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Updates with the SMARTS specs, among others to fix 'Sc' parsing (patc…
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…h by Dazhi Jiao; fixes #2786624)

Change-Id: I34ad117aef815c89978223f7625c5b6558e2d62d

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Apr 12, 2012
1 parent 2c4f244 commit 117377e
Showing 1 changed file with 72 additions and 63 deletions.
135 changes: 72 additions & 63 deletions src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt
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@@ -1,9 +1,9 @@
options {
STATIC=false;
FORCE_LA_CHECK=false;
USER_CHAR_STREAM = false;
UNICODE_INPUT = false;
IGNORE_CASE = false;
USER_CHAR_STREAM=false;
UNICODE_INPUT=false;
IGNORE_CASE=false;
MULTI=true;
VISITOR=true;
NODE_DEFAULT_VOID=true;
Expand Down Expand Up @@ -77,7 +77,6 @@ import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
* @cdk.keyword substructure search
*/
public class SMARTSParser {

/**
* This method parses a Smarts String and returns an instance of
* <code>QueryAtomContainer</code>
Expand All @@ -97,17 +96,22 @@ public class SMARTSParser {
}
return container;
}

}

PARSER_END(SMARTSParser)

TOKEN_MGR_DECLS : {

// Required by SetState
void backup(int n) { input_stream.backup(n); }

}

<*> TOKEN:
{
<#_WS: ( " " | "\t" | "\n" | "\r" ) >
}

<DEFAULT> TOKEN:
{
|
// Logical Operators
<L_AND : ";" >
|
Expand Down Expand Up @@ -138,35 +142,77 @@ PARSER_END(SMARTSParser)
|
< R_BOND : "@" > // any ring bond
|
// Elements
// Explicit Elements
< c: "c" >
| < n: "n" >
| < o: "o" >
| < s: "s" >
| < p: "p" >
| < as: "as" >
| < se: "se" >
| < H: "H" >
| < HE: "He" >
| < LI: "Li" >
| < BE: "Be" >
| < B: "B" >
| < C: "C" >
| < N: "N" >
| < O: "O" >
| < F: "F" >
| < P: "P" >
| < S: "S" >
| < CL: "Cl" >
| < BR: "Br" >
| < I: "I" >
| < WILDCARD: "*" >
| <a : "a" >
| <A : "A" >
| <CARET : "^">
| <Q_MARK : "?" >
|
<DIGIT: ["0"-"9"] >
|
<L_BRACKET : "[" >
|
<L_PAREN : "(" >
|
<R_PAREN : ")" >
|
<R_BRACKET : "]" >
|
<DOLLAR : "$" >
|
<PLUS: "+" >
}

<ATOM_EXPRESSION> TOKEN: {
<h : "h" >
|
<D : "D" >
|
<R : "R" >
|
<r : "r" >
|
<v : "v" >
|
<X : "X" >
|
<x : "x" >
|
<G : "G" >
|
<HX : "#X" >
|
// ELEMENTS
< H: "H" >
| < HE: "He" >
| < LI: "Li" >
| < BE: "Be" >
| < NE: "Ne" >
| < NA: "Na" >
| < MG: "Mg" >
| < AL: "Al" >
| < SI: "Si" >
| < P: "P" >
| < S: "S" >
| < CL: "Cl" >
| < AR: "Ar" >
| < K: "K" >
| < CA: "Ca" >
| < SC: "Sc" >
| < TI: "Ti" >
| < V: "V" >
| < CR: "Cr" >
Expand All @@ -180,7 +226,6 @@ PARSER_END(SMARTSParser)
| < GE: "Ge" >
| < AS: "As" >
| < SE: "Se" >
| < BR: "Br" >
| < KR: "Kr" >
| < RB: "Rb" >
| < SR: "Sr" >
Expand All @@ -198,7 +243,6 @@ PARSER_END(SMARTSParser)
| < SN: "Sn" >
| < SB: "Sb" >
| < TE: "Te" >
| < I: "I" >
| < XE: "Xe" >
| < CS: "Cs" >
| < BA: "Ba" >
Expand Down Expand Up @@ -248,47 +292,9 @@ PARSER_END(SMARTSParser)
| < TM: "Tm" >
| < YB: "Yb" >
| < LU: "Lu" >
| < PR: "Pr" >
// Atomic Primitives
| < WILDCARD: "*" >
|
<h : "h" >
|
<a : "a" >
|
<A : "A" >
|
<D : "D" >
|
<R : "R" >
|
<r : "r" >
|
<v : "v" >
|
<X : "X" >
|
<x : "x" >
|
<G : "G" >
|
<HX : "#X" >
|
<CARET : "^">
|
<DOLLAR : "$" >
|
<L_PAREN : "(" >
|
<R_PAREN : ")" >
|
<L_BRACKET : "[" >
|
<R_BRACKET : "]" >
|
<Q_MARK : "?" >
|
<DIGIT: ["0"-"9"] >
| < PR: "Pr" >
| <SC: "Sc">

}

/**
Expand Down Expand Up @@ -395,7 +401,9 @@ ASTAtom AtomExpression() #Atom :
(
(

<L_BRACKET> { firstToken = getToken(1); secondToken = getToken(2); }
<L_BRACKET> { token_source.SwitchTo(SMARTSParserConstants.ATOM_EXPRESSION);
firstToken = getToken(1);
secondToken = getToken(2); }
( AtomicMass() { massNode = (ASTAtomicMass)jjtree.popNode(); } )?
LowAndExpression()
{
Expand All @@ -405,7 +413,7 @@ ASTAtom AtomExpression() #Atom :
jjtree.pushNode(topNode);
}
}
<R_BRACKET> { rightBracket = token; }
<R_BRACKET> { token_source.SwitchTo(SMARTSParserConstants.DEFAULT); rightBracket = token; }
{
Token HToken = null;
// If the LowAndExpression is "[H]", change it to an ExplicitAtom
Expand Down Expand Up @@ -530,7 +538,8 @@ void NotExpression() #NotExpression :

void RecursiveSmartsExpression() #RecursiveSmartsExpression : {}
{
<DOLLAR> <L_PAREN> SmartsExpression() <R_PAREN>
<DOLLAR> <L_PAREN> {token_source.SwitchTo(SMARTSParserConstants.DEFAULT); }
SmartsExpression() <R_PAREN> {token_source.SwitchTo(SMARTSParserConstants.ATOM_EXPRESSION); }
}

void PrimitiveAtomExpression() : {}
Expand Down

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