--- trunk/src/mdParser/MDTreeParser.cpp	2013/07/16 17:16:45	1902
+++ trunk/src/mdParser/MDTreeParser.cpp	2014/10/22 12:23:59	2026
@@ -1,4 +1,4 @@
-/* $ANTLR 2.7.7 (20121118): "MDTreeParser.g" -> "MDTreeParser.cpp"$ */
+/* $ANTLR 2.7.7 (20131114): "MDTreeParser.g" -> "MDTreeParser.cpp"$ */
 #include "MDTreeParser.hpp"
 #include <antlr/Token.hpp>
 #include <antlr/AST.hpp>
@@ -145,7 +145,7 @@ void MDTreeParser::componentblock(ANTLR_USE_NAMESPACE(
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp2_AST_in = _t;
 		match(_t,COMPONENT);
 		_t = _t->getFirstChild();
-#line 72 "MDTreeParser.g"
+#line 70 "MDTreeParser.g"
 		Component* currComponet = new Component(); blockStack.push(currComponet);
 #line 151 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -168,7 +168,7 @@ void MDTreeParser::componentblock(ANTLR_USE_NAMESPACE(
 		_t = _t->getNextSibling();
 		_t = __t10;
 		_t = _t->getNextSibling();
-#line 74 "MDTreeParser.g"
+#line 72 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);
 #line 174 "MDTreeParser.cpp"
 	}
@@ -188,7 +188,7 @@ void MDTreeParser::moleculeblock(ANTLR_USE_NAMESPACE(a
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp4_AST_in = _t;
 		match(_t,MOLECULE);
 		_t = _t->getFirstChild();
-#line 103 "MDTreeParser.g"
+#line 101 "MDTreeParser.g"
 		MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);
 #line 194 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -211,7 +211,7 @@ void MDTreeParser::moleculeblock(ANTLR_USE_NAMESPACE(a
 		_t = _t->getNextSibling();
 		_t = __t34;
 		_t = _t->getNextSibling();
-#line 105 "MDTreeParser.g"
+#line 103 "MDTreeParser.g"
 		blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);
 #line 217 "MDTreeParser.cpp"
 	}
@@ -231,7 +231,7 @@ void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPAC
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp6_AST_in = _t;
 		match(_t,ZCONSTRAINT);
 		_t = _t->getFirstChild();
-#line 77 "MDTreeParser.g"
+#line 75 "MDTreeParser.g"
 		ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);
 #line 237 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -254,7 +254,7 @@ void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPAC
 		_t = _t->getNextSibling();
 		_t = __t14;
 		_t = _t->getNextSibling();
-#line 79 "MDTreeParser.g"
+#line 77 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);
 #line 260 "MDTreeParser.cpp"
 	}
@@ -274,7 +274,7 @@ void MDTreeParser::restraintblock(ANTLR_USE_NAMESPACE(
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp8_AST_in = _t;
 		match(_t,RESTRAINT);
 		_t = _t->getFirstChild();
-#line 82 "MDTreeParser.g"
+#line 80 "MDTreeParser.g"
 		RestraintStamp* currRestraintStamp = new RestraintStamp(); blockStack.push(currRestraintStamp);
 #line 280 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -297,7 +297,7 @@ void MDTreeParser::restraintblock(ANTLR_USE_NAMESPACE(
 		_t = _t->getNextSibling();
 		_t = __t18;
 		_t = _t->getNextSibling();
-#line 84 "MDTreeParser.g"
+#line 82 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addRestraintStamp(currRestraintStamp);
 #line 303 "MDTreeParser.cpp"
 	}
@@ -317,7 +317,7 @@ void MDTreeParser::flucqblock(ANTLR_USE_NAMESPACE(antl
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp10_AST_in = _t;
 		match(_t,FLUCQ);
 		_t = _t->getFirstChild();
-#line 87 "MDTreeParser.g"
+#line 85 "MDTreeParser.g"
 		FluctuatingChargeParameters* flucQpars = new FluctuatingChargeParameters(); blockStack.push(flucQpars);
 #line 323 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -340,7 +340,7 @@ void MDTreeParser::flucqblock(ANTLR_USE_NAMESPACE(antl
 		_t = _t->getNextSibling();
 		_t = __t22;
 		_t = _t->getNextSibling();
-#line 89 "MDTreeParser.g"
+#line 87 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addFluctuatingChargeParameters(flucQpars);
 #line 346 "MDTreeParser.cpp"
 	}
@@ -360,7 +360,7 @@ void MDTreeParser::rnemdblock(ANTLR_USE_NAMESPACE(antl
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp12_AST_in = _t;
 		match(_t,RNEMD);
 		_t = _t->getFirstChild();
-#line 92 "MDTreeParser.g"
+#line 90 "MDTreeParser.g"
 		RNEMDParameters* rnemdPars = new RNEMDParameters(); blockStack.push(rnemdPars);
 #line 366 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -383,7 +383,7 @@ void MDTreeParser::rnemdblock(ANTLR_USE_NAMESPACE(antl
 		_t = _t->getNextSibling();
 		_t = __t26;
 		_t = _t->getNextSibling();
-#line 94 "MDTreeParser.g"
+#line 92 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addRNEMDParameters(rnemdPars);
 #line 389 "MDTreeParser.cpp"
 	}
@@ -403,7 +403,7 @@ void MDTreeParser::minimizerblock(ANTLR_USE_NAMESPACE(
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp14_AST_in = _t;
 		match(_t,MINIMIZER);
 		_t = _t->getFirstChild();
-#line 97 "MDTreeParser.g"
+#line 95 "MDTreeParser.g"
 		MinimizerParameters* minimizerPars = new MinimizerParameters(); blockStack.push(minimizerPars);
 #line 409 "MDTreeParser.cpp"
 		{ // ( ... )*
@@ -426,7 +426,7 @@ void MDTreeParser::minimizerblock(ANTLR_USE_NAMESPACE(
 		_t = _t->getNextSibling();
 		_t = __t30;
 		_t = _t->getNextSibling();
-#line 99 "MDTreeParser.g"
+#line 97 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addMinimizerParameters(minimizerPars);
 #line 432 "MDTreeParser.cpp"
 	}
@@ -448,7 +448,7 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 	
 	int ival;
 	RealType dval, x, y, z;
-	Vector3d dvec;
+	std::vector<RealType> dvec;
 	
