org.xmlcml.cml
Interface AbstractBond

All Known Subinterfaces:

Bond, BondArray

All Known Implementing Classes:

AbstractBondImpl

public interface AbstractBond

extends AbstractBuiltinContainer, HasAtomRefs

Field Summary

static java.lang.String	AROMATIC aromatic bond
static int	ATOMREF
static int	ATOMREFS
static int	BOND_BUILTIN_COUNT
static int	BOND_FLOATVAL_COUNT
static int	BOND_FLOATVAL_END
static int	BOND_FLOATVAL_START
static int	BOND_INTEGERVAL_COUNT
static int	BOND_INTEGERVAL_END
static int	BOND_INTEGERVAL_START
static int	BOND_STRINGVAL_COUNT
static int	BOND_STRINGVAL_END
static int	BOND_STRINGVAL_START
static double[]	bondOrders
static java.lang.String[]	bondTypeStrings
static java.lang.String	DECREASE
static double	DEFAULTXY2LENGTH default screen bondlength
static double	DEFAULTXYZ3LENGTH default 3d bondlength
static java.lang.String	DELETE
static java.lang.String	DOUBLE double bond
static java.lang.String	HATCH hatch bond
static java.lang.String	INCREASE
static int	LENGTH
static java.lang.String	NOSTEREO nostereo bond
static int	ORDER
static java.lang.String	OVERRUN
static java.lang.String	SINGLE single bond
static int	STEREO
static java.lang.String	TRIPLE triple bond
static java.lang.String	WEDGE wedge bond
static java.lang.String	ZERO zero bond (disjoint == "." in SMILES)

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

Method Summary

void	addAtomRef(Atom atom)
void	deleteAtomRef(Atom atom)
Atom	getAtomRef(int serial)
java.util.Vector	getAtomRefVector()

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.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

Field Detail

BOND_FLOATVAL_START

public static final int BOND_FLOATVAL_START

LENGTH

public static final int LENGTH

BOND_FLOATVAL_END

public static final int BOND_FLOATVAL_END

BOND_FLOATVAL_COUNT

public static final int BOND_FLOATVAL_COUNT

BOND_INTEGERVAL_START

public static final int BOND_INTEGERVAL_START

BOND_INTEGERVAL_END

public static final int BOND_INTEGERVAL_END

BOND_INTEGERVAL_COUNT

public static final int BOND_INTEGERVAL_COUNT

BOND_STRINGVAL_START

public static final int BOND_STRINGVAL_START

ATOMREF

public static final int ATOMREF

ATOMREFS

public static final int ATOMREFS

ORDER

public static final int ORDER

STEREO

public static final int STEREO

BOND_STRINGVAL_END

public static final int BOND_STRINGVAL_END

BOND_STRINGVAL_COUNT

public static final int BOND_STRINGVAL_COUNT

BOND_BUILTIN_COUNT

public static final int BOND_BUILTIN_COUNT

DEFAULTXY2LENGTH

public static final double DEFAULTXY2LENGTH

default screen bondlength

DEFAULTXYZ3LENGTH

public static final double DEFAULTXYZ3LENGTH

default 3d bondlength

SINGLE

public static final java.lang.String SINGLE

single bond

DOUBLE

public static final java.lang.String DOUBLE

double bond

TRIPLE

public static final java.lang.String TRIPLE

triple bond

AROMATIC

public static final java.lang.String AROMATIC

aromatic bond

ZERO

public static final java.lang.String ZERO

zero bond (disjoint == "." in SMILES)

WEDGE

public static final java.lang.String WEDGE

wedge bond

HATCH

public static final java.lang.String HATCH

hatch bond

NOSTEREO

public static final java.lang.String NOSTEREO

nostereo bond

DELETE

public static final java.lang.String DELETE

OVERRUN

public static final java.lang.String OVERRUN

INCREASE

public static final java.lang.String INCREASE

DECREASE

public static final java.lang.String DECREASE

bondTypeStrings

public static final java.lang.String[] bondTypeStrings

bondOrders

public static final double[] bondOrders

Method Detail

getAtomRef

public Atom getAtomRef(int serial)

Specified by:

getAtomRef in interface HasAtomRefs

getAtomRefVector

public java.util.Vector getAtomRefVector()

Specified by:

getAtomRefVector in interface HasAtomRefs

addAtomRef

public void addAtomRef(Atom atom)

Specified by:

addAtomRef in interface HasAtomRefs

deleteAtomRef

public void deleteAtomRef(Atom atom)

Specified by:

deleteAtomRef in interface HasAtomRefs