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[Cdk-commits] SF.net SVN: cdk: [8207] trunk/cdk/src/org/openscience/cdk/smiles/smarts/ SMARTSParser.jj
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From: <sus...@us...> - 2007-04-17 18:46:32
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Revision: 8207
http://svn.sourceforge.net/cdk/?rev=8207&view=rev
Author: sushil_ronghe
Date: 2007-04-17 11:46:21 -0700 (Tue, 17 Apr 2007)
Log Message:
-----------
Operators are added
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj
Modified: trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj
===================================================================
--- trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj 2007-04-16 15:18:19 UTC (rev 8206)
+++ trunk/cdk/src/org/openscience/cdk/smiles/smarts/SMARTSParser.jj 2007-04-17 18:46:21 UTC (rev 8207)
@@ -31,12 +31,14 @@
import org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond;
import org.openscience.cdk.isomorphism.matchers.smarts.RingAtom;
import org.openscience.cdk.isomorphism.matchers.smarts.TotalRingConnectionAtom;
+import org.openscience.cdk.isomorphism.matchers.smarts.OperatorContainer;
+import org.openscience.cdk.isomorphism.matchers.smarts.SMARTSOperatorAtom;
import org.openscience.cdk.tools.LoggingTool;
/* $RCSfile$
* $Original Author: egonw $
* $code extension: sushil ronghe$
- * $Date: 2007-03-26 (Mon, 26 March 2007) $
+ * $Date: 2007-04-18 (Wed, 18 April 2007) $
* $Revision: 6382 $
*
* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
@@ -58,11 +60,9 @@
*/
/**
- * This parser implements a (small) subset of the SMARTS syntax as defined on
+ * This parser implements a nearly complete subset of the SMARTS syntax as defined on
* <a href="http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html">the
- * Daylight website</a>. But note that not all parsed strings are yet converted
- * in the corresponding queries. Not all concepts can yet be represented in
- * SMARTSAtom. This code is very experimental.
+ * Daylight website</a>.
*
* <p>Example code using SMARTS substructure search looks like:
* <pre>
@@ -78,7 +78,7 @@
* @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom
*
* @author Sushil Ronghe
- * @cdk.created 2007-03-29
+ * @cdk.created 2007-04-29
*
* @cdk.require ant1.6
* @cdk.module smarts
@@ -91,11 +91,13 @@
private IQueryAtom previousAtom = null;
private SMARTSBond currentBond = null;
private QueryAtomContainer container = null;
-
+ private QueryAtomContainer opcontainer = new QueryAtomContainer ();
+ private OperatorContainer OperMap = new OperatorContainer();
private final static LoggingTool logger = new LoggingTool(SMARTSParser.class);
public static QueryAtomContainer parse(String stringToParse) throws CDKException {
QueryAtomContainer container = null;
+
StringReader stringReader = new StringReader(stringToParse);
try {
SMARTSParser parser = new SMARTSParser(stringReader);
@@ -179,9 +181,16 @@
JAVACODE
void AddNewDegreeAtom() {
+ DegreeAtom atom;
Token tok = getToken(-1);
logger.debug("Adding SMARTS degree atom: " + tok.image);
- DegreeAtom atom = new DegreeAtom(Integer.parseInt(tok.image));
+ String ss = new String(tok.image);
+ if(ss.equals("D")){
+ atom=new DegreeAtom();
+ }
+ else{
+ atom=new DegreeAtom(Integer.parseInt(tok.image));
+ }
container.addAtom(atom);
if (previousAtom != null) AddCurrentBond(previousAtom, atom);
previousAtom = atom;
@@ -218,9 +227,16 @@
JAVACODE
void AddTotalRingConnectionAtom(){
+TotalRingConnectionAtom atom;
Token tt = getToken(-1);
logger.debug("adding SMARTS format charge atom: "+ tt.image);
-TotalRingConnectionAtom atom = new TotalRingConnectionAtom(Integer.parseInt(tt.image));
+String ss = new String(tt.image);
+if(ss.equals("x")){
+ atom=new TotalRingConnectionAtom();
+}
+else{
+ atom=new TotalRingConnectionAtom(Integer.parseInt(tt.image));
+}
container.addAtom(atom);
if (previousAtom != null) AddCurrentBond(previousAtom, atom);
previousAtom = atom;
@@ -238,9 +254,16 @@
JAVACODE
void AddNewImplicitHCountAtom() {
+ ImplicitHCountAtom atom;
Token tok = getToken(-1);
logger.debug("Adding SMARTS implicit Hcount atom: " + tok.image);
- ImplicitHCountAtom atom = new ImplicitHCountAtom(Integer.parseInt(tok.image));
+ String ss = new String(tok.image);