 #line 454 "MDTreeParser.cpp"
 	
@@ -474,38 +474,6 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 #line 57 "MDTreeParser.g"
 			blockStack.top()->assign(id->getText(), dval);
 #line 477 "MDTreeParser.cpp"
-			break;
-		}
-		case LPAREN:
-		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t8 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp16_AST_in = _t;
-			match(_t,LPAREN);
-			_t = _t->getFirstChild();
-			x=doubleNumber(_t);
-			_t = _retTree;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp17_AST_in = _t;
-			match(_t,COMMA);
-			_t = _t->getNextSibling();
-			y=doubleNumber(_t);
-			_t = _retTree;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp18_AST_in = _t;
-			match(_t,COMMA);
-			_t = _t->getNextSibling();
-			z=doubleNumber(_t);
-			_t = _retTree;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp19_AST_in = _t;
-			match(_t,RPAREN);
-			_t = _t->getNextSibling();
-			_t = __t8;
-			_t = _t->getNextSibling();
-#line 59 "MDTreeParser.g"
-			dvec.x() = x; 
-			dvec.y() = y; 
-			dvec.z() = z; 
-			blockStack.top()->assign(id->getText(), dvec);
-			
-#line 509 "MDTreeParser.cpp"
 			break;
 		}
 		case ID:
@@ -513,9 +481,9 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 			str1 = _t;
 			match(_t,ID);
 			_t = _t->getNextSibling();
-#line 64 "MDTreeParser.g"
+#line 58 "MDTreeParser.g"
 			blockStack.top()->assign(id->getText(), str1->getText());
-#line 519 "MDTreeParser.cpp"
+#line 487 "MDTreeParser.cpp"
 			break;
 		}
 		case StringLiteral:
@@ -523,14 +491,34 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 			str2 = _t;
 			match(_t,StringLiteral);
 			_t = _t->getNextSibling();
-#line 65 "MDTreeParser.g"
+#line 59 "MDTreeParser.g"
 			std::string s =  str2->getText();
 			s = s.substr(1, s.length()-2);
 			blockStack.top()->assign(id->getText(),s);
 			
-#line 532 "MDTreeParser.cpp"
+#line 500 "MDTreeParser.cpp"
 			break;
 		}
+		case LPAREN:
+		{
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t8 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp16_AST_in = _t;
+			match(_t,LPAREN);
+			_t = _t->getFirstChild();
+			dvec=doubleNumberTuple(_t);
+			_t = _retTree;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp17_AST_in = _t;
+			match(_t,RPAREN);
+			_t = _t->getNextSibling();
+			_t = __t8;
+			_t = _t->getNextSibling();
+#line 64 "MDTreeParser.g"
+			
+			blockStack.top()->assign(id->getText(), dvec);
+			
+#line 520 "MDTreeParser.cpp"
+			break;
+		}
 		default:
 		{
 			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
@@ -546,9 +534,9 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 }
 
