org.xmlcml.noncml
Class SDFImpl

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.SDFImpl

public class SDFImpl

extends NonCMLDocumentImpl

implements SDF

class to read and write SDFiles

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.SDF

DATA_HEADER

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

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

SDFImpl(CML outputCML)
form a SDF object from a CML file

Method Summary

Molecule	getMolecule() returns the first Molecule in the document or null if none
void	input(java.io.BufferedReader bReader) input from a Reader.
static void	main(java.lang.String[] args)
java.lang.String	output(java.io.Writer writer) outputs CML as an SDF if possible.
void	setOutputCML(CML outputCML)
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
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

createCMLElement, createMoleculeElement

Methods inherited from class org.xmlcml.cml.CMLDocumentImpl

createCMLDocument, createCMLDocument, debug, 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

SDFImpl

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

form a SDF object from a local file

Throws:

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

SDFImpl

public SDFImpl(CML outputCML)

form a SDF object from a CML file

Method Detail

setOutputCML

public void setOutputCML(CML outputCML)

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

output

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

Parameters:

Writer - writer to output it to

writeData

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

getMolecule

public Molecule getMolecule()

Description copied from interface: CMLDocument

returns the first Molecule in the document or null if none

Overrides:

getMolecule in class CMLDocumentImpl

Tags copied from interface: CMLDocument

Returns:

Molecule the molecule

splitSDF

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

main

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