org.openscience.cdk.smiles.smarts.parser

Class SMARTSParser

java.lang.Object

org.openscience.cdk.smiles.smarts.parser.SMARTSParser

All Implemented Interfaces:

SMARTSParserConstants, SMARTSParserTreeConstants

public class SMARTSParser
extends Object
implements SMARTSParserTreeConstants, SMARTSParserConstants

This parser implements a nearly complete subset of the SMARTS syntax as defined on the Daylight website.

Example code using SMARTS substructure search looks like:

 SmilesParser sp = new SmilesParser();
 AtomContainer atomContainer = sp.parseSmiles("CC(=O)OC(=O)C");
 QueryAtomContainer query = SMARTSParser.parse("C*C");
 boolean queryMatch = UniversalIsomorphismTester.isSubgraph(atomContainer, query);
 

See the cdk.test.smiles.smarts.parser.ParserTest for examples of the implemented subset. This parser is based on JJTree and it generates an AST (Abstract Syntax Tree)

To get the AST, the code looks like:

 SMARTSParser parser = new SMARTSParser(new java.io.StringReader("C*C"));
 ASTStart = parser.start();
 

Author:

Dazhi Jiao

See Also:

SMARTSAtom

Belongs to CDK module:

smarts

Keywords:

SMARTS, substructure search

Created on:

2007-04-23

Requires:

ant1.6

Field Summary

Fields

Modifier and Type	Field and Description
Token	jj_nt Next token.
protected JJTSMARTSParserState	jjtree
Token	token Current token.
SMARTSParserTokenManager	token_source Generated Token Manager.

Fields inherited from interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserTreeConstants

JJTALIPHATIC, JJTANYATOM, JJTAROMATIC, JJTATOM, JJTATOMICMASS, JJTATOMICNUMBER, JJTCHARGE, JJTCHIRALITY, JJTELEMENT, JJTEXPLICITATOM, JJTEXPLICITCONNECTIVITY, JJTEXPLICITHIGHANDBOND, JJTEXPLICITHIGHANDEXPRESSION, JJTGROUP, JJTHYBRDIZATIONNUMBER, JJTIMPLICITHCOUNT, JJTIMPLICITHIGHANDBOND, JJTIMPLICITHIGHANDEXPRESSION, JJTLOWANDBOND, JJTLOWANDEXPRESSION, jjtNodeName, JJTNONCHHEAVYATOM, JJTNOTBOND, JJTNOTEXPRESSION, JJTORBOND, JJTOREXPRESSION, JJTPERIODICGROUPNUMBER, JJTREACTION, JJTRECURSIVESMARTSEXPRESSION, JJTRINGCONNECTIVITY, JJTRINGIDENTIFIER, JJTRINGMEMBERSHIP, JJTSIMPLEBOND, JJTSMALLESTRINGSIZE, JJTSMARTS, JJTSTART, JJTTOTALCONNECTIVITY, JJTTOTALHCOUNT, JJTVALENCE, JJTVOID

Fields inherited from interface org.openscience.cdk.smiles.smarts.parser.SMARTSParserConstants

a, A, AC, AG, AL, AM, ANY_BOND, AR, AR_BOND, as, AS, AT, ATOM_EXPRESSION, AU, B, BA, BE, BI, BK, BR, c, C, CA, CARET, CD, CE, CF, CL, CM, CO, CR, CS, CU, D, D_BOND, DEFAULT, DIGIT, DN_OR_UNSPECIFIED_S_BOND, DN_S_BOND, DOLLAR, DY, EOF, ER, ES, EU, F, FE, FM, FR, G, GA, GD, GE, h, H, H_AND, HE, HF, HG, HO, HX, I, IN, IR, K, KR, L_AND, L_BRACKET, L_PAREN, LA, LI, LR, LU, MD, MG, MN, MO, n, N, NA, NB, ND, NE, NI, NO, NOT, NP, o, O, OR, OS, p, P, PA, PB, PD, PLUS, PM, PO, PR, PT, PU, Q_MARK, r, R, R_BOND, R_BRACKET, R_PAREN, RA, RB, RE, RH, RN, RU, s, S, S_BOND, SB, SC, se, SE, SI, SM, SN, SR, T_BOND, TA, TB, TC, TE, TH, TI, TL, TM, tokenImage, U, UP_OR_UNSPECIFIED_S_BOND, UP_S_BOND, v, V, W, WILDCARD, WS, x, X, XE, Y, YB, ZN, ZR

Constructor Summary

Constructors

Constructor and Description
SMARTSParser(InputStream stream) Constructor with InputStream.
SMARTSParser(InputStream stream, String encoding) Constructor with InputStream and supplied encoding
SMARTSParser(Reader stream) Constructor.
SMARTSParser(SMARTSParserTokenManager tm) Constructor with generated Token Manager.

