org.xmlcml.noncml
Class JMEImpl

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.cml.CMLDocumentImpl
                                      |
                                      +--org.xmlcml.noncml.NonCMLDocumentImpl
                                            |
                                            +--org.xmlcml.noncml.JMEImpl

public class JMEImpl

extends NonCMLDocumentImpl

implements JME

class to read and write JME files (Peter Ertl's applet)

See Also:

Serialized Form

Fields inherited from class org.xmlcml.noncml.NonCMLDocumentImpl

atomList, atomParent, bondList, bondParent, bReader, inputCML, inputCMLMolecule, line, natoms, nbonds, outputCML, outputCMLMolecule

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 org.xmlcml.noncml.NonCMLDocument

JME, MDLMOL, SDF, SMILES, XYZ

Fields inherited from interface org.xmlcml.cml.CMLDocument

PACKAGE_NAME

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

JMEImpl(java.io.BufferedReader bReader, java.lang.String id)
form a JME object from a local file

JMEImpl(Molecule outputCMLMolecule)
form a JME object from a CML file

Method Summary

static java.lang.String	cmlBondOrder(int molNumber) translates jme bond orders into JUMBO-MOL orders
static java.lang.String	cmlBondStereo(int molNumber) translates jme numbers into JUMBO-MOL codes
void	input(java.io.BufferedReader bReader) input from a Reader.
static int	jmeBondOrder(java.lang.String cmlCode) translates "CML" codes into jme numbers
static int	jmeBondStereo(java.lang.String cmlCode) translates JUMBO-MOL codes into jme numbers
static void	main(java.lang.String[] args)
java.lang.String	output(java.io.Writer writer) outputs Molecule as a JME
void	setOutputCMLMolecule(Molecule outputCMLMolecule) to output a CML-Molecule in legacy form the molecule must be added to the NonCMLDocument and then the output() method called
java.lang.String	writeAtoms(java.io.Writer writer)
java.lang.String	writeBonds(java.io.Writer writer)
java.lang.String	writeFooter(java.io.Writer writer)
java.lang.String	writeHeader(java.io.Writer writer)

Methods inherited from class org.xmlcml.noncml.NonCMLDocumentImpl

createCMLElement, createMoleculeElement

Methods inherited from class org.xmlcml.cml.CMLDocumentImpl

createCMLDocument, createCMLDocument, debug, getMolecule, test1

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, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

JMEImpl

public JMEImpl(java.io.BufferedReader bReader,
               java.lang.String id)
        throws java.lang.Exception

form a JME object from a local file

Throws:

java.lang.Exception - file was not a standard JME file

JMEImpl

public JMEImpl(Molecule outputCMLMolecule)

form a JME object from a CML file

Method Detail

setOutputCMLMolecule

public void setOutputCMLMolecule(Molecule outputCMLMolecule)

Description copied from interface: NonCMLDocument

to output a CML-Molecule in legacy form the molecule must be added to the NonCMLDocument and then the output() method called

input

public void input(java.io.BufferedReader bReader)
           throws java.io.IOException,
                  CMLException

Description copied from interface: NonCMLDocument

input from a Reader. If the String value is to be input, use a StringReader. This could be used immediately after a default constructor and may be used in the class constructors

jmeBondOrder

public static int jmeBondOrder(java.lang.String cmlCode)

translates "CML" codes into jme numbers

cmlBondOrder

public static java.lang.String cmlBondOrder(int molNumber)

translates jme bond orders into JUMBO-MOL orders

jmeBondStereo

public static int jmeBondStereo(java.lang.String cmlCode)

translates JUMBO-MOL codes into jme numbers

cmlBondStereo

public static java.lang.String cmlBondStereo(int molNumber)

translates jme numbers into JUMBO-MOL codes

output

public java.lang.String output(java.io.Writer writer)
                        throws CMLException,
                               java.io.IOException

outputs Molecule as a JME

Parameters:

Writer - writer to output it to

writeHeader

public java.lang.String writeHeader(java.io.Writer writer)
                             throws CMLException,
                                    java.io.IOException

writeAtoms

public java.lang.String writeAtoms(java.io.Writer writer)
                            throws CMLException,
                                   java.io.IOException

writeBonds

public java.lang.String writeBonds(java.io.Writer writer)
                            throws CMLException,
                                   java.io.IOException

writeFooter

public java.lang.String writeFooter(java.io.Writer writer)
                             throws CMLException,
                                    java.io.IOException

main

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