--- trunk/src/mdParser/MDTreeParser.cpp	2008/07/04 20:54:29	1275
+++ branches/development/src/mdParser/MDTreeParser.cpp	2012/08/09 15:52:59	1776
@@ -1,4 +1,4 @@
-/* $ANTLR 2.7.4: "MDTreeParser.g" -> "MDTreeParser.cpp"$ */
+/* $ANTLR 2.7.7 (20120725): "MDTreeParser.g" -> "MDTreeParser.cpp"$ */
 #include "MDTreeParser.hpp"
 #include <antlr/Token.hpp>
 #include <antlr/AST.hpp>
@@ -13,7 +13,7 @@ void MDTreeParser::mdfile(ANTLR_USE_NAMESPACE(antlr)Re
 }
 
 void MDTreeParser::mdfile(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST mdfile_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST mdfile_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
 		{ // ( ... )*
@@ -44,7 +44,7 @@ void MDTreeParser::statement(ANTLR_USE_NAMESPACE(antlr
 }
 
 void MDTreeParser::statement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST statement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST statement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -74,6 +74,30 @@ void MDTreeParser::statement(ANTLR_USE_NAMESPACE(antlr
 			_t = _retTree;
 			break;
 		}
+		case RESTRAINT:
+		{
+			restraintblock(_t);
+			_t = _retTree;
+			break;
+		}
+		case FLUCQ:
+		{
+			flucqblock(_t);
+			_t = _retTree;
+			break;
+		}
+		case RNEMD:
+		{
+			rnemdblock(_t);
+			_t = _retTree;
+			break;
+		}
+		case MINIMIZER:
+		{
+			minimizerblock(_t);
+			_t = _retTree;
+			break;
+		}
 		default:
 		{
 			throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);
@@ -89,7 +113,7 @@ void MDTreeParser::assignment(ANTLR_USE_NAMESPACE(antl
 }
 
 void MDTreeParser::assignment(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST assignment_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST assignment_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	ANTLR_USE_NAMESPACE(antlr)RefAST id = ANTLR_USE_NAMESPACE(antlr)nullAST;
 	
 	try {      // for error handling
@@ -114,16 +138,16 @@ void MDTreeParser::componentblock(ANTLR_USE_NAMESPACE(
 }
 
 void MDTreeParser::componentblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST componentblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST componentblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t9 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t10 = _t;
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp2_AST_in = _t;
 		match(_t,COMPONENT);
 		_t = _t->getFirstChild();
-#line 62 "MDTreeParser.g"
+#line 72 "MDTreeParser.g"
 		Component* currComponet = new Component(); blockStack.push(currComponet);
-#line 127 "MDTreeParser.cpp"
+#line 151 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -133,20 +157,20 @@ void MDTreeParser::componentblock(ANTLR_USE_NAMESPACE(
 				_t = _retTree;
 			}
 			else {
-				goto _loop11;
+				goto _loop12;
 			}
 			
 		}
-		_loop11:;
+		_loop12:;
 		} // ( ... )*
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp3_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t9;
+		_t = __t10;
 		_t = _t->getNextSibling();
-#line 64 "MDTreeParser.g"
+#line 74 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addComponent(currComponet);
-#line 150 "MDTreeParser.cpp"
+#line 174 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -157,16 +181,16 @@ void MDTreeParser::moleculeblock(ANTLR_USE_NAMESPACE(a
 }
 
 void MDTreeParser::moleculeblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST moleculeblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST moleculeblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t17 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t34 = _t;
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp4_AST_in = _t;
 		match(_t,MOLECULE);
 		_t = _t->getFirstChild();
-#line 72 "MDTreeParser.g"
+#line 103 "MDTreeParser.g"
 		MoleculeStamp* currMoleculeStamp = new MoleculeStamp(); blockStack.push(currMoleculeStamp);
-#line 170 "MDTreeParser.cpp"
+#line 194 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -176,20 +200,20 @@ void MDTreeParser::moleculeblock(ANTLR_USE_NAMESPACE(a
 				_t = _retTree;
 			}
 			else {
-				goto _loop19;
+				goto _loop36;
 			}
 			
 		}
-		_loop19:;
+		_loop36:;
 		} // ( ... )*
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp5_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t17;
+		_t = __t34;
 		_t = _t->getNextSibling();
-#line 74 "MDTreeParser.g"
+#line 105 "MDTreeParser.g"
 		blockStack.top()->validate(); blockStack.pop(); currConf->addMoleculeStamp(currMoleculeStamp);
-#line 193 "MDTreeParser.cpp"
+#line 217 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -200,16 +224,16 @@ void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPAC
 }
 
 void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST zconstraintblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST zconstraintblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t13 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t14 = _t;
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp6_AST_in = _t;
 		match(_t,ZCONSTRAINT);
 		_t = _t->getFirstChild();
-#line 67 "MDTreeParser.g"
+#line 77 "MDTreeParser.g"
 		ZConsStamp* currZConsStamp = new ZConsStamp(); blockStack.push(currZConsStamp);
-#line 213 "MDTreeParser.cpp"
+#line 237 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -219,20 +243,20 @@ void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPAC
 				_t = _retTree;
 			}
 			else {
-				goto _loop15;
+				goto _loop16;
 			}
 			
