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org.xmlcml.noncml
Class SMILESImpl  

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

All Implemented Interfaces:

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

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public class SMILESImpl

extends NonCMLDocumentImpl

implements SMILES

class to read and write SMILES files

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Field Summary
(package private)  java.util.Hashtable	aromaticTable
protected  java.util.Vector	linkVector
(package private)  java.lang.String	order
(package private)  java.util.Hashtable	serialTable
protected  java.lang.String	smilesString
(package private)  org.xmlcml.cml.subset.SpanningTree	spanningTree

 

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.SMILES

LINKVECTORSIZE, SIMPLE_ELEMENTS

 

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

SMILESImpl()

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

SMILESImpl(org.xmlcml.cml.CMLMolecule outputCMLMolecule)           form a SMILES object from a CML file

 

Method Summary
(package private)  void	addBondToParent(org.xmlcml.cml.CMLAtom atom, org.xmlcml.cml.subset.STElement newatomElement)
(package private)  void	addLink(org.xmlcml.cml.CMLAtom atom)           adds link to smilesString if appropriate
(package private)  int	builtinElementLength(java.lang.String s)           length of builtin SMILES Chemical element? Case-sensitive no match returns 0
static java.lang.String	cmlBondOrder(java.lang.String smilesBond)           translates SMILES bond orders into JUMBO-MOL orders
(package private)  org.xmlcml.cml.CMLAtom	createAtomFromSMILESAtom(SMILESAtom sa)           create a new atom from s.
(package private)  org.xmlcml.cml.CMLAtom	createAtomFromString(java.lang.String s)
static org.xmlcml.cml.CMLMolecule	createMolecule(java.lang.String s)
static SMILES	createSMILESFromString(java.lang.String s)
(package private)  void	interpretString(org.xmlcml.cml.subset.STElement parentElement, java.lang.String s)           interprets a SMILES string
(package private)  boolean	is2LetterElement(java.lang.String s)           is an element a valid SMILES Chemical element?
static void	main(java.lang.String[] args)
java.lang.String	output(java.io.Writer writer)           outputs CMLMolecule as a SMILES
void	parse(java.io.BufferedReader bReader)           input from a Reader.
void	parse(java.lang.String line)           input from the Smiles String
(package private)  void	processLink(org.xmlcml.cml.subset.STElement node2, char number)           process numeric link in SMILES
(package private)  void	processSmilesString()
(package private)  void	processSpanningTree(org.xmlcml.cml.subset.STElement stElement)
(package private)  void	removeElements(java.util.Vector theVector, java.util.Vector removeVector)
(package private)  void	resetLinkVector()           set linkVector to have (10) preset elements, initially null
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

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

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linkVector

protected java.util.Vector linkVector

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smilesString

protected java.lang.String smilesString

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order

java.lang.String order

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spanningTree

org.xmlcml.cml.subset.SpanningTree spanningTree

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aromaticTable

java.util.Hashtable aromaticTable

Constructor Detail

SMILESImpl

public SMILESImpl()

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SMILESImpl

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

form a SMILES object from a local file

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SMILESImpl

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

form a SMILES 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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parse

public void parse(java.lang.String line)
           throws org.xmlcml.cml.CMLException

input from the Smiles String

Specified by:

parse in interface SMILES

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createSMILESFromString

public static SMILES createSMILESFromString(java.lang.String s)
                                     throws org.xmlcml.cml.CMLException

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createMolecule

public static org.xmlcml.cml.CMLMolecule createMolecule(java.lang.String s)
                                                 throws org.xmlcml.cml.CMLException

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interpretString

void interpretString(org.xmlcml.cml.subset.STElement parentElement,
                     java.lang.String s)
               throws org.xmlcml.cml.CMLException

interprets a SMILES string

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createAtomFromSMILESAtom

org.xmlcml.cml.CMLAtom createAtomFromSMILESAtom(SMILESAtom sa)
                                          throws org.xmlcml.cml.CMLException

create a new atom from s. The Node is filled with the new details

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createAtomFromString

org.xmlcml.cml.CMLAtom createAtomFromString(java.lang.String s)
                                      throws org.xmlcml.cml.CMLException

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addBondToParent

void addBondToParent(org.xmlcml.cml.CMLAtom atom,
                     org.xmlcml.cml.subset.STElement newatomElement)
               throws org.xmlcml.cml.CMLException

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processLink

void processLink(org.xmlcml.cml.subset.STElement node2,
                 char number)
           throws org.xmlcml.cml.CMLException

process numeric link in SMILES

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resetLinkVector

void resetLinkVector()

set linkVector to have (10) preset elements, initially null

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builtinElementLength

int builtinElementLength(java.lang.String s)

length of builtin SMILES Chemical element? Case-sensitive no match returns 0

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is2LetterElement

boolean is2LetterElement(java.lang.String s)

is an element a valid SMILES Chemical element?

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processSmilesString

void processSmilesString()

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processSpanningTree

void processSpanningTree(org.xmlcml.cml.subset.STElement stElement)
                   throws org.xmlcml.cml.CMLException

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addLink

void addLink(org.xmlcml.cml.CMLAtom atom)

adds link to smilesString if appropriate

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removeElements

void removeElements(java.util.Vector theVector,
                    java.util.Vector removeVector)

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SMILESBondOrder

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

translates "CML" codes into SMILES symbols

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cmlBondOrder

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

translates SMILES bond orders into JUMBO-MOL orders

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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 SMILES

Specified by:

output in interface NonCMLDocument

Specified by:

output in class NonCMLDocumentImpl

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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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