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org.xmlcml.noncml
Class JMEImpl  

java.lang.Object
  PMRDocumentImpl
      org.xmlcml.cmlimpl.CMLDocumentImpl
          org.xmlcml.noncml.NonCMLDocumentImpl
              org.xmlcml.noncml.JMEImpl

All Implemented Interfaces:

org.xmlcml.cml.CMLDocument, org.w3c.dom.Document, org.xmlcml.cml.mvc.HasController, JME, org.w3c.dom.Node, NonCMLDocument

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public class JMEImpl

extends NonCMLDocumentImpl

implements JME

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

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Field Summary
(package private)  java.util.Hashtable	serialTable

 

Fields inherited from class org.xmlcml.noncml.NonCMLDocumentImpl

ATOM_FACTORY, atomParent, atomVector, BOND_FACTORY, bondParent, bondVector, bReader, convention, currentLine, DOCUMENT_FACTORY, inputCML, inputCMLMolecule, inputDescription2TypeTable, localDictionary, markLine, MOLECULE_FACTORY, natoms, nbonds, nextLine, nLine, nonCmlDoc, outputCML, outputCMLMolecule, outputDescription2TypeTable, parseFile, selector, SPACE40, SPACE80

 

Fields inherited from class org.xmlcml.cmlimpl.CMLDocumentImpl

CML_DICTIONARY, controller, moleculeVector

 

Fields inherited from interface org.xmlcml.noncml.NonCMLDocument

CASTEP, CIF, CML, CMLARRAY, FORMAT, G94, GAMESS, INPUT_DESCRIPTIONS, INPUT_SUFFIXES, INPUT_TYPES, JCAMP, JME, MDLMOL, MIF, MMCIF, MOL2, MOPAC, MOPACIn, OUTPUT_DESCRIPTIONS, OUTPUT_SUFFIXES, OUTPUT_TYPES, PDB, PDBConect, SDF, SMILES, SWISS, TEST, VAMP, XML, XYZ

 

Fields inherited from interface org.xmlcml.cml.CMLDocument

CML_DICTIONARY_FILENAME, CML_DICTIONARY_NAME, CML_DICTIONARY_NAMESPACE_URI, CML_DICTIONARY_PREFIX, PACKAGE_NAME

 

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

JMEImpl()

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

JMEImpl(org.xmlcml.cml.CMLMolecule 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
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 CMLMolecule as a JME
void	parse(java.io.BufferedReader bReader)           input from a Reader.
(package private)  void	readAtoms(java.util.StringTokenizer st)
(package private)  void	readBonds(java.util.StringTokenizer st)
(package private)  void	readFooter(java.util.StringTokenizer st)
(package private)  void	readHeader(java.util.StringTokenizer st)
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

addDataItem, convertFile, convertList, createAndAddCMLElement, createAndAddMoleculeElement, createCMLDocument, createCMLDocument, createCMLDocument, createCMLElement, createMoleculeElement, getAndCheckVectors, getCurrentLine, getDictionary, getInputDescriptions, getInputSuffixes, getInputTypes, getMoleculeVector, getOutputDescriptions, getOutputSuffixes, getOutputTypes, getSelector, getSuffixFromType, getTypeFromFile, getTypesFromFile, makeDataItem, makeFileStem, outform, parse, peekLine, processLinks, readFortranReal, readNextLine, resetMark, setMark, setOutputCML, setOutputCMLMolecule, setParseFile, setSelector

 

Methods inherited from class org.xmlcml.cmlimpl.CMLDocumentImpl

addTracer, arrayify, createCMLDocument, deArrayify, debug, debug, dereferenceDescendantLinks, dereferenceLinks, getController, getDictionaryFileName, getDictionaryName, getDictionaryNamespaceURI, getDictionaryPrefix, getMolecule, getMoleculeFactory, getMoleculeList, getMoleculeVector, hasLinkElements, isTrace, readXMLTest, removeTracer, setController, setMoleculeFactory, setTrace, test1, trace

 

Methods inherited from class java.lang.Object

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

 

Methods inherited from interface org.xmlcml.noncml.NonCMLDocument

createAndAddMoleculeElement, createMoleculeElement, setOutputCML, setOutputCMLMolecule

 

Methods inherited from interface org.xmlcml.cml.CMLDocument

arrayify, deArrayify, debug, debug, dereferenceLinks, getMolecule, getMoleculeFactory, getMoleculeList, getMoleculeVector, hasLinkElements, parse, readXMLTest, setMoleculeFactory

 

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

serialTable

java.util.Hashtable serialTable

Constructor Detail

JMEImpl

public JMEImpl()

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JMEImpl

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

Convenience: form a JME object from a local file

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JMEImpl

public JMEImpl(org.xmlcml.cml.CMLMolecule outputCMLMolecule)

form a JME object from a CML file

Method Detail

parse

public void parse(java.io.BufferedReader bReader)
           throws java.io.IOException,
                  org.xmlcml.cml.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 after a default constructor either immediately or with some additional customisation and may be used in the class constructors. Note that parse(URL) is inherited from CMLDocument

Specified by:

parse in interface NonCMLDocument

Specified by:

parse in class NonCMLDocumentImpl

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readHeader

void readHeader(java.util.StringTokenizer st)
          throws java.io.IOException,
                 org.xmlcml.cml.CMLException

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readAtoms

void readAtoms(java.util.StringTokenizer st)
         throws java.io.IOException,
                org.xmlcml.cml.CMLException

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readBonds

void readBonds(java.util.StringTokenizer st)
         throws java.io.IOException,
                org.xmlcml.cml.CMLException

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readFooter

void readFooter(java.util.StringTokenizer st)
          throws java.io.IOException,
                 org.xmlcml.cml.CMLException

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jmeBondOrder

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

translates "CML" codes into jme numbers

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cmlBondOrder

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

translates jme bond orders into JUMBO-MOL orders

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jmeBondStereo

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

translates JUMBO-MOL codes into jme numbers

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cmlBondStereo

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

translates jme numbers into JUMBO-MOL codes

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output

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

outputs CMLMolecule as a JME

Specified by:

output in interface NonCMLDocument

Specified by:

output in class NonCMLDocumentImpl

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writeHeader

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

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writeAtoms

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

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writeBonds

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

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writeFooter

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

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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 >> [ noncml overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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