 		}
-		_loop15:;
+		_loop16:;
 		} // ( ... )*
 		ANTLR_USE_NAMESPACE(antlr)RefAST tmp7_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t13;
+		_t = __t14;
 		_t = _t->getNextSibling();
-#line 69 "MDTreeParser.g"
+#line 79 "MDTreeParser.g"
 		blockStack.top()->validate();blockStack.pop(); currConf->addZConsStamp(currZConsStamp);
-#line 236 "MDTreeParser.cpp"
+#line 260 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -242,18 +266,191 @@ void MDTreeParser::zconstraintblock(ANTLR_USE_NAMESPAC
 	_retTree = _t;
 }
 
+void MDTreeParser::restraintblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST restraintblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	
+	try {      // for error handling
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t18 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp8_AST_in = _t;
+		match(_t,RESTRAINT);
+		_t = _t->getFirstChild();
+#line 82 "MDTreeParser.g"
+		RestraintStamp* currRestraintStamp = new RestraintStamp(); blockStack.push(currRestraintStamp);
+#line 280 "MDTreeParser.cpp"
+		{ // ( ... )*
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if ((_t->getType() == ASSIGNEQUAL)) {
+				assignment(_t);
+				_t = _retTree;
+			}
+			else {
+				goto _loop20;
+			}
+			
+		}
+		_loop20:;
+		} // ( ... )*
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp9_AST_in = _t;
+		match(_t,ENDBLOCK);
+		_t = _t->getNextSibling();
+		_t = __t18;
+		_t = _t->getNextSibling();
+#line 84 "MDTreeParser.g"
+		blockStack.top()->validate();blockStack.pop(); currConf->addRestraintStamp(currRestraintStamp);
+#line 303 "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::flucqblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST flucqblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	
+	try {      // for error handling
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t22 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp10_AST_in = _t;
+		match(_t,FLUCQ);
+		_t = _t->getFirstChild();
+#line 87 "MDTreeParser.g"
+		FluctuatingChargeParameters* flucQpars = new FluctuatingChargeParameters(); blockStack.push(flucQpars);
+#line 323 "MDTreeParser.cpp"
+		{ // ( ... )*
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if ((_t->getType() == ASSIGNEQUAL)) {
+				assignment(_t);
+				_t = _retTree;
+			}
+			else {
+				goto _loop24;
+			}
+			
+		}
+		_loop24:;
+		} // ( ... )*
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp11_AST_in = _t;
+		match(_t,ENDBLOCK);
+		_t = _t->getNextSibling();
+		_t = __t22;
+		_t = _t->getNextSibling();
+#line 89 "MDTreeParser.g"
+		blockStack.top()->validate();blockStack.pop(); currConf->addFluctuatingChargeParameters(flucQpars);
+#line 346 "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::rnemdblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST rnemdblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	
+	try {      // for error handling
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t26 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp12_AST_in = _t;
+		match(_t,RNEMD);
+		_t = _t->getFirstChild();
+#line 92 "MDTreeParser.g"
+		RNEMDParameters* rnemdPars = new RNEMDParameters(); blockStack.push(rnemdPars);
+#line 366 "MDTreeParser.cpp"
+		{ // ( ... )*
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if ((_t->getType() == ASSIGNEQUAL)) {
+				assignment(_t);
+				_t = _retTree;
+			}
+			else {
+				goto _loop28;
+			}
+			
+		}
+		_loop28:;
+		} // ( ... )*
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp13_AST_in = _t;
+		match(_t,ENDBLOCK);
+		_t = _t->getNextSibling();
+		_t = __t26;
+		_t = _t->getNextSibling();
+#line 94 "MDTreeParser.g"
+		blockStack.top()->validate();blockStack.pop(); currConf->addRNEMDParameters(rnemdPars);
+#line 389 "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::minimizerblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+	ANTLR_USE_NAMESPACE(antlr)RefAST minimizerblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	
+	try {      // for error handling
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t30 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp14_AST_in = _t;
+		match(_t,MINIMIZER);
+		_t = _t->getFirstChild();
+#line 97 "MDTreeParser.g"
+		MinimizerParameters* minimizerPars = new MinimizerParameters(); blockStack.push(minimizerPars);
+#line 409 "MDTreeParser.cpp"
+		{ // ( ... )*
+		for (;;) {
+			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
+				_t = ASTNULL;
+			if ((_t->getType() == ASSIGNEQUAL)) {
+				assignment(_t);
+				_t = _retTree;
+			}
+			else {
+				goto _loop32;
+			}
+			
+		}
+		_loop32:;
+		} // ( ... )*
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp15_AST_in = _t;
+		match(_t,ENDBLOCK);
+		_t = _t->getNextSibling();
+		_t = __t30;
+		_t = _t->getNextSibling();
+#line 99 "MDTreeParser.g"
+		blockStack.top()->validate();blockStack.pop(); currConf->addMinimizerParameters(minimizerPars);
+#line 432 "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::constant(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
 	ANTLR_USE_NAMESPACE(antlr)RefAST id
 ) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST constant_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST constant_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	ANTLR_USE_NAMESPACE(antlr)RefAST str1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
 	ANTLR_USE_NAMESPACE(antlr)RefAST str2 = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 47 "MDTreeParser.g"
+#line 50 "MDTreeParser.g"
 	
 	int ival;
-	RealType dval;
+	RealType dval, x, y, z;
+	Vector3d dvec;
 	