Method Summary

Methods

Modifier and Type	Method and Description
void	Aliphatic()
void	AnyAtom()
void	Aromatic()
org.openscience.cdk.smiles.smarts.parser.ASTAtom	AtomExpression()
void	AtomicMass()
void	AtomicNumber()
void	Charge()
void	Chirality()
void	disable_tracing() Disable tracing.
void	enable_tracing() Enable tracing.
void	ExplicitAtomExpression()
void	ExplicitConnectivity()
void	ExplicitHighAndBond()
void	ExplicitHighAndExpression()
ParseException	generateParseException() Generate ParseException.
Token	getNextToken() Get the next Token.
Token	getToken(int index) Get the specific Token.
void	GroupExpression()
void	HybridizationNumber()
void	ImplicitHCount()
void	ImplicitHighAndBond()
void	ImplicitHighAndExpression()
void	LowAndBond()
void	LowAndExpression()
void	NoHydrogenElement()
void	NonCHHeavyAtom()
void	NotBond()
void	NotExpression()
void	OrBond()
void	OrExpression()
static QueryAtomContainer	parse(String smarts, IChemObjectBuilder builder) This method parses a Smarts String and returns an instance of QueryAtomContainer
void	PeriodicGroupNumber()
void	PrimitiveAtomExpression()
void	ReactionExpression()
void	RecursiveSmartsExpression()
void	ReInit(InputStream stream) Reinitialise.
void	ReInit(InputStream stream, String encoding) Reinitialise.
void	ReInit(Reader stream) Reinitialise.
void	ReInit(SMARTSParserTokenManager tm) Reinitialise.
void	RingConnectivity()
void	RingIdentifier()
void	RingMembership()
void	SimpleBond()
void	SmallestRingSize()
void	SmartsExpression()
org.openscience.cdk.smiles.smarts.parser.ASTStart	Start() Start ::= <ReactionExpression> <#_WS> ReactionExpression ::= <GroupExpression>? (">" <GroupExpression>? ">" <GroupExpression>?)? GroupExpression ::= ["("] <SmartsExpresion> [")"] ( "." ["("] <SmartsExpression> [")"] )* SmartsExpression ::= <AtomExpression> ( ( [ <LowAndBond> ] ( <Digit> | <AtomExpression> ) ) | ( "(" [ <LowAndBond> ] <SmartsExpression> ")" ) )* AtomExpression ::= ( "[" [ <AtomicMass> ] <LowAndExpression> [:<Digit>+] "]" ) | <ExplicitAtomExpression> LowAndBond ::= <OrBond> [ ";" <AndBond> ] OrBond ::= <ExplicitHighAndBond> [ "," <OrBond> ] ExplicitHighAndBond ::= <ImplicitHighAndBond> [ "&" <ExplicitHighAndBond> ] ImplicitHighAndBond ::= <NotBond> [ <ImplicitHighAndBond> ] NotBond ::= [ "!" ] <SimpleBond> SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@" ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I" | "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ] LowAndExpression ::= <OrExpression> ( ";" <LowAndExpression> )? OrExpression ::= <ExplicitHighAndExpression> ( "," <OrExpression> ) ? ExplicitHighAndExpression ::= <ImplicitHighAndExpression> ( "&" <ExplicitHighAndExpression> )? ImplicitHighAndExpression ::= <NotExpression> ( <ImplicitHighAndExpression> ) ? NotExpression ::= "!" ( <PrimitiveAtomExpression> | <RecursiveSmartsExpression> ) RecursiveSmartsExpression ::= "$" "(" <SmartsExpression> ")" PrimitiveAtomExpression ::= <NonHydrogenElement> | "*" | "A" | "a" | "D" (<Digits>)? | "H" (<Digits>)? | "h" (<Digits>)? | "R" (<Digit>+)? | "r" (<Digit>+)? | "v" (<Digit>+)? | "#X" | "G" (<DIGIT>+) | "X" (<Digit>+)? | "x" (<Digit>+)? | "^" (<DIGIT>) | ("+" | "-") (<Digit>+)? | "#" (<Digit>+) | "@" | "@@" | <Digit>+ Digit ::= ( "0" - "9") NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" | "TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" | "SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" | "PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" | "HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" | "PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" | "B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" | "c" | "o" | "n" | "p" | "as" | "se" ]
void	TotalConnectivity()
void	TotalHCount()
void	Valence()

Methods inherited from class java.lang.Object

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

Field Detail

jjtree

protected JJTSMARTSParserState jjtree

token_source

public SMARTSParserTokenManager token_source

Generated Token Manager.

token

public Token token

Current token.

jj_nt

public Token jj_nt

Next token.

