
java.lang.String	getElementType()           CORE Method DOM Method get ElementType.
java.lang.String[]	getElementTypeList()           CORE Method Query Method get ElementTypeList.
int	getFormalCharge()           CORE Method DOM Method get Formal charge
int[]	getFormalChargeList()           Query Method get list of Formal charges
int	getHydrogenCount()           Query Method DOM Method get hydrogen counts.
int[]	getHydrogenCountList()           CORE Method DOM Method get list of hydrogen counts.
CMLIsotope	getIsotope()           CORE Method DOM Method get Isotope
java.lang.Double	getLength(CMLAtom atom)           convenience method to get interatomic distance
CMLAtom	getLigand(int i)           convenience method to get element of ligand vector
int	getLigandCount()           get ligand count
CMLAtom[]	getLigandList()
java.util.Vector	getLigandVector()
CMLMolecule	getMolecule()           CORE Method an atom must normally be associated with a CMLMolecule
int	getNonHydrogenCount()           DOM Method get nonhydrogen count.
int[]	getNonHydrogenCountList()           DOM Method get nonhydrogen count.
CMLAtom[]	getNonHydrogenLigandList()
java.util.Vector	getNonHydrogenLigandVector()           get Vector of non-hydrogen ligands
double	getOccupancy()           CORE Method DOM Method get Occupancy
java.lang.String	getResidueID()
java.lang.String	getResidueType()           =======================================================
CMLCoordinate2	getXY2()           CORE Method DOM Method get Coordinate
CMLCoordinate3	getXYZ3()           CORE Method DOM Method get 3-D Cartesian Coordinate (default Angstrom)
CMLCoordinate3	getXYZFract()           CORE Method DOM Method get Fractional Coordinate
void	setAtomParity(CMLAtomParity parity)           CORE Method DOM Method set AtomParity.
void	setElementType(java.lang.String elementType)           CORE Method DOM Method set ElementType.
void	setElementTypeList(java.lang.String[] elementType)           CORE Method Query Method set ElementTypeList.
void	setFormalCharge(int charge)           CORE Method DOM Method set Formal charge
void	setFormalChargeList(int[] charge)           CORE Method set Formal charge list
void	setHydrogenCount(int hydrogenCount)           CORE Method DOM Method set hydrogen count.
void	setHydrogenCountList(int[] hydrogenCount)           CORE Method set hydrogen count list.
void	setIsotope(CMLIsotope isotope)           CORE Method DOM Method set Isotope
void	setNonHydrogenCount(int nonHydrogenCount)           DOM Method set nonhydrogen count.
void	setNonHydrogenCountList(int[] nonHydrogenCount)           DOM Method set nonhydrogen count.
void	setOccupancy(double occ)           CORE Method DOM Method set Occupancy
void	setResidueID(java.lang.String residueID)
void	setResidueType(java.lang.String residueType)
void	setXY2(CMLCoordinate2 xy2)           CORE Method DOM Method set 2D Coordinate.
void	setXY2(double x2, double y2)           CORE Method DOM Method set 2D Coordinate
void	setXYZ3(CMLCoordinate3 xyz3)           CORE Method DOM Method set 3D Cartesian Coordinate.
void	setXYZ3(double x3, double y3, double z3)           CORE Method DOM Method set 3D Cartesian Coordinates.
void	setXYZFract(CMLCoordinate3 xyzFract)           CORE Method DOM Method set 3D Fractional Coordinate.
void	setXYZFract(double x3, double y3, double z3)           CORE Method DOM Method set 3D Fractional Coordinates.

 

Methods inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChild, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinCount, getBuiltinVal, getNonBuiltinVal, removeBuiltinChild, setBuiltinFloatChild, setBuiltinIntegerChild, setBuiltinStringChild, setBuiltinVal, setNonBuiltinVal

 

Methods inherited from interface org.xmlcml.cml.AbstractBase

addTracer, debug, debug, getDisplay, processDOM, readXMLTest, removeTracer, setDOMNeedsProcessing, setDOMNeedsUpdating, updateDOM

 

Methods inherited from interface org.w3c.dom.Element

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

 

Methods inherited from interface org.w3c.dom.Node

appendChild, cloneNode, compareDocumentPosition, getAttributes, getBaseURI, getChildNodes, getFeature, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, getTextContent, getUserData, hasAttributes, hasChildNodes, insertBefore, isDefaultNamespace, isEqualNode, isSameNode, isSupported, lookupNamespaceURI, lookupPrefix, normalize, removeChild, replaceChild, setNodeValue, setPrefix, setTextContent, setUserData

 

Methods inherited from interface org.xmlcml.cml.AttributeTitle

getTitle, processDOMHasTitle, setTitle, updateDOMHasTitle

 

Methods inherited from interface org.xmlcml.cml.AttributeDictRef

getDictRef, processDOMHasDictRef, setDictRef, updateDOMHasDictRef

 

Methods inherited from interface org.xmlcml.cml.AttributeId

getId, processDOMHasId, setId, updateDOMHasId

 

Methods inherited from interface org.xmlcml.cml.AttributeConvention

getConventionName, processDOMHasConvention, setConventionName, updateDOMHasConvention

 

Methods inherited from interface org.xmlcml.cml.AttributeCount

getCount, processDOMHasCount, setCount, updateDOMHasCount

 

Method Detail

cloneAtom

public CMLAtom cloneAtom(CMLMolecule newMolecule)
                  throws CMLException

creates a new Atom - can use a Factory method internally if required. Adds atom to newMolecule.