 int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 296 "MDTreeParser.g"
+#line 312 "MDTreeParser.g"
 	int ival;
-#line 552 "MDTreeParser.cpp"
+#line 540 "MDTreeParser.cpp"
 	ANTLR_USE_NAMESPACE(antlr)RefAST intConst_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	ANTLR_USE_NAMESPACE(antlr)RefAST i1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
 	ANTLR_USE_NAMESPACE(antlr)RefAST i2 = ANTLR_USE_NAMESPACE(antlr)nullAST;
@@ -562,9 +550,9 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 			i1 = _t;
 			match(_t,NUM_INT);
 			_t = _t->getNextSibling();
-#line 297 "MDTreeParser.g"
+#line 313 "MDTreeParser.g"
 			ival = lexi_cast<int>(i1->getText());
-#line 568 "MDTreeParser.cpp"
+#line 556 "MDTreeParser.cpp"
 			break;
 		}
 		case NUM_LONG:
@@ -572,9 +560,9 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 			i2 = _t;
 			match(_t,NUM_LONG);
 			_t = _t->getNextSibling();
-#line 298 "MDTreeParser.g"
+#line 314 "MDTreeParser.g"
 			ival = lexi_cast<int>(i2->getText());
-#line 578 "MDTreeParser.cpp"
+#line 566 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -593,9 +581,9 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 }
 
 RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 308 "MDTreeParser.g"
+#line 324 "MDTreeParser.g"
 	RealType dval;
-#line 599 "MDTreeParser.cpp"
+#line 587 "MDTreeParser.cpp"
 	ANTLR_USE_NAMESPACE(antlr)RefAST floatConst_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	ANTLR_USE_NAMESPACE(antlr)RefAST d1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
 	ANTLR_USE_NAMESPACE(antlr)RefAST d2 = ANTLR_USE_NAMESPACE(antlr)nullAST;
@@ -609,9 +597,9 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 			d1 = _t;
 			match(_t,NUM_FLOAT);
 			_t = _t->getNextSibling();
-#line 309 "MDTreeParser.g"
+#line 325 "MDTreeParser.g"
 			dval = lexi_cast<RealType>(d1->getText());
-#line 615 "MDTreeParser.cpp"
+#line 603 "MDTreeParser.cpp"
 			break;
 		}
 		case NUM_DOUBLE:
@@ -619,9 +607,9 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 			d2 = _t;
 			match(_t,NUM_DOUBLE);
 			_t = _t->getNextSibling();
-#line 310 "MDTreeParser.g"
+#line 326 "MDTreeParser.g"
 			dval = lexi_cast<RealType>(d2->getText());
-#line 625 "MDTreeParser.cpp"
+#line 613 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -639,45 +627,38 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 	return dval;
 }
 
-RealType  MDTreeParser::doubleNumber(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 302 "MDTreeParser.g"
+vector<RealType>  MDTreeParser::doubleNumberTuple(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+#line 296 "MDTreeParser.g"
+	vector<RealType> dvec;
+#line 634 "MDTreeParser.cpp"
+	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumberTuple_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 296 "MDTreeParser.g"
+	
 	RealType dval;
-#line 646 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumber_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-	ANTLR_USE_NAMESPACE(antlr)RefAST ic = ANTLR_USE_NAMESPACE(antlr)nullAST;
-	ANTLR_USE_NAMESPACE(antlr)RefAST fc = ANTLR_USE_NAMESPACE(antlr)nullAST;
 	
+#line 640 "MDTreeParser.cpp"
+	
 	try {      // for error handling
-		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
-			_t = ASTNULL;
-		switch ( _t->getType()) {
-		case NUM_INT:
-		case NUM_LONG:
-		{
-			ic = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-			intConst(_t);
-			_t = _retTree;
-#line 303 "MDTreeParser.g"
-			dval = lexi_cast<RealType>(ic->getText());
-#line 663 "MDTreeParser.cpp"
-			break;
-		}
-		case NUM_FLOAT:
-		case NUM_DOUBLE:
-		{
-			fc = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-			floatConst(_t);
-			_t = _retTree;
-#line 304 "MDTreeParser.g"
-			dval = lexi_cast<RealType>(fc->getText());
-#line 674 "MDTreeParser.cpp"
-			break;
-		}
-		default:
-		{
-			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
+		{ // ( ... )+
+		int _cnt95=0;
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if (((_t->getType() >= NUM_INT && _t->getType() <= NUM_DOUBLE))) {
+				dval=doubleNumber(_t);
+				_t = _retTree;
+#line 300 "MDTreeParser.g"
+				dvec.push_back(dval);
+#line 653 "MDTreeParser.cpp"
+			}
+			else {
+				if ( _cnt95>=1 ) { goto _loop95; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
+			}
+			
+			_cnt95++;
 		}
-		}
+		_loop95:;
+		}  // ( ... )+
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -685,7 +666,7 @@ RealType  MDTreeParser::doubleNumber(ANTLR_USE_NAMESPA
 			_t = _t->getNextSibling();
 	}
 	_retTree = _t;
-	return dval;
+	return dvec;
 }
 
