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org.xmlcml.cml
Interface CMLBond  

All Superinterfaces:

AbstractBase, AbstractBond, AbstractBuiltinContainer, AttributeAtomRefs, AttributeConvention, AttributeDictRef, AttributeId, AttributeTitle, BuiltinContainer, org.w3c.dom.Element, org.w3c.dom.Node

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public interface CMLBond

extends AbstractBond

CORE Interface
DTD Class
main class: supports <bond> elements

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Field Summary

 

Fields inherited from interface org.xmlcml.cml.AbstractBond

AROMATIC, ATOMREF, ATOMREF_NAME, ATOMREFS, ATOMREFS_NAME, BOND_BUILTIN_COUNT, BOND_FLOATVAL_COUNT, BOND_FLOATVAL_END, BOND_FLOATVAL_START, BOND_INTEGERVAL_COUNT, BOND_INTEGERVAL_END, BOND_INTEGERVAL_START, BOND_STRINGVAL_COUNT, BOND_STRINGVAL_END, BOND_STRINGVAL_START, BONDID, bondOrders, bondTypeStrings, builtinFloatValNames, builtinIntegerValNames, builtinStringValNames, CIS, DECREASE, DEFAULTXY2LENGTH, DEFAULTXYZ3LENGTH, DELETE, DOUBLE, HATCH, ID_NAME, INCREASE, LENGTH, LENGTH_NAME, NOSTEREO, ORDER, ORDER_NAME, OVERRUN, SINGLE, STEREO, STEREO_NAME, TRANS, TRIPLE, UNKNOWN, WEDGE, ZERO

 

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

 

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.AttributeAtomRefs

ATOM_REFS

 

Method Summary
CMLBond	cloneBond(java.util.HashMap map)           clone the bond.
boolean	contains(CMLAtom atom)           true if bond contains this atom
CMLAtom	getAtom(int i)           CORE Method
double	getBondLength()           CORE Method
CMLMolecule	getMolecule()           CORE Method
java.lang.String	getOrder()           CORE Method
CMLAtom	getOtherAtom(CMLAtom atom)           returns other atom in a 2-atom bond else null
CMLBondStereo	getStereo()           CORE Method
CMLStringVal	getStringVal(int i)
java.lang.String	hashKey()
boolean	hasOrder()           convenience method to test if bond order is known
void	processAtomRefs(CMLMolecule molecule)
void	setBondLength(double length)           CORE Method
void	setOrder(java.lang.String order)           CORE Method
void	setStereo(CMLBondStereo stereo, CMLAtom sharpAtom)           CORE Method
void	setStringVal(int i, CMLStringVal stringVal)

 

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.AttributeAtomRefs

addAtomRef, deleteAtomRef, getAtomRef, getAtomRefVector, processDOMHasAtomRefs, updateDOMHasAtomRefs

 

Method Detail

cloneBond

public CMLBond cloneBond(java.util.HashMap map)
                  throws CMLException

clone the bond. HashMap maps old atoms to new atoms. Factory methods can be used internally.

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getStringVal

public CMLStringVal getStringVal(int i)

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setStringVal

public void setStringVal(int i,
                         CMLStringVal stringVal)

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getAtom

public CMLAtom getAtom(int i)

CORE Method

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getOtherAtom

public CMLAtom getOtherAtom(CMLAtom atom)

returns other atom in a 2-atom bond else null

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contains

public boolean contains(CMLAtom atom)

true if bond contains this atom

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processAtomRefs

public void processAtomRefs(CMLMolecule molecule)
                     throws CMLException

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getMolecule

public CMLMolecule getMolecule()

CORE Method

Specified by:

getMolecule in interface AttributeAtomRefs

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hashKey

public java.lang.String hashKey()

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getOrder

public java.lang.String getOrder()
                          throws CMLException

CORE Method

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setOrder

public void setOrder(java.lang.String order)
              throws CMLException

CORE Method

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getStereo

public CMLBondStereo getStereo()

CORE Method

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setStereo

public void setStereo(CMLBondStereo stereo,
                      CMLAtom sharpAtom)
               throws CMLException

CORE Method

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getBondLength

public double getBondLength()
                     throws CMLException

CORE Method

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setBondLength

public void setBondLength(double length)
                   throws CMLException

CORE Method

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hasOrder

public boolean hasOrder()

convenience method to test if bond order is known

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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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