org.xmlcml.noncml
Class SMILESImpl

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.SMILESImpl

public class SMILESImpl

extends NonCMLDocumentImpl

implements SMILES

class to read and write SMILES files

See Also:

Serialized Form

Field Summary

protected java.util.Vector	linkVector
protected java.lang.String	smilesString

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.SMILES

LINKVECTORSIZE, SIMPLE_ELEMENTS

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

SMILESImpl()

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

SMILESImpl(Molecule outputCMLMolecule)
form a SMILES object from a CML file

Method Summary

static java.lang.String	cmlBondOrder(java.lang.String smilesBond) translates SMILES bond orders into JUMBO-MOL orders
void	input(java.io.BufferedReader bReader) input from a Reader.
void	input(java.lang.String smilesString) input from the Smiles String
static void	main(java.lang.String[] args)
java.lang.String	output(java.io.Writer writer) outputs Molecule as a SMILES
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 java.lang.String	SMILESBondOrder(java.lang.String cmlCode) translates "CML" codes into SMILES symbols
java.lang.String	writeAtoms(java.io.Writer writer)
java.lang.String	writeBonds(java.io.Writer writer)
java.lang.String	writeFooter(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

Field Detail

linkVector

protected java.util.Vector linkVector

smilesString

protected java.lang.String smilesString

Constructor Detail

SMILESImpl

public SMILESImpl()

SMILESImpl

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

form a SMILES object from a local file

Throws:

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

SMILESImpl

public SMILESImpl(Molecule outputCMLMolecule)

form a SMILES 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

input

public void input(java.lang.String smilesString)
           throws CMLException,
                  java.io.IOException

input from the Smiles String

Specified by:

input in interface SMILES

SMILESBondOrder

public static java.lang.String SMILESBondOrder(java.lang.String cmlCode)

translates "CML" codes into SMILES symbols

cmlBondOrder

public static java.lang.String cmlBondOrder(java.lang.String smilesBond)

translates SMILES bond orders into JUMBO-MOL orders

output

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

outputs Molecule as a SMILES

Parameters:

Writer - writer to output it to

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)