 void MDTreeParser::moleculestatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
@@ -749,6 +730,12 @@ void MDTreeParser::moleculestatement(ANTLR_USE_NAMESPA
 			_t = _retTree;
 			break;
 		}
+		case CONSTRAINT:
+		{
+			constraintblock(_t);
+			_t = _retTree;
+			break;
+		}
 		default:
 		{
 			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
@@ -765,22 +752,22 @@ void MDTreeParser::atomblock(ANTLR_USE_NAMESPACE(antlr
 
 void MDTreeParser::atomblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST atomblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 119 "MDTreeParser.g"
+#line 118 "MDTreeParser.g"
 	
 	int index;
 	
-#line 773 "MDTreeParser.cpp"
+#line 760 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t39 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp20_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp18_AST_in = _t;
 		match(_t,ATOM);
 		_t = _t->getFirstChild();
 		index=intConst(_t);
 		_t = _retTree;
-#line 123 "MDTreeParser.g"
+#line 122 "MDTreeParser.g"
 		AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);
-#line 784 "MDTreeParser.cpp"
+#line 771 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -796,19 +783,19 @@ void MDTreeParser::atomblock(ANTLR_USE_NAMESPACE(antlr
 		}
 		_loop41:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp21_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp19_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t39;
 		_t = _t->getNextSibling();
-#line 125 "MDTreeParser.g"
+#line 124 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addAtomStamp(currAtomStamp); 
 		
-#line 812 "MDTreeParser.cpp"
+#line 799 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -823,12 +810,12 @@ void MDTreeParser::bondblock(ANTLR_USE_NAMESPACE(antlr
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t46 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp22_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp20_AST_in = _t;
 		match(_t,BOND);
 		_t = _t->getFirstChild();
-#line 145 "MDTreeParser.g"
+#line 144 "MDTreeParser.g"
 		BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);
-#line 832 "MDTreeParser.cpp"
+#line 819 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -844,18 +831,18 @@ void MDTreeParser::bondblock(ANTLR_USE_NAMESPACE(antlr
 		}
 		_loop48:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp23_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp21_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t46;
 		_t = _t->getNextSibling();
-#line 147 "MDTreeParser.g"
+#line 146 "MDTreeParser.g"
 		
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addBondStamp(currBondStamp); 
 		
-#line 859 "MDTreeParser.cpp"
+#line 846 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -870,12 +857,12 @@ void MDTreeParser::bendblock(ANTLR_USE_NAMESPACE(antlr
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t52 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp24_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp22_AST_in = _t;
 		match(_t,BEND);
 		_t = _t->getFirstChild();
-#line 163 "MDTreeParser.g"
+#line 162 "MDTreeParser.g"
 		BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);
-#line 879 "MDTreeParser.cpp"
+#line 866 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -891,19 +878,19 @@ void MDTreeParser::bendblock(ANTLR_USE_NAMESPACE(antlr
 		}
 		_loop54:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp25_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp23_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t52;
 		_t = _t->getNextSibling();
-#line 165 "MDTreeParser.g"
+#line 164 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addBendStamp(currBendStamp); 
 		
-#line 907 "MDTreeParser.cpp"
+#line 894 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -918,12 +905,12 @@ void MDTreeParser::torsionblock(ANTLR_USE_NAMESPACE(an
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t58 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp26_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp24_AST_in = _t;
 		match(_t,TORSION);
 		_t = _t->getFirstChild();
-#line 182 "MDTreeParser.g"
+#line 181 "MDTreeParser.g"
 		TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);
-#line 927 "MDTreeParser.cpp"
+#line 914 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -939,19 +926,19 @@ void MDTreeParser::torsionblock(ANTLR_USE_NAMESPACE(an
 		}
 		_loop60:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp27_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp25_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t58;
 		_t = _t->getNextSibling();
-#line 184 "MDTreeParser.g"
+#line 183 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addTorsionStamp(currTorsionStamp); 
 		