Constructor Detail

SMARTSParser

public SMARTSParser(InputStream stream)

Constructor with InputStream.

SMARTSParser

public SMARTSParser(InputStream stream,
            String encoding)

Constructor with InputStream and supplied encoding

SMARTSParser

public SMARTSParser(Reader stream)

Constructor.

SMARTSParser

public SMARTSParser(SMARTSParserTokenManager tm)

Constructor with generated Token Manager.

Method Detail

parse

public static QueryAtomContainer parse(String smarts,
                       IChemObjectBuilder builder)

This method parses a Smarts String and returns an instance of QueryAtomContainer

Start

public final org.openscience.cdk.smiles.smarts.parser.ASTStart Start()
                                                              throws ParseException

Start ::= <ReactionExpression> <#_WS>
        ReactionExpression ::= <GroupExpression>? (">" <GroupExpression>? ">" <GroupExpression>?)?
           GroupExpression ::= ["("] <SmartsExpresion> [")"] ( "." ["("] <SmartsExpression> [")"] )*
          SmartsExpression ::= <AtomExpression> ( 
                                                                        ( [ <LowAndBond> ] ( <Digit> | <AtomExpression> ) ) |
                                                                        ( "(" [ <LowAndBond> ] <SmartsExpression> ")" ) )*
                      AtomExpression ::= ( "[" [ <AtomicMass> ] <LowAndExpression> [:<Digit>+] "]" ) | <ExplicitAtomExpression>
                LowAndBond ::= <OrBond> [ ";" <AndBond> ]
                    OrBond ::= <ExplicitHighAndBond> [ "," <OrBond> ]
       ExplicitHighAndBond ::= <ImplicitHighAndBond> [ "&" <ExplicitHighAndBond> ]
       ImplicitHighAndBond ::= <NotBond> [ <ImplicitHighAndBond> ]
                   NotBond ::= [ "!" ] <SimpleBond>
                SimpleBond ::= "/" | "\\" | "/?" | "\\?" | "=" | "#" | "~" | "@"
    ExplicitAtomExpression ::= [ "B" | "C" | "N" | "O" | "P" | "S" | "F" | "CL" | "BR" | "I" 
                               | "c" | "o" | "n" | "*" | "A" | "a" | "p" | "as" | "se" ] 
          LowAndExpression ::= <OrExpression> ( ";" <LowAndExpression> )?
              OrExpression ::= <ExplicitHighAndExpression> ( "," <OrExpression> ) ?
 ExplicitHighAndExpression ::= <ImplicitHighAndExpression> ( "&" <ExplicitHighAndExpression> )?
 ImplicitHighAndExpression ::= <NotExpression> ( <ImplicitHighAndExpression> ) ?
             NotExpression ::= "!" ( <PrimitiveAtomExpression> | <RecursiveSmartsExpression> )
 RecursiveSmartsExpression ::= "$" "(" <SmartsExpression> ")"
   PrimitiveAtomExpression ::= <NonHydrogenElement> | "*" | "A" | "a" | "D" (<Digits>)? | "H" (<Digits>)? | "h" (<Digits>)?
                               | "R" (<Digit>+)? | "r" (<Digit>+)? | "v" (<Digit>+)? | "#X" | "G" (<DIGIT>+)  
                               | "X" (<Digit>+)? | "x" (<Digit>+)? | "^" (<DIGIT>)
                               | ("+" | "-") (<Digit>+)? | "#" (<Digit>+) | "@" | "@@" | <Digit>+
                     Digit ::= ( "0" - "9")
        NonHydrogenElement ::= [ "HE" | "LI" | "BE" | "NE" | "NA" | "MG" | "AL" | "SI" | "AR" | "CA" | "SC" |
                               "TI" | "CR" | "MN" | "FE" | "CO" | "NI" | "CU" | "ZN" | "GA" | "GE" | "AS" |
                               "SE" | "BR" | "KR" | "RB" | "SR" | "ZR" | "NB" | "MO" | "TC" | "RU" | "RH" |
                               "PD" | "AG" | "CD" | "IN" | "SN" | "SB" | "TE" | "XE" | "CS" | "BA" | "LA" |
                               "HF" | "TA" | "RE" | "OS" | "IR" | "PT" | "AU" | "HG" | "TL" | "PB" | "BI" |
                               "PO" | "AT" | "RN" | "FR" | "RA" | "AC" | "TH" | "PA" |
                               "B" | "C" | "N" | "O" | "F" | "P" | "S" | "K" | "V" | "Y" | "I" | "U" |
                               "c" | "o" | "n" | "p" | "as" | "se" ]
 