-#line 257 "MDTreeParser.cpp"
+#line 454 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -264,9 +461,9 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 		{
 			ival=intConst(_t);
 			_t = _retTree;
-#line 52 "MDTreeParser.g"
+#line 56 "MDTreeParser.g"
 			blockStack.top()->assign(id->getText(), ival);
-#line 270 "MDTreeParser.cpp"
+#line 467 "MDTreeParser.cpp"
 			break;
 		}
 		case NUM_FLOAT:
@@ -274,19 +471,51 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 		{
 			dval=floatConst(_t);
 			_t = _retTree;
-#line 53 "MDTreeParser.g"
+#line 57 "MDTreeParser.g"
 			blockStack.top()->assign(id->getText(), dval);
-#line 280 "MDTreeParser.cpp"
+#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:
 		{
 			str1 = _t;
 			match(_t,ID);
 			_t = _t->getNextSibling();
-#line 54 "MDTreeParser.g"
+#line 64 "MDTreeParser.g"
 			blockStack.top()->assign(id->getText(), str1->getText());
-#line 290 "MDTreeParser.cpp"
+#line 519 "MDTreeParser.cpp"
 			break;
 		}
 		case StringLiteral:
@@ -294,12 +523,12 @@ void MDTreeParser::constant(ANTLR_USE_NAMESPACE(antlr)
 			str2 = _t;
 			match(_t,StringLiteral);
 			_t = _t->getNextSibling();
-#line 55 "MDTreeParser.g"
+#line 65 "MDTreeParser.g"
 			std::string s =  str2->getText();
 			s = s.substr(1, s.length()-2);
 			blockStack.top()->assign(id->getText(),s);
 			
-#line 303 "MDTreeParser.cpp"
+#line 532 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -317,10 +546,10 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 }
 
 int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 262 "MDTreeParser.g"
+#line 294 "MDTreeParser.g"
 	int ival;
-#line 323 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST intConst_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 552 "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;
 	
@@ -333,9 +562,9 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 			i1 = _t;
 			match(_t,NUM_INT);
 			_t = _t->getNextSibling();
-#line 263 "MDTreeParser.g"
+#line 295 "MDTreeParser.g"
 			ival = lexi_cast<int>(i1->getText());
-#line 339 "MDTreeParser.cpp"
+#line 568 "MDTreeParser.cpp"
 			break;
 		}
 		case NUM_LONG:
@@ -343,9 +572,9 @@ int  MDTreeParser::intConst(ANTLR_USE_NAMESPACE(antlr)
 			i2 = _t;
 			match(_t,NUM_LONG);
 			_t = _t->getNextSibling();
-#line 264 "MDTreeParser.g"
+#line 296 "MDTreeParser.g"
 			ival = lexi_cast<int>(i2->getText());
-#line 349 "MDTreeParser.cpp"
+#line 578 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -364,10 +593,10 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 }
 
 RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 276 "MDTreeParser.g"
+#line 306 "MDTreeParser.g"
 	RealType dval;
-#line 370 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST floatConst_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 599 "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;
 	
@@ -380,9 +609,9 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 			d1 = _t;
 			match(_t,NUM_FLOAT);
 			_t = _t->getNextSibling();
-#line 277 "MDTreeParser.g"
+#line 307 "MDTreeParser.g"
 			dval = lexi_cast<RealType>(d1->getText());
-#line 386 "MDTreeParser.cpp"
+#line 615 "MDTreeParser.cpp"
 			break;
 		}
 		case NUM_DOUBLE:
@@ -390,9 +619,9 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 			d2 = _t;
 			match(_t,NUM_DOUBLE);
 			_t = _t->getNextSibling();
-#line 278 "MDTreeParser.g"
+#line 308 "MDTreeParser.g"
 			dval = lexi_cast<RealType>(d2->getText());
-#line 396 "MDTreeParser.cpp"
+#line 625 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -410,8 +639,57 @@ RealType  MDTreeParser::floatConst(ANTLR_USE_NAMESPACE
 	return dval;
 }
 
+RealType  MDTreeParser::doubleNumber(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
+#line 300 "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;
+	
+	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 301 "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 302 "MDTreeParser.g"
+			dval = lexi_cast<RealType>(fc->getText());
+#line 674 "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::moleculestatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST moleculestatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST moleculestatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -486,23 +764,23 @@ 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 == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 88 "MDTreeParser.g"
+	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"
 	
 	int index;
 	