-#line 955 "MDTreeParser.cpp"
+#line 942 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -966,12 +953,12 @@ void MDTreeParser::inversionblock(ANTLR_USE_NAMESPACE(
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t64 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp28_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp26_AST_in = _t;
 		match(_t,INVERSION);
 		_t = _t->getFirstChild();
-#line 201 "MDTreeParser.g"
+#line 200 "MDTreeParser.g"
 		InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);
-#line 975 "MDTreeParser.cpp"
+#line 962 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -987,19 +974,19 @@ void MDTreeParser::inversionblock(ANTLR_USE_NAMESPACE(
 		}
 		_loop66:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp29_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp27_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t64;
 		_t = _t->getNextSibling();
-#line 203 "MDTreeParser.g"
+#line 202 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addInversionStamp(currInversionStamp); 
 		
-#line 1003 "MDTreeParser.cpp"
+#line 990 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -1011,22 +998,22 @@ void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(
 
 void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodyblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 222 "MDTreeParser.g"
+#line 221 "MDTreeParser.g"
 	
 	int index;
 	
-#line 1019 "MDTreeParser.cpp"
+#line 1006 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t71 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp30_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp28_AST_in = _t;
 		match(_t,RIGIDBODY);
 		_t = _t->getFirstChild();
 		index=intConst(_t);
 		_t = _retTree;
-#line 226 "MDTreeParser.g"
+#line 225 "MDTreeParser.g"
 		RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);
-#line 1030 "MDTreeParser.cpp"
+#line 1017 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1042,19 +1029,19 @@ void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(
 		}
 		_loop73:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp31_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp29_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t71;
 		_t = _t->getNextSibling();
-#line 228 "MDTreeParser.g"
+#line 227 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp); 
 		
-#line 1058 "MDTreeParser.cpp"
+#line 1045 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -1069,12 +1056,12 @@ void MDTreeParser::cutoffgroupblock(ANTLR_USE_NAMESPAC
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t77 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp32_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp30_AST_in = _t;
 		match(_t,CUTOFFGROUP);
 		_t = _t->getFirstChild();
-#line 245 "MDTreeParser.g"
+#line 244 "MDTreeParser.g"
 		CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);
-#line 1078 "MDTreeParser.cpp"
+#line 1065 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1090,19 +1077,19 @@ void MDTreeParser::cutoffgroupblock(ANTLR_USE_NAMESPAC
 		}
 		_loop79:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp33_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp31_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t77;
 		_t = _t->getNextSibling();
-#line 247 "MDTreeParser.g"
+#line 246 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp); 
 		
-#line 1106 "MDTreeParser.cpp"
+#line 1093 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -1114,20 +1101,20 @@ void MDTreeParser::fragmentblock(ANTLR_USE_NAMESPACE(a
 
 void MDTreeParser::fragmentblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST fragmentblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 264 "MDTreeParser.g"
+#line 263 "MDTreeParser.g"
 	int ival;
-#line 1120 "MDTreeParser.cpp"
+#line 1107 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		ANTLR_USE_NAMESPACE(antlr)RefAST __t83 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp34_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp32_AST_in = _t;
 		match(_t,FRAGMENT);
 		_t = _t->getFirstChild();
 		ival=intConst(_t);
 		_t = _retTree;
-#line 265 "MDTreeParser.g"
+#line 264 "MDTreeParser.g"
 		FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);
-#line 1131 "MDTreeParser.cpp"
+#line 1118 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1143,19 +1130,19 @@ void MDTreeParser::fragmentblock(ANTLR_USE_NAMESPACE(a
 		}
 		_loop85:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp35_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp33_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
 		_t = __t83;
 		_t = _t->getNextSibling();
-#line 267 "MDTreeParser.g"
+#line 266 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addFragmentStamp(currFragmentStamp); 
 		
-#line 1159 "MDTreeParser.cpp"
+#line 1146 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -1165,15 +1152,62 @@ void MDTreeParser::fragmentblock(ANTLR_USE_NAMESPACE(a
 	_retTree = _t;
 }
 
