diff --git a/formrsctl.cc b/formrsctl.cc
index 7ca391e..45a9a5d 100644
--- a/formrsctl.cc
+++ b/formrsctl.cc
@@ -189,8 +189,8 @@ bool FormRSCTL::hasOper(Oper op) const
     else
     {
         bool result = false;
-        if (arg[0] != NULL) result = arg[0]->hasOper(op);
-        if (!result && arg[1] != NULL) result = arg[1]->hasOper(op);
+        if (arg[0] != nullptr) result = arg[0]->hasOper(op);
+        if (!result && arg[1] != nullptr) result = arg[1]->hasOper(op);
         return result;
     }
 }
@@ -249,7 +249,7 @@ bool FormRSCTL::isERSCTL(void) const
 
 std::string FormRSCTL::getActionsStr(void) const
 {
-	if (actions != NULL)
+	if (actions != nullptr)
 	{
 	    std::string r = "[ ";
 	    bool firstact = true;
@@ -271,7 +271,7 @@ std::string FormRSCTL::getActionsStr(void) const
 		r += " ]";		
 	    return r;
 	}
-	else if (boolCtx != NULL)
+	else if (boolCtx != nullptr)
 	{
 		return "< " + boolCtx->toStr() + " >";
 	}
@@ -285,11 +285,11 @@ void FormRSCTL::encodeActions(const SymRS *srs)
 {
     if (RSCTL_COND_ACT(oper))
     {
-        if (actions_bdd != NULL) forgetActionsBDD();
+        if (actions_bdd != nullptr) forgetActionsBDD();
         actions_bdd = new BDD(srs->getBDDfalse());
-        assert(actions != NULL || boolCtx != NULL);
-		assert(!(actions != NULL && boolCtx != NULL));
-		if (actions != NULL)
+        assert(actions != nullptr || boolCtx != nullptr);
+		assert(!(actions != nullptr && boolCtx != nullptr));
+		if (actions != nullptr)
 		{
 	        for (ActionsVec_f::iterator act = actions->begin(); act != actions->end(); ++act)
 	        {
@@ -302,7 +302,7 @@ void FormRSCTL::encodeActions(const SymRS *srs)
 	            *actions_bdd += single_action;
 	        }
 		}
-		else if (boolCtx != NULL)
+		else if (boolCtx != nullptr)
 		{
 			*actions_bdd = boolCtx->getBDD(srs);
 		}
diff --git a/formrsctl.hh b/formrsctl.hh
index fbbd92d..eac1723 100644
--- a/formrsctl.hh
+++ b/formrsctl.hh
@@ -82,8 +82,8 @@ public:
 	{
 		oper = BCTX_PV;
 		name = varName;
-        arg[0] = NULL;
-        arg[1] = NULL;
+        arg[0] = nullptr;
+        arg[1] = nullptr;
 	}
 	
    /**
@@ -94,8 +94,8 @@ public:
    BoolContexts(bool val) {
        oper = BCTX_TF;
        tf = val;
-       arg[0] = NULL;
-       arg[1] = NULL;
+       arg[0] = nullptr;
+       arg[1] = nullptr;
    }
 
    /**
@@ -105,7 +105,7 @@ public:
        assert(op == BCTX_NOT);
        oper = op;
        arg[0] = form1;
-       arg[1] = NULL;
+       arg[1] = nullptr;
    }
 
