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org.xmlcml.cmlimpl.topology
Class TopologyImpl  

java.lang.Object
  PMRDocumentImpl
      org.xmlcml.cmlimpl.subset.SpanningTreeImpl
          org.xmlcml.cmlimpl.topology.TopologyImpl

All Implemented Interfaces:

org.w3c.dom.Document, org.w3c.dom.Node, org.xmlcml.cml.subset.SpanningTree, org.xmlcml.cml.topology.Topology

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public class TopologyImpl

extends org.xmlcml.cmlimpl.subset.SpanningTreeImpl

implements org.xmlcml.cml.topology.Topology

Topology adapts a SpanningTree to have increased function for connection table analysis

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Nested Class Summary
(package private) static class	TopologyImpl.Primes           generates prime numbers for uniquification
class	TopologyImpl.RankMap

 

Field Summary
protected  java.util.HashSet	bondSetSet
protected  int	chainCount
protected  java.util.Vector	chainVector
protected  ChainSetImpl	chMax
protected  int	ringCount
protected  java.util.Vector	ringNucleusVector
protected  java.util.Vector	ringVector
protected  RingNucleusImpl	rnMax

 

Fields inherited from class org.xmlcml.cmlimpl.subset.SpanningTreeImpl

acyclicBondSet, atomElementTable, bondSet, cyclicBondSet, cyclicBondVector, linkTable, linkVector, molecule, startingAtomSet, stElementVector, usedBondSet

 

Fields inherited from interface org.xmlcml.cml.subset.SpanningTree

RESTRUCTURE

 

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

 

Constructor Summary

TopologyImpl()

TopologyImpl(org.xmlcml.cml.subset.BondSet bondSet, org.xmlcml.cml.CMLAtom rootAtom, org.xmlcml.cml.CMLAtom parentAtom)

TopologyImpl(org.xmlcml.cml.CMLMolecule molecule)           adapter promotes SpanningTree to Toplogy; do not reuse sTree

TopologyImpl(org.xmlcml.cml.CMLMolecule molecule, org.xmlcml.cml.subset.AtomSet atomSet)

TopologyImpl(org.xmlcml.cml.CMLMolecule molecule, org.xmlcml.cml.CMLAtom atom)

 

Method Summary
void	addChainSet(org.xmlcml.cml.topology.ChainSet chain)           this adds an *existing* chain to the vector (i.e.
(package private)  void	addSubstituents(org.xmlcml.cml.subset.BondSet bs, java.util.HashSet bondSetSet)
void	calculateCoordinates(boolean update)
void	calculateTopology(boolean update)           get all cyclic bonds after spanning tree is created.
(package private)  void	findChains()           find the chains
void	findRingNuclei()
void	findRings()
(package private)  java.util.HashMap	getAtomInvariants(org.xmlcml.cml.subset.AtomSet atomSet)
org.xmlcml.cml.topology.ChainSet[]	getChainList()           get chains
java.util.Vector	getChainVector()
(package private)  java.lang.String	getInvariant(org.xmlcml.cml.CMLAtom atom)
(package private)  java.util.HashMap	getRankedMap(java.util.ArrayList list)
org.xmlcml.cml.topology.Ring[]	getRingList()           get rings
org.xmlcml.cml.topology.RingNucleus[]	getRingNucleusList()           get ringNuclei
java.util.Vector	getRingNucleusVector()           get all cyclic bonds after spanning tree is created.
java.util.Vector	getRingVector()           get rings
java.util.TreeMap	getUniqueNumbering()           get unique numbering (cf.
static void	main(java.lang.String[] args)
(package private)  void	removeOverlaps()
private  void	storeBonds(java.util.Vector atomVector, int count, org.xmlcml.cml.topology.Ring ring)
java.lang.String	toString()           Convert this Object to a human-readable String.
(package private)  void	updateCoordinates(org.xmlcml.cml.subset.BondSet bondSet)

 

Methods inherited from class org.xmlcml.cmlimpl.subset.SpanningTreeImpl

addAtom, addLink, createSpanningTreeVector, getAcyclicAtomSet, getAcyclicBondSet, getAtomAncestorVector, getAtomElementTable, getAtomSet, getBondSet, getCyclicAtomSet, getCyclicBondSet, getLinkVector, getMolecule, getNonRingAtomSet, getSTElement, getSTElementVector, makeRootElement, processSpTreeVector, toSMILES

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

 

Methods inherited from interface org.xmlcml.cml.subset.SpanningTree

addAtom, addLink, getAcyclicAtomSet, getAcyclicBondSet, getAtomAncestorVector, getAtomElementTable, getAtomSet, getBondSet, getCyclicAtomSet, getCyclicBondSet, getLinkVector, getMolecule, getNonRingAtomSet, getSTElementVector, toSMILES

 

Methods inherited from interface org.w3c.dom.Document

adoptNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createElement, createElementNS, createEntityReference, createProcessingInstruction, createTextNode, getDoctype, getDocumentElement, getDocumentURI, getDomConfig, getElementById, getElementsByTagName, getElementsByTagNameNS, getImplementation, getInputEncoding, getStrictErrorChecking, getXmlEncoding, getXmlStandalone, getXmlVersion, importNode, normalizeDocument, renameNode, setDocumentURI, setStrictErrorChecking, setXmlStandalone, setXmlVersion