+ if(ss.equals("h")){
+ atom=new ImplicitHCountAtom();
+ }
+ else{
+ atom=new ImplicitHCountAtom(Integer.parseInt(tok.image));
+ }
container.addAtom(atom);
if (previousAtom != null) AddCurrentBond(previousAtom, atom);
previousAtom = atom;
@@ -248,13 +271,62 @@
JAVACODE
void AddNewTotalHCountAtom() {
+ TotalHCountAtom atom;
Token tok = getToken(-1);
logger.debug("Adding SMARTS total Hcount atom: " + tok.image);
- TotalHCountAtom atom = new TotalHCountAtom(Integer.parseInt(tok.image));
+ String ss = new String(tok.image);
+ if(ss.equals("h")){
+ atom=new TotalHCountAtom();
+ }
+ else{
+ atom=new TotalHCountAtom(Integer.parseInt(tok.image));
+ }
container.addAtom(atom);
if (previousAtom != null) AddCurrentBond(previousAtom, atom);
previousAtom = atom;
}
+JAVACODE
+void AddOperator(){
+ Token tok = getToken(-1);
+ try{
+ OperMap.addElement(new String(tok.image));
+ opcontainer.addAtom (previousAtom);
+ container.removeAtom(previousAtom);
+ previousAtom = null;
+ }
+ catch(java.lang.NullPointerException NPT){
+ //System.out.println("error caught");
+ NPT.printStackTrace();
+ }
+
+}
+JAVACODE
+void AddOperatorAtom(){
+ Token tok = getToken(-1);
+ logger.debug("Adding SMARTS total OP atom: " + tok.image);
+ previousAtom.setOperator("!");
+
+}
+JAVACODE
+void AddFinalOperatorExpression(){
+ Token tok = getToken(-1);
+ logger.debug("Adding SMARTS total OPF atom: " + tok.image);
+ if(OperMap.size()!=0 && opcontainer.getAtomCount()!=0){
+ opcontainer.addAtom (previousAtom);
+ container.removeAtom(previousAtom);
+ SMARTSOperatorAtom atom = new SMARTSOperatorAtom(opcontainer,OperMap);
+ container.addAtom(atom);
+ if (previousAtom != null) AddCurrentBond(previousAtom, atom);
+ previousAtom = atom;
+ }
+ OperMap = new OperatorContainer();
+ opcontainer = new QueryAtomContainer ();
+}
+JAVACODE
+void AddOperatorExpression(){
+ Token tok = getToken(-1);
+ logger.debug("Adding SMARTS total OPEX atom: " + tok.image);
+}
JAVACODE
void SetCurrentBondToOrderQuery(double order) {
@@ -311,6 +383,14 @@
{}
{
"["
+ FinalOperatorExpression()
+
+ "]"
+}
+
+void ExpressionAtom():
+{}
+{
(Degree() |
TotalHCount() |
ImplicitHCount() |
@@ -318,16 +398,33 @@
Element() |
ChargeAtom() |
RingAtom() |
- TotalRingConnection())
- "]"
+ TotalRingConnection() )
}
+void OperatorAtom():
+{}
+{
+ <excl> ExpressionAtom() AddOperatorAtom()
+}
void AtomicNumber() :
{}
{
- "#" (<DIGIT> | <DIGITS>) AddNewNumberAtom()
+ <HASH> (<DIGIT> | <DIGITS>) AddNewNumberAtom()
}
+void OperatorExpression():
+{}
+{
+ ( Operator() (OperatorAtom() | ExpressionAtom()))*
+ AddOperatorExpression()
+}
+void FinalOperatorExpression():
+{}
+{
+ (OperatorAtom() | ExpressionAtom()) [OperatorExpression()]
+ AddFinalOperatorExpression()
+}
+
void TotalHCount() :
{}
{
@@ -337,30 +434,30 @@
void ChargeAtom():
{Token t;}
{
- ("n" ("+"|"-") | <SIGNS>) AddNewFormalChargeAtom()
+ (("+"|"-") | <SIGNS>) AddNewFormalChargeAtom()
}
void ImplicitHCount() :
{}
{
- "h" [<DIGIT>] AddNewImplicitHCountAtom()
+ <h> [<DIGIT>] AddNewImplicitHCountAtom()
}
void Degree() :
{}
{
- "D" [<DIGIT>] AddNewDegreeAtom()
+ <D> [<DIGIT>] AddNewDegreeAtom()
}
void RingAtom() :
{}
{
- "r" [<DIGIT>] AddNewRingAtom()
+ <r> [<DIGIT>] AddNewRingAtom()
}
void TotalRingConnection():
{}
{
- "x" [<DIGIT>] AddTotalRingConnectionAtom()
+ <x> [<DIGIT>] AddTotalRingConnectionAtom()
}
void Element() :
{}
@@ -374,7 +471,7 @@
{
("-" SetCurrentBondToOrderQuery(1.0) ) |
("=" SetCurrentBondToOrderQuery(2.0) ) |
- ("#" SetCurrentBondToOrderQuery(3.0) ) |
+ (<HASH> SetCurrentBondToOrderQuery(3.0) ) |
(":" SetCurrentBondToAromatic() ) |
("~" SetCurrentBondToAnyOrder() )
}
@@ -395,8 +492,12 @@
{
<H> | <B> | <C> | <N> | <O> | <F> | <P> | <S> | <K> | <V> | <Y> | <I> | <U>
}
+void Operator():
+{}
+{
+ (<coln>|<coma>|<amps>) AddOperator()
+}
-
TOKEN:
{
< DIGIT: ["0"-"9"] >
@@ -412,22 +513,40 @@
}
TOKEN: /* Opetator*/
{
- < Exclamation: "!" >
+ < excl: "!" >
}
TOKEN:
{
- < Amps :"&" >
+ < amps :"&" >
}
TOKEN:
{
- <Comma:",">
+ <coma:",">
}
TOKEN:
{
- <Colon:";">
+ <coln:";">
}
-
-
+TOKEN:
+{
+ <h:"h">
+}
+TOKEN:
+{
+ <D:"D">
+}
+TOKEN:
+{
+ <r:"r">
+}
+TOKEN:
+{
+ <x:"x">
+}
+TOKEN:
+{
+ <HASH:"#">
+}
TOKEN :
{
< DIGITS: (["0"-"9"])+ >
@@ -514,4 +633,3 @@
| < PA: "Pa" >
| < U: "U" >
}
-
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