org.xmlcml.tools
Interface SpanningTree

All Known Implementing Classes:

SpanningTreeImpl

public interface SpanningTree

extends PMRDocument

simple Spanning tree, independent of Molecule (contains pointer into that). based on CMLDocument

Fields inherited from interface uk.co.demon.ursus.dom.PMRDocument

PACKAGENAME

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

STElement	addAtom(STElement parent, Atom atom) create new STElement (contains atom) and add to parent
void	addChainSet(ChainSet chain)
void	addLink(Bond bond)
void	calculateTopology()
AtomSet	getAcyclicAtomSet() get atoms in acyclic bonds
BondSet	getAcyclicBondSet() get bonds not in rings
AtomSet	getAtomSet() get all atoms
BondSet	getBondSet() get all bonds
AtomSet	getCyclicAtomSet() get atoms only in rings
BondSet	getCyclicBondSet() get bonds in rings
java.util.Vector	getLinkVector()
Molecule	getMolecule()
AtomSet	getNonRingAtomSet() get atoms not in rings
java.util.Vector	getRingNucleusVector()
java.lang.String	toSMILES()

Methods inherited from interface org.w3c.dom.Document

createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createElement, createElementNS, createEntityReference, createProcessingInstruction, createTextNode, getDoctype, getDocumentElement, getElementById, getElementsByTagName, getElementsByTagNameNS, getImplementation, importNode

Methods inherited from interface org.w3c.dom.Node

appendChild, cloneNode, getAttributes, getChildNodes, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, hasChildNodes, insertBefore, normalize, removeChild, replaceChild, setNodeValue, setPrefix, supports

Method Detail

addAtom

public STElement addAtom(STElement parent,
                         Atom atom)

create new STElement (contains atom) and add to parent

addLink

public void addLink(Bond bond)

getMolecule

public Molecule getMolecule()

toSMILES

public java.lang.String toSMILES()
                          throws CMLException

getLinkVector

public java.util.Vector getLinkVector()

getBondSet

public BondSet getBondSet()

get all bonds

getCyclicBondSet

public BondSet getCyclicBondSet()

get bonds in rings

getAcyclicBondSet

public BondSet getAcyclicBondSet()

get bonds not in rings

getAtomSet

public AtomSet getAtomSet()

get all atoms

getNonRingAtomSet

public AtomSet getNonRingAtomSet()

get atoms not in rings

getCyclicAtomSet

public AtomSet getCyclicAtomSet()

get atoms only in rings

getAcyclicAtomSet

public AtomSet getAcyclicAtomSet()

get atoms in acyclic bonds

getRingNucleusVector

public java.util.Vector getRingNucleusVector()
                                      throws CMLException

calculateTopology

public void calculateTopology()
                       throws CMLException

addChainSet

public void addChainSet(ChainSet chain)