-#line 495 "MDTreeParser.cpp"
+#line 773 "MDTreeParser.cpp"
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t22 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp8_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t39 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp20_AST_in = _t;
 		match(_t,ATOM);
 		_t = _t->getFirstChild();
 		index=intConst(_t);
 		_t = _retTree;
-#line 92 "MDTreeParser.g"
+#line 123 "MDTreeParser.g"
 		AtomStamp* currAtomStamp = new AtomStamp(index); blockStack.push(currAtomStamp);
-#line 506 "MDTreeParser.cpp"
+#line 784 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -512,25 +790,25 @@ void MDTreeParser::atomblock(ANTLR_USE_NAMESPACE(antlr
 				_t = _retTree;
 			}
 			else {
-				goto _loop24;
+				goto _loop41;
 			}
 			
 		}
-		_loop24:;
+		_loop41:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp9_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp21_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t22;
+		_t = __t39;
 		_t = _t->getNextSibling();
-#line 94 "MDTreeParser.g"
+#line 125 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addAtomStamp(currAtomStamp); 
 		
-#line 534 "MDTreeParser.cpp"
+#line 812 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -541,16 +819,16 @@ void MDTreeParser::bondblock(ANTLR_USE_NAMESPACE(antlr
 }
 
 void MDTreeParser::bondblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST bondblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST bondblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t29 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp10_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t46 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp22_AST_in = _t;
 		match(_t,BOND);
 		_t = _t->getFirstChild();
-#line 114 "MDTreeParser.g"
+#line 145 "MDTreeParser.g"
 		BondStamp* currBondStamp = new BondStamp(); blockStack.push(currBondStamp);
-#line 554 "MDTreeParser.cpp"
+#line 832 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -560,24 +838,24 @@ void MDTreeParser::bondblock(ANTLR_USE_NAMESPACE(antlr
 				_t = _retTree;
 			}
 			else {
-				goto _loop31;
+				goto _loop48;
 			}
 			
 		}
-		_loop31:;
+		_loop48:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp11_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp23_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t29;
+		_t = __t46;
 		_t = _t->getNextSibling();
-#line 116 "MDTreeParser.g"
+#line 147 "MDTreeParser.g"
 		
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addBondStamp(currBondStamp); 
 		
-#line 581 "MDTreeParser.cpp"
+#line 859 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -588,16 +866,16 @@ void MDTreeParser::bendblock(ANTLR_USE_NAMESPACE(antlr
 }
 
 void MDTreeParser::bendblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST bendblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST bendblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t35 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp12_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t52 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp24_AST_in = _t;
 		match(_t,BEND);
 		_t = _t->getFirstChild();
-#line 132 "MDTreeParser.g"
+#line 163 "MDTreeParser.g"
 		BendStamp* currBendStamp = new BendStamp(); blockStack.push(currBendStamp);
-#line 601 "MDTreeParser.cpp"
+#line 879 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -607,25 +885,25 @@ void MDTreeParser::bendblock(ANTLR_USE_NAMESPACE(antlr
 				_t = _retTree;
 			}
 			else {
-				goto _loop37;
+				goto _loop54;
 			}
 			
 		}
-		_loop37:;
+		_loop54:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp13_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp25_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t35;
+		_t = __t52;
 		_t = _t->getNextSibling();
-#line 134 "MDTreeParser.g"
+#line 165 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addBendStamp(currBendStamp); 
 		
-#line 629 "MDTreeParser.cpp"
+#line 907 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -636,16 +914,16 @@ void MDTreeParser::torsionblock(ANTLR_USE_NAMESPACE(an
 }
 
 void MDTreeParser::torsionblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST torsionblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST torsionblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t41 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp14_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t58 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp26_AST_in = _t;
 		match(_t,TORSION);
 		_t = _t->getFirstChild();
-#line 151 "MDTreeParser.g"
+#line 182 "MDTreeParser.g"
 		TorsionStamp* currTorsionStamp = new TorsionStamp(); blockStack.push(currTorsionStamp);
-#line 649 "MDTreeParser.cpp"
+#line 927 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -655,25 +933,25 @@ void MDTreeParser::torsionblock(ANTLR_USE_NAMESPACE(an
 				_t = _retTree;
 			}
 			else {
-				goto _loop43;
+				goto _loop60;
 			}
 			
 		}
-		_loop43:;
+		_loop60:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp15_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp27_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t41;
+		_t = __t58;
 		_t = _t->getNextSibling();
-#line 153 "MDTreeParser.g"
+#line 184 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addTorsionStamp(currTorsionStamp); 
 		
