Class NomParser

java.lang.Object
org.openscience.cdk.iupac.parser.NomParser
All Implemented Interfaces:
NomParserConstants

public class NomParser extends Object implements NomParserConstants
Deprecated.
The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.
A class partly generated by JavaCC which breaks down the chemical name into computable subparts and passes these parts to the MoleculeBuilder.
Author:
David Robinson (University of Manchester), Bhupinder Sandhu, Stephen Tomkinson
Keywords:
IUPAC name
  • Field Details

    • token_source

      public NomParserTokenManager token_source
      Deprecated.
      Generated Token Manager.
    • token

      public Token token
      Deprecated.
      Current token.
    • jj_nt

      public Token jj_nt
      Deprecated.
      Next token.
  • Constructor Details

    • NomParser

      public NomParser(InputStream stream)
      Deprecated.
      Constructor with InputStream.
    • NomParser

      public NomParser(InputStream stream, String encoding)
      Deprecated.
      Constructor with InputStream and supplied encoding
    • NomParser

      public NomParser(Reader stream)
      Deprecated.
      Constructor.
    • NomParser

      public NomParser(NomParserTokenManager tm)
      Deprecated.
      Constructor with generated Token Manager.
  • Method Details

    • generate

      public static IAtomContainer generate(String stringToParse) throws ParseException, CDKException
      Deprecated.
      Parses the chemical name and returns the built molecule. It uses the DefaultChemObjectBuilder to create a data model.
      Parameters:
      stringToParse - A case-insensitive name of the chemical to build.
      Returns:
      A molecule which represents the interpretation of the name.
      Throws:
      ParseException - Any error which occur in the parsing get wrapped up in a ParseException and thrown.
      CDKException
    • generate

      public static IAtomContainer generate(String stringToParse, IChemObjectBuilder builder) throws ParseException, CDKException
      Deprecated.
      Parses the chemical name and returns the built molecule. It uses the given IChemObjectBuilder to create a data model.
      Parameters:
      stringToParse - A case-insensitive name of the chemical to build.
      Returns:
      A molecule which represents the interpretation of the name.
      Throws:
      ParseException - Any error which occur in the parsing get wrapped up in a ParseException and thrown.
      CDKException
    • completeChemicalName

      public final void completeChemicalName() throws ParseException
      Deprecated.
      The general form all chemical names must follow.
      Throws:
      ParseException
    • prefixConstruct

      public final void prefixConstruct() throws ParseException
      Deprecated.
      Allows 1 or more prefixes
      Throws:
      ParseException
    • prefixType

      public final void prefixType() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • subChain

      public final void subChain() throws ParseException
      Deprecated.
      The substituent part of the prefix
      Throws:
      ParseException
    • attachLocationSpecified

      public final void attachLocationSpecified() throws ParseException
      Deprecated.
      An attach position has been specified using a comma seperated list followed by a dash
      Throws:
      ParseException
    • oneAttachLocation

      public final void oneAttachLocation() throws ParseException
      Deprecated.
      Only one attach location specified, should be followed by a dash.
      Throws:
      ParseException
    • twoOrThreeAttachLocations

      public final void twoOrThreeAttachLocations() throws ParseException
      Deprecated.
      Two or three attach locations specidied, handle the second and if needed, the third one here.
      Throws:
      ParseException
    • chainPrefix

      public final void chainPrefix() throws ParseException
      Deprecated.
      A list of known tokens denoting a chain's length.
      Throws:
      ParseException
    • specialCase

      public final void specialCase() throws ParseException
      Deprecated.
      Deal with special cases where the rules don't apply.
      Throws:
      ParseException
    • allBaseNumbers

      public final void allBaseNumbers() throws ParseException
      Deprecated.
      The usual numbers .
      Throws:
      ParseException
    • tensNoUnits

      public final void tensNoUnits() throws ParseException
      Deprecated.
      Deal with fragments refering to the positioning of the base numbers (denoting their magnitude)
      Throws:
      ParseException
    • tensWithUnits

      public final void tensWithUnits() throws ParseException
      Deprecated.
      Deals with numbers above 30 where the base numbers set appear twice. For example, in the tens and the units.
      Throws:
      ParseException
    • functionalGroupPrefix

      public final void functionalGroupPrefix() throws ParseException
      Deprecated.
      The functional group part of the prefix
      Throws:
      ParseException
    • mainChainConstruct

      public final void mainChainConstruct() throws ParseException
      Deprecated.
      Main chains are compulsary and consist of an optional "cyclo", a length prefix and a posfix denoting functional groups.
      Throws:
      ParseException
    • cycle

      public final void cycle() throws ParseException
      Deprecated.
      Deals with cyclic main chains.
      Throws:
      ParseException
    • mainChainPrefix

      public final void mainChainPrefix() throws ParseException
      Deprecated.
      Deal with the main chain's length.
      Throws:
      ParseException
    • bondType

      public final void bondType() throws ParseException
      Deprecated.
      Tokens which affect the bond order of the first bond.
      Throws:
      ParseException
    • mainChainSuffix

      public final void mainChainSuffix() throws ParseException
      Deprecated.
      Figure out the functional group by the main chain's suffix.
      Throws:
      ParseException
    • endFunctionalGroups

      public final void endFunctionalGroups() throws ParseException
      Deprecated.
      Functional groups which occur at the end of the main chain and need a connecting "an".
      Throws:
      ParseException
    • connectingFunctionalGroupsConstruct

      public final void connectingFunctionalGroupsConstruct() throws ParseException
      Deprecated.
      The layout of a functional group(s) which can connect anywhere. No number specified, or a number list specified.
      Throws:
      ParseException
    • connectingFunctionalGroupSuffix

      public final void connectingFunctionalGroupSuffix() throws ParseException
      Deprecated.
      Functional groups suffixs for groups which can be connected anywhere along the main chain.
      Throws:
      ParseException
    • prefixFunctionalGroups

      public final void prefixFunctionalGroups() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • prioritySubstituentsFunGroups

      public final void prioritySubstituentsFunGroups() throws ParseException
      Deprecated.
      Things which have sub chains branching off them and the molecule does have a main chain.
      Throws:
      ParseException
    • prioritySubstituents

      public final void prioritySubstituents() throws ParseException
      Deprecated.
      Things which have sub chains branching off them but the molecule has no main chain.
      Throws:
      ParseException
    • groupOneMetals

      public final void groupOneMetals() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • groupTwoMetals

      public final void groupTwoMetals() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • dBlockMetals

      public final void dBlockMetals() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • pBlockMetals

      public final void pBlockMetals() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • fBlockMetals

      public final void fBlockMetals() throws ParseException
      Deprecated.
      Throws:
      ParseException
    • ReInit

      public void ReInit(InputStream stream)
      Deprecated.
      Reinitialise.
    • ReInit

      public void ReInit(InputStream stream, String encoding)
      Deprecated.
      Reinitialise.
    • ReInit

      public void ReInit(Reader stream)
      Deprecated.
      Reinitialise.
    • ReInit

      public void ReInit(NomParserTokenManager tm)
      Deprecated.
      Reinitialise.
    • getNextToken

      public final Token getNextToken()
      Deprecated.
      Get the next Token.
    • getToken

      public final Token getToken(int index)
      Deprecated.
      Get the specific Token.
    • generateParseException

      public ParseException generateParseException()
      Deprecated.
      Generate ParseException.
    • enable_tracing

      public final void enable_tracing()
      Deprecated.
      Enable tracing.
    • disable_tracing

      public final void disable_tracing()
      Deprecated.
      Disable tracing.