Throws:

ParseException

ReactionExpression

public final void ReactionExpression()
                              throws ParseException

Throws:

ParseException

GroupExpression

public final void GroupExpression()
                           throws ParseException

Throws:

ParseException

SmartsExpression

public final void SmartsExpression()
                            throws ParseException

Throws:

ParseException

AtomExpression

public final org.openscience.cdk.smiles.smarts.parser.ASTAtom AtomExpression()
                                                                      throws ParseException

Throws:

ParseException

LowAndBond

public final void LowAndBond()
                      throws ParseException

Throws:

ParseException

OrBond

public final void OrBond()
                  throws ParseException

Throws:

ParseException

ExplicitHighAndBond

public final void ExplicitHighAndBond()
                               throws ParseException

Throws:

ParseException

ImplicitHighAndBond

public final void ImplicitHighAndBond()
                               throws ParseException

Throws:

ParseException

NotBond

public final void NotBond()
                   throws ParseException

Throws:

ParseException

SimpleBond

public final void SimpleBond()
                      throws ParseException

Throws:

ParseException

ExplicitAtomExpression

public final void ExplicitAtomExpression()
                                  throws ParseException

Throws:

ParseException

LowAndExpression

public final void LowAndExpression()
                            throws ParseException

Throws:

ParseException

OrExpression

public final void OrExpression()
                        throws ParseException

Throws:

ParseException

ExplicitHighAndExpression

public final void ExplicitHighAndExpression()
                                     throws ParseException

Throws:

ParseException

ImplicitHighAndExpression

public final void ImplicitHighAndExpression()
                                     throws ParseException

Throws:

ParseException

NotExpression

public final void NotExpression()
                         throws ParseException

Throws:

ParseException

RecursiveSmartsExpression

public final void RecursiveSmartsExpression()
                                     throws ParseException

Throws:

ParseException

PrimitiveAtomExpression

public final void PrimitiveAtomExpression()
                                   throws ParseException

Throws:

ParseException

TotalHCount

public final void TotalHCount()
                       throws ParseException

Throws:

ParseException

ImplicitHCount

public final void ImplicitHCount()
                          throws ParseException

Throws:

ParseException

ExplicitConnectivity

public final void ExplicitConnectivity()
                                throws ParseException

Throws:

ParseException

AtomicNumber

public final void AtomicNumber()
                        throws ParseException

Throws:

ParseException

HybridizationNumber

public final void HybridizationNumber()
                               throws ParseException

Throws:

ParseException

Charge

public final void Charge()
                  throws ParseException

Throws:

ParseException

RingConnectivity

public final void RingConnectivity()
                            throws ParseException

Throws:

ParseException

PeriodicGroupNumber

public final void PeriodicGroupNumber()
                               throws ParseException,
                                      ParseException

Throws:

ParseException

TotalConnectivity

public final void TotalConnectivity()
                             throws ParseException

Throws:

ParseException

Valence

public final void Valence()
                   throws ParseException

Throws:

ParseException

RingMembership

public final void RingMembership()
                          throws ParseException

Throws:

ParseException

SmallestRingSize

public final void SmallestRingSize()
                            throws ParseException

Throws:

ParseException

Aliphatic

public final void Aliphatic()
                     throws ParseException

Throws:

ParseException

NonCHHeavyAtom

public final void NonCHHeavyAtom()
                          throws ParseException

Throws:

ParseException

Aromatic

public final void Aromatic()
                    throws ParseException

Throws:

ParseException

AnyAtom

public final void AnyAtom()
                   throws ParseException

Throws:

ParseException

AtomicMass

public final void AtomicMass()
                      throws ParseException

Throws:

ParseException

RingIdentifier

public final void RingIdentifier()
                          throws ParseException

Throws:

ParseException

Chirality

public final void Chirality()
                     throws ParseException

Throws:

ParseException

NoHydrogenElement

public final void NoHydrogenElement()
                             throws ParseException

Throws:

ParseException

ReInit

public void ReInit(InputStream stream)

Reinitialise.

ReInit

public void ReInit(InputStream stream,
          String encoding)

Reinitialise.

ReInit

public void ReInit(Reader stream)

Reinitialise.

ReInit

public void ReInit(SMARTSParserTokenManager tm)

Reinitialise.

getNextToken

public final Token getNextToken()

Get the next Token.

getToken

public final Token getToken(int index)

Get the specific Token.

generateParseException

public ParseException generateParseException()

Generate ParseException.

enable_tracing

public final void enable_tracing()

Enable tracing.

disable_tracing

public final void disable_tracing()

Disable tracing.