-#line 677 "MDTreeParser.cpp"
+#line 955 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -684,16 +962,16 @@ void MDTreeParser::inversionblock(ANTLR_USE_NAMESPACE(
 }
 
 void MDTreeParser::inversionblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST inversionblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST inversionblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t47 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp16_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t64 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp28_AST_in = _t;
 		match(_t,INVERSION);
 		_t = _t->getFirstChild();
-#line 170 "MDTreeParser.g"
+#line 201 "MDTreeParser.g"
 		InversionStamp* currInversionStamp = new InversionStamp(); blockStack.push(currInversionStamp);
-#line 697 "MDTreeParser.cpp"
+#line 975 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -703,25 +981,25 @@ void MDTreeParser::inversionblock(ANTLR_USE_NAMESPACE(
 				_t = _retTree;
 			}
 			else {
-				goto _loop49;
+				goto _loop66;
 			}
 			
 		}
-		_loop49:;
+		_loop66:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp17_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp29_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t47;
+		_t = __t64;
 		_t = _t->getNextSibling();
-#line 172 "MDTreeParser.g"
+#line 203 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addInversionStamp(currInversionStamp); 
 		
-#line 725 "MDTreeParser.cpp"
+#line 1003 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -732,23 +1010,23 @@ void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(
 }
 
 void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodyblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 189 "MDTreeParser.g"
+	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodyblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 220 "MDTreeParser.g"
 	
 	int index;
 	
-#line 741 "MDTreeParser.cpp"
+#line 1019 "MDTreeParser.cpp"
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t53 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp18_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t70 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp30_AST_in = _t;
 		match(_t,RIGIDBODY);
 		_t = _t->getFirstChild();
 		index=intConst(_t);
 		_t = _retTree;
-#line 193 "MDTreeParser.g"
+#line 224 "MDTreeParser.g"
 		RigidBodyStamp* currRigidBodyStamp = new RigidBodyStamp(index); blockStack.push(currRigidBodyStamp);
-#line 752 "MDTreeParser.cpp"
+#line 1030 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -758,25 +1036,25 @@ void MDTreeParser::rigidbodyblock(ANTLR_USE_NAMESPACE(
 				_t = _retTree;
 			}
 			else {
-				goto _loop55;
+				goto _loop72;
 			}
 			
 		}
-		_loop55:;
+		_loop72:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp19_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp31_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t53;
+		_t = __t70;
 		_t = _t->getNextSibling();
-#line 195 "MDTreeParser.g"
+#line 226 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addRigidBodyStamp(currRigidBodyStamp); 
 		
-#line 780 "MDTreeParser.cpp"
+#line 1058 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -787,16 +1065,16 @@ void MDTreeParser::cutoffgroupblock(ANTLR_USE_NAMESPAC
 }
 
 void MDTreeParser::cutoffgroupblock(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST cutoffgroupblock_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST cutoffgroupblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t59 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp20_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t76 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp32_AST_in = _t;
 		match(_t,CUTOFFGROUP);
 		_t = _t->getFirstChild();
-#line 212 "MDTreeParser.g"
+#line 243 "MDTreeParser.g"
 		CutoffGroupStamp* currCutoffGroupStamp = new CutoffGroupStamp(); blockStack.push(currCutoffGroupStamp);
-#line 800 "MDTreeParser.cpp"
+#line 1078 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -806,25 +1084,25 @@ void MDTreeParser::cutoffgroupblock(ANTLR_USE_NAMESPAC
 				_t = _retTree;
 			}
 			else {
-				goto _loop61;
+				goto _loop78;
 			}
 			
 		}
-		_loop61:;
+		_loop78:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp21_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp33_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t59;
+		_t = __t76;
 		_t = _t->getNextSibling();
-#line 214 "MDTreeParser.g"
+#line 245 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addCutoffGroupStamp(currCutoffGroupStamp); 
 		
-#line 828 "MDTreeParser.cpp"
+#line 1106 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -835,21 +1113,21 @@ 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 == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 231 "MDTreeParser.g"
+	ANTLR_USE_NAMESPACE(antlr)RefAST fragmentblock_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 262 "MDTreeParser.g"
 	int ival;
-#line 842 "MDTreeParser.cpp"
+#line 1120 "MDTreeParser.cpp"
 	
 	try {      // for error handling
-		ANTLR_USE_NAMESPACE(antlr)RefAST __t65 = _t;
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp22_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST __t82 = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp34_AST_in = _t;
 		match(_t,FRAGMENT);
 		_t = _t->getFirstChild();
 		ival=intConst(_t);
 		_t = _retTree;
-#line 232 "MDTreeParser.g"
+#line 263 "MDTreeParser.g"
 		FragmentStamp* currFragmentStamp = new FragmentStamp(ival); blockStack.push(currFragmentStamp);
-#line 853 "MDTreeParser.cpp"
+#line 1131 "MDTreeParser.cpp"
 		{ // ( ... )*
 		for (;;) {
 			if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -859,25 +1137,25 @@ void MDTreeParser::fragmentblock(ANTLR_USE_NAMESPACE(a
 				_t = _retTree;
 			}
 			else {
-				goto _loop67;
+				goto _loop84;
 			}
 			