+void MDTreeParser::constraintblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST constraintblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	
+	try {      // for error handling
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t88 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp34_AST_in = _t;
+		match(_t,CONSTRAINT);
+		_t = _t->getFirstChild();
+#line 277 "MDTreeParser.g"
+		ConstraintStamp* currConstraintStamp = new ConstraintStamp(); blockStack.push(currConstraintStamp);
+#line 1166 "MDTreeParser.cpp"
+		{ // ( ... )*
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if ((_t->getType() == MEMBERS || _t->getType() == ASSIGNEQUAL)) {
+				constraintstatement(_t);
+				_t = _retTree;
+			}
+			else {
+				goto _loop90;
+			}
+			
+		}
+		_loop90:;
+		} // ( ... )*
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp35_AST_in = _t;
+		match(_t,ENDBLOCK);
+		_t = _t->getNextSibling();
+		_t = __t88;
+		_t = _t->getNextSibling();
+#line 279 "MDTreeParser.g"
+		
+		blockStack.pop(); 
+		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
+		currMoleculeStamp->addConstraintStamp(currConstraintStamp); 
+		
+#line 1193 "MDTreeParser.cpp"
+	}
+	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
+		reportError(ex);
+		if ( _t != ANTLR_USE_NAMESPACE(antlr)nullAST )
+			_t = _t->getNextSibling();
+	}
+	_retTree = _t;
+}
+
 void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST atomstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 133 "MDTreeParser.g"
+#line 132 "MDTreeParser.g"
 	
 	vector<RealType> dvec;
 	AtomStamp* currAtomStamp =  static_cast<AtomStamp*>(blockStack.top());
 	
 	
-#line 1177 "MDTreeParser.cpp"
+#line 1211 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1195,9 +1229,9 @@ void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(a
 			_t = _retTree;
 			_t = __t43;
 			_t = _t->getNextSibling();
-#line 140 "MDTreeParser.g"
+#line 139 "MDTreeParser.g"
 			currAtomStamp->setPosition(dvec);
-#line 1201 "MDTreeParser.cpp"
+#line 1235 "MDTreeParser.cpp"
 			break;
 		}
 		case ORIENTATION:
@@ -1210,9 +1244,9 @@ void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(a
 			_t = _retTree;
 			_t = __t44;
 			_t = _t->getNextSibling();
-#line 141 "MDTreeParser.g"
+#line 140 "MDTreeParser.g"
 			currAtomStamp->setOrientation(dvec);
-#line 1216 "MDTreeParser.cpp"
+#line 1250 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1229,56 +1263,14 @@ void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(a
 	_retTree = _t;
 }
 
-vector<RealType>  MDTreeParser::doubleNumberTuple(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 280 "MDTreeParser.g"
-	vector<RealType> dvec;
-#line 1236 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumberTuple_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 280 "MDTreeParser.g"
-	
-	RealType dval;
-	
-#line 1242 "MDTreeParser.cpp"
-	
-	try {      // for error handling
-		{ // ( ... )+
-		int _cnt89=0;
-		for (;;) {
-			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
-				_t = ASTNULL;
-			if (((_t->getType() >= NUM_INT && _t->getType() <= NUM_DOUBLE))) {
-				dval=doubleNumber(_t);
-				_t = _retTree;
-#line 284 "MDTreeParser.g"
-				dvec.push_back(dval);
-#line 1255 "MDTreeParser.cpp"
-			}
-			else {
-				if ( _cnt89>=1 ) { goto _loop89; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
-			}
-			
-			_cnt89++;
-		}
-		_loop89:;
-		}  // ( ... )+
-	}
-	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
-		reportError(ex);
-		if ( _t != ANTLR_USE_NAMESPACE(antlr)nullAST )
-			_t = _t->getNextSibling();
-	}
-	_retTree = _t;
-	return dvec;
-}
-
 void MDTreeParser::bondstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST bondstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 154 "MDTreeParser.g"
+#line 153 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
 	
-#line 1282 "MDTreeParser.cpp"
+#line 1274 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1300,9 +1292,9 @@ void MDTreeParser::bondstatement(ANTLR_USE_NAMESPACE(a
 			_t = _retTree;
 			_t = __t50;
 			_t = _t->getNextSibling();
-#line 160 "MDTreeParser.g"
+#line 159 "MDTreeParser.g"
 			currBondStamp->setMembers(ivec);
-#line 1306 "MDTreeParser.cpp"
+#line 1298 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1320,36 +1312,36 @@ vector<int>  MDTreeParser::inttuple(ANTLR_USE_NAMESPAC
 }
 
 vector<int>  MDTreeParser::inttuple(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 288 "MDTreeParser.g"
+#line 304 "MDTreeParser.g"
 	vector<int> ivec;
-#line 1326 "MDTreeParser.cpp"
+#line 1318 "MDTreeParser.cpp"
 	ANTLR_USE_NAMESPACE(antlr)RefAST inttuple_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 288 "MDTreeParser.g"
+#line 304 "MDTreeParser.g"
 	
 	int ival;
 	
