org.openscience.cdk.iupac.parser

Class NomParser

java.lang.Object

org.openscience.cdk.iupac.parser.NomParser

All Implemented Interfaces:

NomParserConstants

Deprecated.

The OPSIN (http://opsin.ch.cam.ac.uk/) tool offers a more comprehensive alternative to this parsers functionality.

public class NomParser
extends Object
implements NomParserConstants

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 Summary

Fields

Modifier and Type	Field and Description
Token	jj_nt Deprecated. Next token.
Token	token Deprecated. Current token.
NomParserTokenManager	token_source Deprecated. Generated Token Manager.

Fields inherited from interface org.openscience.cdk.iupac.parser.NomParserConstants

A, ACTINIUM, AL, ALUMINIUM, ALUMINO, AMERCIUM, AMIDE, AMINE, AMINO, AN, ANTIMONY, ARSENIC, BARIUM, BERKELIUM, BERYLLIUM, BISMUTH, BOHRIUM, BROMO, BUT, CADMIUM, CALCIUM, CALIFORNIUM, CERIUM, CESIUM, CHLORO, CHROMIUM, COBALT, COMMA, CONSTANT, CONT, COPPER, COS, CURIUM, CYCLO, DASH, DEC, DEFAULT, DI, DIGIT, DO, DUBNIUM, DYSPROSIUM, E, EICOS, EINSTEINIUM, EN, EOF, EOL, ERBIUM, ETH, EUROPIUM, FERMIUM, FLUORO, FRANCIUM, GADOLINIUM, GALLIUM, GERMAINIUM, GOLD, HAFNIUM, HASSIUM, HEN, HENICOS, HEPT, HEX, HOLMIUM, HYDROXY, INDIUM, IODO, IRIDIUM, IRON, LANTHANUM, LAWRENCIUM, LEAD, LITHIUM, LITHO, LUTETIUM, MAGNESIUM, MANGANESE, MECURY, MEITMERIUM, MENDELEVIUM, METH, MOLYBDENUM, NEODYMIUM, NEPTUNIUM, NICKEL, NIOBIUM, NITRILE, NITRO, NOBELIUM, NON, OATE, OCT, OICACID, OL, ONE, OSMIUM, OXO, OYLCHLORIDE, PALLADIUM, PENT, PHENYL, PLATINUM, PLUTONIUM, POLONIUM, POTASSIUM, PRASEODYMIUM, PROMETHIUM, PROP, PROTACTINIUM, RADIUM, RHENIUM, RHODIUM, RUBIDIUM, RUTHENIUM, RUTHERFORDIUM, SANARIUM, SCANDIUM, SEABORGIUM, SELENIUM, SILVER, SODIUM, SPACE, STRONTIUM, TANTALUM, TECHNETIUM, TELLURIUM, TERBIUM, TETR, THALLIUM, THORIUM, THULIUM, TIN, TITANIUM, tokenImage, TRI, TUNGSTEN, UNDEC, URANIUM, VANADIUM, YL, YN, YTTERBIUM, YTTRIUM, ZINC, ZIRCONIUM

Constructor Summary

Constructors

Constructor and Description
NomParser(InputStream stream) Deprecated. Constructor with InputStream.
NomParser(InputStream stream, String encoding) Deprecated. Constructor with InputStream and supplied encoding
NomParser(NomParserTokenManager tm) Deprecated. Constructor with generated Token Manager.
NomParser(Reader stream) Deprecated. Constructor.

Method Summary

Modifier and Type	Method and Description
void	allBaseNumbers() Deprecated. The usual numbers .
void	attachLocationSpecified() Deprecated. An attach position has been specified using a comma seperated list followed by a dash
void	bondType() Deprecated. Tokens which affect the bond order of the first bond.
void	chainPrefix() Deprecated. A list of known tokens denoting a chain's length.
void	completeChemicalName() Deprecated. The general form all chemical names must follow.
void	connectingFunctionalGroupsConstruct() Deprecated. The layout of a functional group(s) which can connect anywhere.
void	connectingFunctionalGroupSuffix() Deprecated. Functional groups suffixs for groups which can be connected anywhere along the main chain.
void	cycle() Deprecated. Deals with cyclic main chains.
void	dBlockMetals() Deprecated.
void	disable_tracing() Deprecated. Disable tracing.
void	enable_tracing() Deprecated. Enable tracing.
void	endFunctionalGroups() Deprecated. Functional groups which occur at the end of the main chain and need a connecting "an".
void	fBlockMetals() Deprecated.
void	functionalGroupPrefix() Deprecated. The functional group part of the prefix
static IAtomContainer	generate(String stringToParse) Deprecated. Parses the chemical name and returns the built molecule.
static IAtomContainer	generate(String stringToParse, IChemObjectBuilder builder) Deprecated. Parses the chemical name and returns the built molecule.
ParseException	generateParseException() Deprecated. Generate ParseException.
Token	getNextToken() Deprecated. Get the next Token.
Token	getToken(int index) Deprecated. Get the specific Token.
void	groupOneMetals() Deprecated.
void	groupTwoMetals() Deprecated.
void	mainChainConstruct() Deprecated. Main chains are compulsary and consist of an optional "cyclo", a length prefix and a posfix denoting functional groups.
void	mainChainPrefix() Deprecated. Deal with the main chain's length.
void	mainChainSuffix() Deprecated. Figure out the functional group by the main chain's suffix.
void	oneAttachLocation() Deprecated. Only one attach location specified, should be followed by a dash.
void	pBlockMetals() Deprecated.
void	prefixConstruct() Deprecated. Allows 1 or more prefixes
void	prefixFunctionalGroups() Deprecated.
void	prefixType() Deprecated.
void	prioritySubstituents() Deprecated. Things which have sub chains branching off them but the molecule has no main chain.
void	prioritySubstituentsFunGroups() Deprecated. Things which have sub chains branching off them and the molecule does have a main chain.
void	ReInit(InputStream stream) Deprecated. Reinitialise.
void	ReInit(InputStream stream, String encoding) Deprecated. Reinitialise.
void	ReInit(NomParserTokenManager tm) Deprecated. Reinitialise.
void	ReInit(Reader stream) Deprecated. Reinitialise.
void	specialCase() Deprecated. Deal with special cases where the rules don't apply.
void	subChain() Deprecated. The substituent part of the prefix
void	tensNoUnits() Deprecated. Deal with fragments refering to the positioning of the base numbers (denoting their magnitude)
void	tensWithUnits() Deprecated. Deals with numbers above 30 where the base numbers set appear twice.
void	twoOrThreeAttachLocations() Deprecated. Two or three attach locations specidied, handle the second and if needed, the third one here.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail

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 Detail

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.