 		}
-		_loop67:;
+		_loop84:;
 		} // ( ... )*
-		ANTLR_USE_NAMESPACE(antlr)RefAST tmp23_AST_in = _t;
+		ANTLR_USE_NAMESPACE(antlr)RefAST tmp35_AST_in = _t;
 		match(_t,ENDBLOCK);
 		_t = _t->getNextSibling();
-		_t = __t65;
+		_t = __t82;
 		_t = _t->getNextSibling();
-#line 234 "MDTreeParser.g"
+#line 265 "MDTreeParser.g"
 		
 		blockStack.top()->validate();
 		blockStack.pop(); 
 		MoleculeStamp* currMoleculeStamp = static_cast<MoleculeStamp*>(blockStack.top());
 		currMoleculeStamp->addFragmentStamp(currFragmentStamp); 
 		
-#line 881 "MDTreeParser.cpp"
+#line 1159 "MDTreeParser.cpp"
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
 		reportError(ex);
@@ -888,14 +1166,14 @@ void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(a
 }
 
 void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST atomstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 102 "MDTreeParser.g"
+	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"
 	
 	vector<RealType> dvec;
 	AtomStamp* currAtomStamp =  static_cast<AtomStamp*>(blockStack.top());
 	
 	
-#line 899 "MDTreeParser.cpp"
+#line 1177 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -909,32 +1187,32 @@ void MDTreeParser::atomstatement(ANTLR_USE_NAMESPACE(a
 		}
 		case POSITION:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t26 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp24_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t43 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp36_AST_in = _t;
 			match(_t,POSITION);
 			_t = _t->getFirstChild();
 			dvec=doubleNumberTuple(_t);
 			_t = _retTree;
-			_t = __t26;
+			_t = __t43;
 			_t = _t->getNextSibling();
-#line 109 "MDTreeParser.g"
+#line 140 "MDTreeParser.g"
 			currAtomStamp->setPosition(dvec);
-#line 923 "MDTreeParser.cpp"
+#line 1201 "MDTreeParser.cpp"
 			break;
 		}
 		case ORIENTATION:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t27 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp25_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t44 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp37_AST_in = _t;
 			match(_t,ORIENTATION);
 			_t = _t->getFirstChild();
 			dvec=doubleNumberTuple(_t);
 			_t = _retTree;
-			_t = __t27;
+			_t = __t44;
 			_t = _t->getNextSibling();
-#line 110 "MDTreeParser.g"
+#line 141 "MDTreeParser.g"
 			currAtomStamp->setOrientation(dvec);
-#line 938 "MDTreeParser.cpp"
+#line 1216 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -952,36 +1230,36 @@ vector<RealType>  MDTreeParser::doubleNumberTuple(ANTL
 }
 
 vector<RealType>  MDTreeParser::doubleNumberTuple(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 247 "MDTreeParser.g"
+#line 278 "MDTreeParser.g"
 	vector<RealType> dvec;
-#line 958 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumberTuple_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 247 "MDTreeParser.g"
+#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 278 "MDTreeParser.g"
 	
 	RealType dval;
 	
-#line 964 "MDTreeParser.cpp"
+#line 1242 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		{ // ( ... )+
-		int _cnt71=0;
+		int _cnt88=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 251 "MDTreeParser.g"
+#line 282 "MDTreeParser.g"
 				dvec.push_back(dval);
-#line 977 "MDTreeParser.cpp"
+#line 1255 "MDTreeParser.cpp"
 			}
 			else {
-				if ( _cnt71>=1 ) { goto _loop71; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
+				if ( _cnt88>=1 ) { goto _loop88; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
 			}
 			
-			_cnt71++;
+			_cnt88++;
 		}
-		_loop71:;
+		_loop88:;
 		}  // ( ... )+
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
@@ -994,13 +1272,13 @@ void MDTreeParser::bondstatement(ANTLR_USE_NAMESPACE(a
 }
 
 void MDTreeParser::bondstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST bondstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 123 "MDTreeParser.g"
+	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"
 	
 	vector<int> ivec;
 	BondStamp* currBondStamp = static_cast<BondStamp*>(blockStack.top());
 	
-#line 1004 "MDTreeParser.cpp"
+#line 1282 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1014,17 +1292,17 @@ void MDTreeParser::bondstatement(ANTLR_USE_NAMESPACE(a
 		}
 		case MEMBERS:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t33 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp26_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t50 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp38_AST_in = _t;
 			match(_t,MEMBERS);
 			_t = _t->getFirstChild();
 			ivec=inttuple(_t);
 			_t = _retTree;
-			_t = __t33;
+			_t = __t50;
 			_t = _t->getNextSibling();
-#line 129 "MDTreeParser.g"
+#line 160 "MDTreeParser.g"
 			currBondStamp->setMembers(ivec);
-#line 1028 "MDTreeParser.cpp"
+#line 1306 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1042,36 +1320,36 @@ vector<int>  MDTreeParser::inttuple(ANTLR_USE_NAMESPAC
 }
 
 vector<int>  MDTreeParser::inttuple(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 254 "MDTreeParser.g"
+#line 286 "MDTreeParser.g"
 	vector<int> ivec;
-#line 1048 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST inttuple_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 254 "MDTreeParser.g"
+#line 1326 "MDTreeParser.cpp"
+	ANTLR_USE_NAMESPACE(antlr)RefAST inttuple_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 286 "MDTreeParser.g"
 	
 	int ival;
 	