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getAtomRefVector

public java.util.Vector getAtomRefVector()

CORE Method
Vector of elements which refer to this atom; possibly better located in CMLMolecule and perhaps protected

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getXY2

public CMLCoordinate2 getXY2()

CORE Method DOM Method
get Coordinate

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getXYZ3

public CMLCoordinate3 getXYZ3()

CORE Method DOM Method
get 3-D Cartesian Coordinate (default Angstrom)

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getXYZFract

public CMLCoordinate3 getXYZFract()

CORE Method DOM Method
get Fractional Coordinate

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setXY2

public void setXY2(double x2,
                   double y2)

CORE Method DOM Method
set 2D Coordinate

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setXY2

public void setXY2(CMLCoordinate2 xy2)

CORE Method DOM Method
set 2D Coordinate. If already present, overwrites current value.

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setXYZ3

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

CORE Method DOM Method
set 3D Cartesian Coordinates. If already present, overwrites current value.

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setXYZ3

public void setXYZ3(CMLCoordinate3 xyz3)

CORE Method DOM Method
set 3D Cartesian Coordinate. If already present, overwrites current value.

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setXYZFract

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

CORE Method DOM Method
set 3D Fractional Coordinates. If already present, overwrites current value.

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setXYZFract

public void setXYZFract(CMLCoordinate3 xyzFract)

CORE Method DOM Method
set 3D Fractional Coordinate. If already present, overwrites current value.

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getOccupancy

public double getOccupancy()
                    throws CMLException

CORE Method DOM Method
get Occupancy

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setOccupancy

public void setOccupancy(double occ)

CORE Method DOM Method
set Occupancy

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getIsotope

public CMLIsotope getIsotope()
                      throws CMLException

CORE Method DOM Method
get Isotope

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setIsotope

public void setIsotope(CMLIsotope isotope)

CORE Method DOM Method
set Isotope

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getFormalCharge

public int getFormalCharge()

CORE Method DOM Method
get Formal charge

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getFormalChargeList

public int[] getFormalChargeList()

Query Method get list of Formal charges

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setFormalCharge

public void setFormalCharge(int charge)

CORE Method DOM Method
set Formal charge

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setFormalChargeList

public void setFormalChargeList(int[] charge)

CORE Method set Formal charge list

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getHydrogenCount

public int getHydrogenCount()
                     throws CMLException

Query Method DOM Method
get hydrogen counts. NOTE: this is the total count of attached hydrogens, not the number of ligands which have elementTypes "H"

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getHydrogenCountList

public int[] getHydrogenCountList()

CORE Method DOM Method
get list of hydrogen counts. NOTE: this is the total count of attached hydrogens, not the number of ligands which have elementTypes "H"

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setHydrogenCount

public void setHydrogenCount(int hydrogenCount)

CORE Method DOM Method
set hydrogen count. NOTE: this is the total count of attached hydrogens, not the number of ligands which have elementTypes "H"

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setHydrogenCountList

public void setHydrogenCountList(int[] hydrogenCount)

CORE Method set hydrogen count list. NOTE: this is the total count of attached hydrogens, not the number of ligands which have elementTypes "H"

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getNonHydrogenCount

public int getNonHydrogenCount()
                        throws CMLException

DOM Method
get nonhydrogen count. This is for defining generic atoms

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getNonHydrogenCountList

public int[] getNonHydrogenCountList()

DOM Method
get nonhydrogen count. This is for defining generic atoms

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setNonHydrogenCount

public void setNonHydrogenCount(int nonHydrogenCount)

DOM Method
set nonhydrogen count. This is for defining generic atoms

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setNonHydrogenCountList

public void setNonHydrogenCountList(int[] nonHydrogenCount)

DOM Method
set nonhydrogen count. This is for defining generic atoms

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getAtomParity

public CMLAtomParity getAtomParity()
                            throws CMLException

DOM Method
[CMLCore] get AtomParity.

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setAtomParity

public void setAtomParity(CMLAtomParity parity)

CORE Method DOM Method
set AtomParity.

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getElementType

public java.lang.String getElementType()
                                throws CMLException

CORE Method DOM Method
get ElementType. Element types are described elsewhere are are normally drawn from the IUPAC periodic table ( case-sensitive) with D, T and "Dummy".

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getElementTypeList

public java.lang.String[] getElementTypeList()

CORE Method Query Method
get ElementTypeList. Element types are described elsewhere are are normally drawn from the IUPAC periodic table ( case-sensitive) with D, T and "Dummy".

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setElementType

public void setElementType(java.lang.String elementType)

CORE Method DOM Method
set ElementType.

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setElementTypeList

public void setElementTypeList(java.lang.String[] elementType)

CORE Method Query Method
set ElementTypeList.

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getMolecule

public CMLMolecule getMolecule()

CORE Method
an atom must normally be associated with a CMLMolecule

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getResidueType

public java.lang.String getResidueType()
                                throws CMLException

=======================================================

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setResidueType

public void setResidueType(java.lang.String residueType)

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getResidueID

public java.lang.String getResidueID()
                              throws CMLException

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setResidueID

public void setResidueID(java.lang.String residueID)

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generateId

public java.lang.String generateId(int serial)

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

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createBondToLigand

public CMLBond createBondToLigand(CMLAtom ligand)
                           throws CMLException

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

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addLigand

public void addLigand(CMLAtom ligand)
               throws CMLException

add ligand. If already known, ignore.

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getLigandVector

public java.util.Vector getLigandVector()

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getLigandList

public CMLAtom[] getLigandList()

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getLigandCount

public int getLigandCount()

get ligand count

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getLigand

public CMLAtom getLigand(int i)

convenience method to get element of ligand vector

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getNonHydrogenLigandVector

public java.util.Vector getNonHydrogenLigandVector()

get Vector of non-hydrogen ligands

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getNonHydrogenLigandList

public CMLAtom[] getNonHydrogenLigandList()

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getLength

public java.lang.Double getLength(CMLAtom atom)

convenience method to get interatomic distance

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ cml overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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