    /**
@@ -132,12 +132,12 @@ public:
        return oper;
    }
    BoolContexts *getLeftSF(void) const {
-       assert(arg[0] != NULL);
+       assert(arg[0] != nullptr);
        return arg[0];
    }
    BoolContexts *getRightSF(void) const {
        assert(BCTX_COND_2ARG(oper));
-       assert(arg[1] != NULL);
+       assert(arg[1] != nullptr);
        return arg[1];
    }
 };
@@ -162,12 +162,12 @@ public:
     FormRSCTL(std::string varName) {
         oper = RSCTL_PV;
         name = varName;
-        arg[0] = NULL;
-        arg[1] = NULL;
-        bdd = NULL;
-        actions = NULL;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        arg[0] = nullptr;
+        arg[1] = nullptr;
+        bdd = nullptr;
+        actions = nullptr;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
     /**
@@ -178,12 +178,12 @@ public:
     FormRSCTL(bool val) {
         oper = RSCTL_TF;
         tf = val;
-        arg[0] = NULL;
-        arg[1] = NULL;
-        bdd = NULL;
-        actions = NULL;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        arg[0] = nullptr;
+        arg[1] = nullptr;
+        bdd = nullptr;
+        actions = nullptr;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
     /**
@@ -195,41 +195,41 @@ public:
         oper = op;
         arg[0] = form1;
         arg[1] = form2;
-        bdd = NULL;
-        actions = NULL;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        bdd = nullptr;
+        actions = nullptr;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
     /**
      * @brief Constructor for two-argument formula with action restrictions.
      */
     FormRSCTL(Oper op, ActionsVec_f *acts, FormRSCTL *form1, FormRSCTL *form2) {
-        assert(acts != NULL);
+        assert(acts != nullptr);
         assert(RSCTL_COND_2ARG(op));
         assert(RSCTL_COND_ACT(op));
         oper = op;
         arg[0] = form1;
         arg[1] = form2;
-        bdd = NULL;
+        bdd = nullptr;
         actions = acts;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
    /**
     * @brief Constructor for two-argument formula with Boolean context restrictions.
     */
    FormRSCTL(Oper op, BoolContexts *bctx, FormRSCTL *form1, FormRSCTL *form2) {
-       assert(bctx != NULL);
+       assert(bctx != nullptr);
        assert(RSCTL_COND_2ARG(op));
        assert(RSCTL_COND_ACT(op));
        oper = op;
        arg[0] = form1;
        arg[1] = form2;
-       bdd = NULL;
-       actions = NULL;
-       actions_bdd = NULL;
+       bdd = nullptr;
+       actions = nullptr;
+       actions_bdd = nullptr;
 	   boolCtx = bctx;
    }
 
@@ -241,42 +241,42 @@ public:
         assert(!RSCTL_COND_ACT(op));
         oper = op;
         arg[0] = form1;
-        arg[1] = NULL;
-        bdd = NULL;
-        actions = NULL;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        arg[1] = nullptr;
+        bdd = nullptr;
+        actions = nullptr;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
     /**
      * @brief Constructor for one-argument formula with action restrictions.
      */
     FormRSCTL(Oper op, ActionsVec_f *acts, FormRSCTL *form1) {
-        assert(acts != NULL);
+        assert(acts != nullptr);
         assert(RSCTL_COND_1ARG(op));
         assert(RSCTL_COND_ACT(op));
         oper = op;
         arg[0] = form1;
-        arg[1] = NULL;
-        bdd = NULL;
+        arg[1] = nullptr;
+        bdd = nullptr;
         actions = acts;
-        actions_bdd = NULL;
-		boolCtx = NULL;
+        actions_bdd = nullptr;
+		boolCtx = nullptr;
     }
 
    /**
     * @brief Constructor for one-argument formula with Boolean context restrictions.
     */
    FormRSCTL(Oper op, BoolContexts *bctx, FormRSCTL *form1) {
-       assert(bctx != NULL);
+       assert(bctx != nullptr);
        assert(RSCTL_COND_1ARG(op));
        assert(RSCTL_COND_ACT(op));
        oper = op;
        arg[0] = form1;
-       arg[1] = NULL;
-       bdd = NULL;
-       actions = NULL;
-       actions_bdd = NULL;
+       arg[1] = nullptr;
+       bdd = nullptr;
+       actions = nullptr;
+       actions_bdd = nullptr;
 	   boolCtx = bctx;
 	}
 