-#line 1054 "MDTreeParser.cpp"
+#line 1332 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		{ // ( ... )+
-		int _cnt74=0;
+		int _cnt91=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 258 "MDTreeParser.g"
+#line 290 "MDTreeParser.g"
 				ivec.push_back(ival);
-#line 1067 "MDTreeParser.cpp"
+#line 1345 "MDTreeParser.cpp"
 			}
 			else {
-				if ( _cnt74>=1 ) { goto _loop74; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
+				if ( _cnt91>=1 ) { goto _loop91; } else {throw ANTLR_USE_NAMESPACE(antlr)NoViableAltException(_t);}
 			}
 			
-			_cnt74++;
+			_cnt91++;
 		}
-		_loop74:;
+		_loop91:;
 		}  // ( ... )+
 	}
 	catch (ANTLR_USE_NAMESPACE(antlr)RecognitionException& ex) {
@@ -1084,13 +1362,13 @@ 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 == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 142 "MDTreeParser.g"
+	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"
 	
 	vector<int> ivec;
 	BendStamp* currBendStamp = static_cast<BendStamp*>(blockStack.top());
 	
-#line 1094 "MDTreeParser.cpp"
+#line 1372 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1104,17 +1382,17 @@ void MDTreeParser::bendstatement(ANTLR_USE_NAMESPACE(a
 		}
 		case MEMBERS:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t39 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp27_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t56 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp39_AST_in = _t;
 			match(_t,MEMBERS);
 			_t = _t->getFirstChild();
 			ivec=inttuple(_t);
 			_t = _retTree;
-			_t = __t39;
+			_t = __t56;
 			_t = _t->getNextSibling();
-#line 148 "MDTreeParser.g"
+#line 179 "MDTreeParser.g"
 			currBendStamp->setMembers(ivec);
-#line 1118 "MDTreeParser.cpp"
+#line 1396 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1132,13 +1410,13 @@ void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPAC
 }
 
 void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST torsionstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 161 "MDTreeParser.g"
+	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"
 	
 	vector<int> ivec;
 	TorsionStamp* currTorsionStamp = static_cast<TorsionStamp*>(blockStack.top());
 	
-#line 1142 "MDTreeParser.cpp"
+#line 1420 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1152,17 +1430,17 @@ void MDTreeParser::torsionstatement(ANTLR_USE_NAMESPAC
 		}
 		case MEMBERS:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t45 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp28_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t62 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp40_AST_in = _t;
 			match(_t,MEMBERS);
 			_t = _t->getFirstChild();
 			ivec=inttuple(_t);
 			_t = _retTree;
-			_t = __t45;
+			_t = __t62;
 			_t = _t->getNextSibling();
-#line 167 "MDTreeParser.g"
+#line 198 "MDTreeParser.g"
 			currTorsionStamp->setMembers(ivec);
-#line 1166 "MDTreeParser.cpp"
+#line 1444 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1180,13 +1458,13 @@ void MDTreeParser::inversionstatement(ANTLR_USE_NAMESP
 }
 
 void MDTreeParser::inversionstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST inversionstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 180 "MDTreeParser.g"
+	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"
 	
 	int icent;
 	InversionStamp* currInversionStamp = static_cast<InversionStamp*>(blockStack.top());
 	
-#line 1190 "MDTreeParser.cpp"
+#line 1468 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1200,17 +1478,17 @@ void MDTreeParser::inversionstatement(ANTLR_USE_NAMESP
 		}
 		case CENTER:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t51 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp29_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t68 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp41_AST_in = _t;
 			match(_t,CENTER);
 			_t = _t->getFirstChild();
 			icent=intConst(_t);
 			_t = _retTree;
-			_t = __t51;
+			_t = __t68;
 			_t = _t->getNextSibling();
-#line 186 "MDTreeParser.g"
+#line 217 "MDTreeParser.g"
 			currInversionStamp->setCenter(icent);
-#line 1214 "MDTreeParser.cpp"
+#line 1492 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1228,13 +1506,13 @@ void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESP
 }
 
 void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodystatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 203 "MDTreeParser.g"
+	ANTLR_USE_NAMESPACE(antlr)RefAST rigidbodystatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 234 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	RigidBodyStamp* currRigidBodyStamp = static_cast<RigidBodyStamp*>(blockStack.top());
 	