 

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

 

Field Detail

ringCount

protected int ringCount

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ringNucleusVector

protected java.util.Vector ringNucleusVector

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chainCount

protected int chainCount

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chainVector

protected java.util.Vector chainVector

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ringVector

protected java.util.Vector ringVector

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rnMax

protected RingNucleusImpl rnMax

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chMax

protected ChainSetImpl chMax

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bondSetSet

protected java.util.HashSet bondSetSet

Constructor Detail

TopologyImpl

public TopologyImpl()

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TopologyImpl

public TopologyImpl(org.xmlcml.cml.CMLMolecule molecule)
             throws org.xmlcml.cml.CMLException

adapter promotes SpanningTree to Toplogy; do not reuse sTree

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TopologyImpl

public TopologyImpl(org.xmlcml.cml.CMLMolecule molecule,
                    org.xmlcml.cml.CMLAtom atom)
             throws org.xmlcml.cml.CMLException

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TopologyImpl

public TopologyImpl(org.xmlcml.cml.CMLMolecule molecule,
                    org.xmlcml.cml.subset.AtomSet atomSet)
             throws org.xmlcml.cml.CMLException

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TopologyImpl

public TopologyImpl(org.xmlcml.cml.subset.BondSet bondSet,
                    org.xmlcml.cml.CMLAtom rootAtom,
                    org.xmlcml.cml.CMLAtom parentAtom)
             throws org.xmlcml.cml.CMLException

Method Detail

findRings

public void findRings()
               throws org.xmlcml.cml.CMLException

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storeBonds

private void storeBonds(java.util.Vector atomVector,
                        int count,
                        org.xmlcml.cml.topology.Ring ring)
                 throws org.xmlcml.cml.CMLException

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calculateTopology

public void calculateTopology(boolean update)
                       throws org.xmlcml.cml.CMLException

get all cyclic bonds after spanning tree is created.

Specified by:

calculateTopology in interface org.xmlcml.cml.topology.Topology

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calculateCoordinates

public void calculateCoordinates(boolean update)

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removeOverlaps

void removeOverlaps()

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updateCoordinates

void updateCoordinates(org.xmlcml.cml.subset.BondSet bondSet)

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addSubstituents

void addSubstituents(org.xmlcml.cml.subset.BondSet bs,
                     java.util.HashSet bondSetSet)

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getRingVector

public java.util.Vector getRingVector()

get rings

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getRingList

public org.xmlcml.cml.topology.Ring[] getRingList()

get rings

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getRingNucleusVector

public java.util.Vector getRingNucleusVector()
                                      throws org.xmlcml.cml.CMLException

get all cyclic bonds after spanning tree is created.

Specified by:

getRingNucleusVector in interface org.xmlcml.cml.topology.Topology

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getRingNucleusList

public org.xmlcml.cml.topology.RingNucleus[] getRingNucleusList()
                                                         throws org.xmlcml.cml.CMLException

get ringNuclei

Specified by:

getRingNucleusList in interface org.xmlcml.cml.topology.Topology

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getChainVector

public java.util.Vector getChainVector()
                                throws org.xmlcml.cml.CMLException

Specified by:

getChainVector in interface org.xmlcml.cml.topology.Topology

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getChainList

public org.xmlcml.cml.topology.ChainSet[] getChainList()
                                                throws org.xmlcml.cml.CMLException

get chains

Specified by:

getChainList in interface org.xmlcml.cml.topology.Topology

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findChains

void findChains()
          throws org.xmlcml.cml.CMLException

find the chains

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findRingNuclei

public void findRingNuclei()
                    throws org.xmlcml.cml.CMLException

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addChainSet

public void addChainSet(org.xmlcml.cml.topology.ChainSet chain)

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

Specified by:

addChainSet in interface org.xmlcml.cml.topology.Topology

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getUniqueNumbering

public java.util.TreeMap getUniqueNumbering()

get unique numbering (cf. Weininger)

Specified by:

getUniqueNumbering in interface org.xmlcml.cml.topology.Topology

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getRankedMap

java.util.HashMap getRankedMap(java.util.ArrayList list)

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getAtomInvariants

java.util.HashMap getAtomInvariants(org.xmlcml.cml.subset.AtomSet atomSet)

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getInvariant

java.lang.String getInvariant(org.xmlcml.cml.CMLAtom atom)

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toString

public java.lang.String toString()

Description copied from class: java.lang.Object

Convert this Object to a human-readable String. There are no limits placed on how long this String should be or what it should contain. We suggest you make it as intuitive as possible to be able to place it into System.out.println() 55 and such.

It is typical, but not required, to ensure that this method never completes abruptly with a java.lang.RuntimeException.

This method will be called when performing string concatenation with this object. If the result is null, string concatenation will instead use "null".

The default implementation returns getClass().getName() + "@" + Integer.toHexString(hashCode()).

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main

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

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

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