org.xmlcml.tools
Class SpanningTreeImpl

java.lang.Object
  |
  +--org.apache.xerces.dom.NodeImpl
        |
        +--org.apache.xerces.dom.ParentNode
              |
              +--org.apache.xerces.dom.DocumentImpl
                    |
                    +--uk.co.demon.ursus.dom.AbstractDocumentImpl
                          |
                          +--uk.co.demon.ursus.dom.PMRDocumentImpl
                                |
                                +--org.xmlcml.tools.SpanningTreeImpl

public class SpanningTreeImpl

extends PMRDocumentImpl

implements SpanningTree

See Also:

Serialized Form

Fields inherited from class uk.co.demon.ursus.dom.AbstractDocumentImpl

DEFAULT_PARSER_NAME, docElement

Fields inherited from class org.apache.xerces.dom.DocumentImpl

allowGrammarAccess, docElement, docType, errorChecking, identifiers, iterators, kidOK, ranges, treeWalkers, userData

Fields inherited from class org.apache.xerces.dom.ParentNode

changes, firstChild, nodeListIndex, nodeListLength, nodeListNode, ownerDocument

Fields inherited from class org.apache.xerces.dom.NodeImpl

ELEMENT_DEFINITION_NODE, FIRSTCHILD, flags, IGNORABLEWS, MUTATION_AGGREGATE, MUTATION_ALL, MUTATION_LOCAL, MUTATION_NONE, MUTATIONEVENTS, OWNED, ownerNode, READONLY, SETVALUE, SPECIFIED, SYNCCHILDREN, SYNCDATA

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

Constructor Summary

SpanningTreeImpl()

SpanningTreeImpl(Molecule molecule)
new spanning tree, starting at first atom and including all its descendants

SpanningTreeImpl(Molecule molecule, Atom start)
new spanning tree, starting at start and including all its descendants

SpanningTreeImpl(Molecule molecule, Atom rootAtom, Atom parentAtom)
new spanning tree, starting at rootAtom.

Method Summary

STElement	addAtom(STElement parentElement, Atom atom) create new STElement (contains atom) and add to parent
void	addChainSet(ChainSet chain) this adds an *existing* chain to the vector (i.e.
void	addLink(Bond bond) add link - check if bond alreay used and create vector if null
void	calculateTopology() get all cyclic bonds after spanning tree is created.
void	findRingNuclei()
void	findRings()
AtomSet	getAcyclicAtomSet() get atoms in acyclic bonds
BondSet	getAcyclicBondSet() get bonds not in rings
AtomSet	getAtomSet() get atoms
BondSet	getBondSet() get 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() get all cyclic bonds after spanning tree is created.
java.util.Vector	getRingVector() get rings
STElement	getSTElement(Atom atom)
static void	main(java.lang.String[] args)
java.lang.String	toSMILES()
java.lang.String	toString()

Methods inherited from class uk.co.demon.ursus.dom.PMRDocumentImpl

createDocument, createDocument, testBuild, testRead

Methods inherited from class org.apache.xerces.dom.DocumentImpl

adoptNode, clone, cloneNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createDocumentType, createElement, createElementDefinition, createElementNS, createEntity, createEntityReference, createEvent, createNodeIterator, createNodeIterator, createNotation, createProcessingInstruction, createRange, createTextNode, createTreeWalker, createTreeWalker, getDoctype, getDocumentElement, getElementById, getElementsByTagName, getElementsByTagNameNS, getErrorChecking, getIdentifier, getIdentifiers, getImplementation, getNodeIterators, getNodeName, getNodeType, getOwnerDocument, getRanges, getTreeWalkers, getUserData, importNode, insertBefore, isKidOK, isXMLName, putIdentifier, removeChild, removeIdentifier, removeTreeWalker, setErrorChecking, setUserData