-#line 1238 "MDTreeParser.cpp"
+#line 1516 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1248,17 +1526,17 @@ void MDTreeParser::rigidbodystatement(ANTLR_USE_NAMESP
 		}
 		case MEMBERS:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t57 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp30_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t74 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp42_AST_in = _t;
 			match(_t,MEMBERS);
 			_t = _t->getFirstChild();
 			ivec=inttuple(_t);
 			_t = _retTree;
-			_t = __t57;
+			_t = __t74;
 			_t = _t->getNextSibling();
-#line 209 "MDTreeParser.g"
+#line 240 "MDTreeParser.g"
 			currRigidBodyStamp->setMembers(ivec);
-#line 1262 "MDTreeParser.cpp"
+#line 1540 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1276,13 +1554,13 @@ void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAME
 }
 
 void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST cutoffgroupstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 222 "MDTreeParser.g"
+	ANTLR_USE_NAMESPACE(antlr)RefAST cutoffgroupstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+#line 253 "MDTreeParser.g"
 	
 	vector<int> ivec;
 	CutoffGroupStamp* currCutoffGroupStamp = static_cast<CutoffGroupStamp*>(blockStack.top());
 	
-#line 1286 "MDTreeParser.cpp"
+#line 1564 "MDTreeParser.cpp"
 	
 	try {      // for error handling
 		if (_t == ANTLR_USE_NAMESPACE(antlr)nullAST )
@@ -1296,17 +1574,17 @@ void MDTreeParser::cutoffgroupstatement(ANTLR_USE_NAME
 		}
 		case MEMBERS:
 		{
-			ANTLR_USE_NAMESPACE(antlr)RefAST __t63 = _t;
-			ANTLR_USE_NAMESPACE(antlr)RefAST tmp31_AST_in = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST __t80 = _t;
+			ANTLR_USE_NAMESPACE(antlr)RefAST tmp43_AST_in = _t;
 			match(_t,MEMBERS);
 			_t = _t->getFirstChild();
 			ivec=inttuple(_t);
 			_t = _retTree;
-			_t = __t63;
+			_t = __t80;
 			_t = _t->getNextSibling();
-#line 228 "MDTreeParser.g"
+#line 259 "MDTreeParser.g"
 			currCutoffGroupStamp->setMembers(ivec);
-#line 1310 "MDTreeParser.cpp"
+#line 1588 "MDTreeParser.cpp"
 			break;
 		}
 		default:
@@ -1324,7 +1602,7 @@ void MDTreeParser::fragmentstatement(ANTLR_USE_NAMESPA
 }
 
 void MDTreeParser::fragmentstatement(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-	ANTLR_USE_NAMESPACE(antlr)RefAST fragmentstatement_AST_in = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
+	ANTLR_USE_NAMESPACE(antlr)RefAST fragmentstatement_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
 	
 	try {      // for error handling
 		assignment(_t);
@@ -1338,55 +1616,6 @@ void MDTreeParser::fragmentstatement(ANTLR_USE_NAMESPA
 	_retTree = _t;
 }
 
-RealType  MDTreeParser::doubleNumber(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 268 "MDTreeParser.g"
-	RealType dval;
-#line 1345 "MDTreeParser.cpp"
-	ANTLR_USE_NAMESPACE(antlr)RefAST doubleNumber_AST_in = (_t == 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 270 "MDTreeParser.g"
-			dval = lexi_cast<RealType>(ic->getText());
-#line 1362 "MDTreeParser.cpp"
-			break;
-		}
-		case NUM_FLOAT:
-		case NUM_DOUBLE:
-		{
-			fc = (_t == ASTNULL) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-			floatConst(_t);
-			_t = _retTree;
-#line 271 "MDTreeParser.g"
-			dval = lexi_cast<RealType>(fc->getText());
-#line 1373 "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& )
 {
 }
@@ -1398,6 +1627,7 @@ const char* MDTreeParser::tokenNames[] = {
 	"\"component\"",
 	"\"molecule\"",
 	"\"zconstraint\"",
+	"\"restraint\"",
 	"\"atom\"",
 	"\"bond\"",
 	"\"bend\"",
@@ -1410,6 +1640,9 @@ const char* MDTreeParser::tokenNames[] = {
 	"\"center\"",
 	"\"position\"",
 	"\"orientation\"",
+	"\"flucQ\"",
+	"\"RNEMD\"",
+	"\"minimizer\"",
 	"ENDBLOCK",
 	"ID",
 	"ASSIGNEQUAL",
@@ -1447,10 +1680,11 @@ const char* MDTreeParser::tokenNames[] = {
 	0
 };
 
-const unsigned long MDTreeParser::_tokenSet_0_data_[] = { 2097264UL, 0UL, 0UL, 0UL };
-// "component" "molecule" "zconstraint" ASSIGNEQUAL 
+const unsigned long MDTreeParser::_tokenSet_0_data_[] = { 40894704UL, 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_[] = { 2129792UL, 0UL, 0UL, 0UL };
+const unsigned long MDTreeParser::_tokenSet_1_data_[] = { 33619712UL, 0UL, 0UL, 0UL };
 // "atom" "bond" "bend" "torsion" "inversion" "rigidBody" "cutoffGroup" 
 // "fragment" ASSIGNEQUAL 
 const ANTLR_USE_NAMESPACE(antlr)BitSet MDTreeParser::_tokenSet_1(_tokenSet_1_data_,4);