-#line 1332 "MDTreeParser.cpp"
+#line 1324 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		{ // ( ... )+
-		int _cnt92=0;
+		int _cnt98=0;
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
 				_t = ASTNULL;
 			if ((_t->getType() == NUM_INT || _t->getType() == NUM_LONG)) {
 				ival=intConst(_t);
 				_t = _retTree;
-#line 292 "MDTreeParser.g"
+#line 308 "MDTreeParser.g"
 				ivec.push_back(ival);
-#line 1345 "MDTreeParser.cpp"
+#line 1337 "MDTreeParser.cpp"
 			}
 			else {
-				if ( _cnt92>=1 ) { goto _loop92; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
+				if ( _cnt98>=1 ) { goto _loop98; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
 			}
 			
-			_cnt92++;
+			_cnt98++;
 		}
-		_loop92:;
+		_loop98:;
 		}  // ( ... )+
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
@@ -1363,12 +1355,12 @@ void MDTreeParser::bendstatement(ANTLR_USE_NAMESPACE(a
 
 void MDTreeParser::bendstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST bendstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 173 "MDTreeParser.g"
+#line 172 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
 	
-#line 1372 "MDTreeParser.cpp"
+#line 1364 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1390,9 +1382,9 @@ void MDTreeParser::bendstatement(ANTLR_USE_NAMESPACE(a
 			_t = _retTree;
 			_t = __t56;
 			_t = _t->getNextSibling();
-#line 179 "MDTreeParser.g"
+#line 178 "MDTreeParser.g"
 			currBendStamp->setMembers(ivec);
-#line 1396 "MDTreeParser.cpp"
+#line 1388 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1411,12 +1403,12 @@ void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPAC
 
 void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST torsionstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 192 "MDTreeParser.g"
+#line 191 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
 	
-#line 1420 "MDTreeParser.cpp"
+#line 1412 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1438,9 +1430,9 @@ void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPAC
 			_t = _retTree;
 			_t = __t62;
 			_t = _t->getNextSibling();
-#line 198 "MDTreeParser.g"
+#line 197 "MDTreeParser.g"
 			currTorsionStamp->setMembers(ivec);
-#line 1444 "MDTreeParser.cpp"
+#line 1436 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1459,13 +1451,13 @@ void MDTreeParser::inversionstatement(ANTLR_USE_NAMESP
 
 void MDTreeParser::inversionstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST inversionstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 211 "MDTreeParser.g"
+#line 210 "MDTreeParser.g"
 	
 	int icent;
 	vector<int> ivec;
 	InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
 	
-#line 1469 "MDTreeParser.cpp"
+#line 1461 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1487,9 +1479,9 @@ void MDTreeParser::inversionstatement(ANTLR_USE_NAMESP
 			_t = _retTree;
 			_t = __t68;
 			_t = _t->getNextSibling();
-#line 218 "MDTreeParser.g"
+#line 217 "MDTreeParser.g"
 			currInversionStamp->setCenter(icent);
-#line 1493 "MDTreeParser.cpp"
+#line 1485 "MDTreeParser.cpp"
 			break;
 		}
 		case SATELLITES:
@@ -1502,9 +1494,9 @@ void MDTreeParser::inversionstatement(ANTLR_USE_NAMESP
 			_t = _retTree;
 			_t = __t69;
 			_t = _t->getNextSibling();
-#line 219 "MDTreeParser.g"
+#line 218 "MDTreeParser.g"
 			currInversionStamp->setSatellites(ivec);
-#line 1508 "MDTreeParser.cpp"
+#line 1500 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1523,12 +1515,12 @@ void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESP
 
 void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodystatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 236 "MDTreeParser.g"
+#line 235 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
 	
-#line 1532 "MDTreeParser.cpp"
+#line 1524 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1550,9 +1542,9 @@ void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESP
 			_t = _retTree;
 			_t = __t75;
 			_t = _t->getNextSibling();
-#line 242 "MDTreeParser.g"
+#line 241 "MDTreeParser.g"
 			currRigidBodyStamp->setMembers(ivec);
-#line 1556 "MDTreeParser.cpp"
+#line 1548 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1571,12 +1563,12 @@ void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAME
 
 void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
 	ANTLR_USE_NAMESPACE(antlr)RefAST cutoffgroupstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 255 "MDTreeParser.g"
+#line 254 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
 	
-#line 1580 "MDTreeParser.cpp"
+#line 1572 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1598,9 +1590,9 @@ void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAME
 			_t = _retTree;
 			_t = __t81;
 			_t = _t->getNextSibling();
-#line 261 "MDTreeParser.g"
+#line 260 "MDTreeParser.g"
 			currCutoffGroupStamp->setMembers(ivec);
-#line 1604 "MDTreeParser.cpp"
+#line 1596 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1632,6 +1624,103 @@ void MDTreeParser::fragmentstatement(ANTLR_USE_NAMESPA
 	_retTree = _t;
 }
 
