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org.xmlcml.noncml
Class SDFImpl  

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

All Implemented Interfaces:

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

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public class SDFImpl

extends NonCMLDocumentImpl

implements SDF

class to read and write SDFiles

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Field Summary
(package private)  java.lang.String	id
(package private)  MDLMol	mdlMol

 

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.SDF

DATA_HEADER

 

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

SDFImpl()

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

SDFImpl(org.xmlcml.cml.CML outputCML)           form a SDF object from a CML file

 

Method Summary
org.xmlcml.cml.CMLMolecule	getMolecule()           convenience method: returns the first CMLMolecule in the document or null if none
static void	main(java.lang.String[] args)
java.lang.String	output(java.io.Writer writer)           outputs CML as an SDF if possible.
(package private)  void	output(java.io.Writer writer, org.xmlcml.cml.CMLList list)
void	parse(java.io.BufferedReader bReader)           input from a Reader.
(package private)  void	readData()
static void	splitSDF(java.io.BufferedReader bReader, java.lang.String idBase)
java.lang.String	writeData(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, 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, 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

mdlMol

MDLMol mdlMol

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id

java.lang.String id

Constructor Detail

SDFImpl

public SDFImpl()

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SDFImpl

public SDFImpl(java.io.BufferedReader bReader,
               java.lang.String id)
        throws java.io.IOException,
               org.xmlcml.cml.CMLException

form a SDF object from a local file

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SDFImpl

public SDFImpl(org.xmlcml.cml.CML outputCML)

form a SDF 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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readData

void readData()
        throws java.io.IOException,
               org.xmlcml.cml.CMLException

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output

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

outputs CML as an SDF if possible. This is NOT a faithful representation as I haven't read the spec completely

Specified by:

output in interface NonCMLDocument

Specified by:

output in class NonCMLDocumentImpl

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writeData

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

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output

void output(java.io.Writer writer,
            org.xmlcml.cml.CMLList list)
      throws org.xmlcml.cml.CMLException,
             java.io.IOException

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getMolecule

public org.xmlcml.cml.CMLMolecule getMolecule()

Description copied from interface: org.xmlcml.cml.CMLDocument

convenience method: returns the first CMLMolecule in the document or null if none

Specified by:

getMolecule in interface org.xmlcml.cml.CMLDocument

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splitSDF

public static void splitSDF(java.io.BufferedReader bReader,
                            java.lang.String idBase)
                     throws java.io.IOException,
                            org.xmlcml.cml.CMLException

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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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