Methods inherited from class org.apache.xerces.dom.ParentNode

changed, changes, getChildNodes, getFirstChild, getLastChild, getLength, hasChildNodes, item, normalize, replaceChild, setReadOnly, synchronizeChildren, synchronizeChildren

Methods inherited from class org.apache.xerces.dom.NodeImpl

addEventListener, appendChild, dispatchEvent, finalize, getAttributes, getLocalName, getNamespaceURI, getNextSibling, getNodeValue, getParentNode, getPrefix, getPreviousSibling, getReadOnly, getUserData, removeEventListener, setNodeValue, setPrefix, setUserData, supports, synchronizeData

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SpanningTreeImpl

public SpanningTreeImpl()

SpanningTreeImpl

public SpanningTreeImpl(Molecule molecule,
                        Atom rootAtom,
                        Atom parentAtom)
                 throws CMLException

new spanning tree, starting at rootAtom. Do not include parent and its descendants (unless reached by other routes). If parent == null, explore all atoms connected to start

SpanningTreeImpl

public SpanningTreeImpl(Molecule molecule,
                        Atom start)
                 throws CMLException

new spanning tree, starting at start and including all its descendants

SpanningTreeImpl

public SpanningTreeImpl(Molecule molecule)
                 throws CMLException

new spanning tree, starting at first atom and including all its descendants

Method Detail

getMolecule

public Molecule getMolecule()

Specified by:

getMolecule in interface SpanningTree

getLinkVector

public java.util.Vector getLinkVector()

Specified by:

getLinkVector in interface SpanningTree

getBondSet

public BondSet getBondSet()

get bonds

Specified by:

getBondSet in interface SpanningTree

getCyclicBondSet

public BondSet getCyclicBondSet()

get bonds in rings

Specified by:

getCyclicBondSet in interface SpanningTree

getAcyclicBondSet

public BondSet getAcyclicBondSet()

get bonds not in rings

Specified by:

getAcyclicBondSet in interface SpanningTree

getAtomSet

public AtomSet getAtomSet()

get atoms

Specified by:

getAtomSet in interface SpanningTree

getNonRingAtomSet

public AtomSet getNonRingAtomSet()

get atoms not in rings

Specified by:

getNonRingAtomSet in interface SpanningTree

getCyclicAtomSet

public AtomSet getCyclicAtomSet()

get atoms only in rings

Specified by:

getCyclicAtomSet in interface SpanningTree

getAcyclicAtomSet

public AtomSet getAcyclicAtomSet()

get atoms in acyclic bonds

Specified by:

getAcyclicAtomSet in interface SpanningTree

addAtom

public STElement addAtom(STElement parentElement,
                         Atom atom)

Description copied from interface: SpanningTree

create new STElement (contains atom) and add to parent

Specified by:

addAtom in interface SpanningTree

getSTElement

public STElement getSTElement(Atom atom)

addLink

public void addLink(Bond bond)

add link - check if bond alreay used and create vector if null

Specified by:

addLink in interface SpanningTree

findRings

public void findRings()
               throws CMLException

calculateTopology

public void calculateTopology()
                       throws CMLException

get all cyclic bonds after spanning tree is created.

Specified by:

calculateTopology in interface SpanningTree

getRingVector

public java.util.Vector getRingVector()

get rings

getRingNucleusVector

public java.util.Vector getRingNucleusVector()
                                      throws CMLException

get all cyclic bonds after spanning tree is created.

Specified by:

getRingNucleusVector in interface SpanningTree

findRingNuclei

public void findRingNuclei()
                    throws CMLException

addChainSet

public void addChainSet(ChainSet chain)

this adds an *existing* chain to the vector (i.e. does not create it). Called from Chain()

Specified by:

addChainSet in interface SpanningTree

toSMILES

public java.lang.String toSMILES()
                          throws CMLException

Specified by:

toSMILES in interface SpanningTree

toString

public java.lang.String toString()

Overrides:

toString in class org.apache.xerces.dom.NodeImpl

main

public static void main(java.lang.String[] args)