+void MDTreeParser::constraintstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST constraintstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 286 "MDTreeParser.g"
+	
+	vector<int> ivec;
+	ConstraintStamp* currConstraintStamp = static_cast<ConstraintStamp*>(blockStack.top());
+	
+#line 1635 "MDTreeParser.cpp"
+	
+	try {      // for error handling
+		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+			_t = ASTNULL;
+		switch ( _t->getType()) {
+		case ASSIGNEQUAL:
+		{
+			assignment(_t);
+			_t = _retTree;
+			break;
+		}
+		case MEMBERS:
+		{
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t92 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp45_AST_in = _t;
+			match(_t,MEMBERS);
+			_t = _t->getFirstChild();
+			ivec=inttuple(_t);
+			_t = _retTree;
+			_t = __t92;
+			_t = _t->getNextSibling();
+#line 292 "MDTreeParser.g"
+			currConstraintStamp->setMembers(ivec);
+#line 1659 "MDTreeParser.cpp"
+			break;
+		}
+		default:
+		{
+			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
+		}
+		}
+	}
+	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
+		reportError(ex);
+		if ( _t != ANTLR_USE_NAMESPACE(antlr)nullAST )
+			_t = _t->getNextSibling();
+	}
+	_retTree = _t;
+}
+
+RealType  MDTreeParser::doubleNumber(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+#line 318 "MDTreeParser.g"
+	RealType dval;
+#line 1679 "MDTreeParser.cpp"
+	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumber_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST ic = ANTLR_USE_NAMESPACE(antlr)nullAST;
+	ANTLR_USE_NAMESPACE(antlr)RefAST fc = ANTLR_USE_NAMESPACE(antlr)nullAST;
+	
+	try {      // for error handling
+		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+			_t = ASTNULL;
+		switch ( _t->getType()) {
+		case NUM_INT:
+		case NUM_LONG:
+		{
+			ic = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+			intConst(_t);
+			_t = _retTree;
+#line 319 "MDTreeParser.g"
+			dval = lexi_cast<RealType>(ic->getText());
+#line 1696 "MDTreeParser.cpp"
+			break;
+		}
+		case NUM_FLOAT:
+		case NUM_DOUBLE:
+		{
+			fc = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+			floatConst(_t);
+			_t = _retTree;
+#line 320 "MDTreeParser.g"
+			dval = lexi_cast<RealType>(fc->getText());
+#line 1707 "MDTreeParser.cpp"
+			break;
+		}
+		default:
+		{
+			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
+		}
+		}
+	}
+	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
+		reportError(ex);
+		if ( _t != ANTLR_USE_NAMESPACE(antlr)nullAST )
+			_t = _t->getNextSibling();
+	}
+	_retTree = _t;
+	return dval;
+}
+
 void MDTreeParser::initializeASTFactory( ANTLR_USE_NAMESPACE(antlr)ASTFactory& )
 {
 }
@@ -1651,6 +1740,8 @@ const char* MDTreeParser::tokenNames[] = {
 	"\"inversion\"",
 	"\"rigidBody\"",
 	"\"cutoffGroup\"",
+	"\"constraint\"",
+	"\"distance\"",
 	"\"fragment\"",
 	"\"members\"",
 	"\"center\"",
@@ -1697,13 +1788,13 @@ const char* MDTreeParser::tokenNames[] = {
 	0
 };
 
-const unsigned long MDTreeParser::_tokenSet_0_data_[] = { 81789168UL, 0UL, 0UL, 0UL };
+const unsigned long MDTreeParser::_tokenSet_0_data_[] = { 327155952UL, 0UL, 0UL, 0UL };
 // "component" "molecule" "zconstraint" "restraint" "flucQ" "RNEMD" "minimizer" 
 // ASSIGNEQUAL 
 const ANTLR_USE_NAMESPACE(antlr)BitSet MDTreeParser::_tokenSet_0(_tokenSet_0_data_,4);
-const unsigned long MDTreeParser::_tokenSet_1_data_[] = { 67174144UL, 0UL, 0UL, 0UL };
+const unsigned long MDTreeParser::_tokenSet_1_data_[] = { 268631808UL, 0UL, 0UL, 0UL };
 // "atom" "bond" "bend" "torsion" "inversion" "rigidBody" "cutoffGroup" 
-// "fragment" ASSIGNEQUAL 
+// "constraint" "fragment" ASSIGNEQUAL 
 const ANTLR_USE_NAMESPACE(antlr)BitSet MDTreeParser::_tokenSet_1(_tokenSet_1_data_,4);