@@ -295,12 +295,12 @@ public:
     bool hasOper(Oper op) const;
     const BDD *getBDD(void) const {
         assert(oper == RSCTL_PV);
-        assert(bdd != NULL);
+        assert(bdd != nullptr);
         return bdd;
     }
     const BDD *getActionsBDD(void) const {
         assert(RSCTL_COND_ACT(oper));
-        assert(actions_bdd != NULL);
+        assert(actions_bdd != nullptr);
         return actions_bdd;
     }
     Oper getOper(void) const {
@@ -308,12 +308,12 @@ public:
         return oper;
     }
     FormRSCTL *getLeftSF(void) const {
-        assert(arg[0] != NULL);
+        assert(arg[0] != nullptr);
         return arg[0];
     }
     FormRSCTL *getRightSF(void) const {
         assert(RSCTL_COND_2ARG(oper));
-        assert(arg[1] != NULL);
+        assert(arg[1] != nullptr);
         return arg[1];
     }
     std::string getActionsStr(void) const;
@@ -324,7 +324,7 @@ public:
     void encodeEntities(const SymRS *srs);
     void encodeActions(const SymRS *srs);
     void forgetActionsBDD(void) {
-        if (actions_bdd != NULL) delete actions_bdd;
+        if (actions_bdd != nullptr) delete actions_bdd;
     }
     bool isERSCTL(void) const;
 };
diff --git a/macro.hh b/macro.hh
index 0c133c7..4a78a70 100644
--- a/macro.hh
+++ b/macro.hh
@@ -1,6 +1,8 @@
 #ifndef __MY_MACROS__
 #define __MY_MACROS__
 
+#include <cassert>
+
 #define LINENUM std::cout << __FILE__ <<  " (function " << __func__ << "), line " << __LINE__ << std::endl;
 /* Fatal error */
 #define FERROR(s) \
@@ -14,16 +16,19 @@
 }
 
 #define VERB(s) \
+assert(opts != nullptr); \
 if (opts->verbose > 0) { \
 	std::cerr << "ii VERBOSE(1): " << __FILE__ << " (" << __func__ << ":" << __LINE__ << "): " << s << std::endl;		\
 }
 
 #define VERB_L2(s) \
+assert(opts != nullptr); \
 if (opts->verbose > 1) { \
 	std::cerr << "ii VERBOSE(2): " << __FILE__ << " (" << __func__ << ":" << __LINE__ << "): " << s << std::endl;		\
 }
 
 #define VERB_L3(s) \
+assert(opts != nullptr); \
 if (opts->verbose > 2) { \
 	std::cerr << "ii VERBOSE(3): " << __FILE__ << " (" << __func__ << ":" << __LINE__ << "): " << s << std::endl;		\
 }
diff --git a/main.cc b/main.cc
index 2e2927c..2f8e3f1 100644
--- a/main.cc
+++ b/main.cc
@@ -10,12 +10,10 @@
 
 int main(int argc, char **argv)
 {
-
-
-    RctSys rs;
-    rsin_driver driver(&rs);
+    rsin_driver driver;
 
     Options *opts = new Options;
+	driver.setOptions(opts);
 
     bool show_reactions = false;
     bool rstl_model_checking = false;
@@ -95,10 +93,8 @@ int main(int argc, char **argv)
             default:
                 usage_error = true;
         }
-    }
-
-    rs.setOptions(opts);
-
+    }	
+	
     std::string inputfile;
     if (optind < argc)
     {
@@ -113,9 +109,9 @@ int main(int argc, char **argv)
     if (usage_error)
     {
         cout << endl
-             << " **********************************" << endl
-             << " **Reaction Systems Model Checker**" << endl
-             << " **********************************" << endl
+             << " ------------------------------------" << endl
+             << " -- Reaction Systems Model Checker --" << endl
+             << " ------------------------------------" << endl
              << endl
              << "   Version:   " << VERSION << endl
              << "   Contact:   " << AUTHOR << endl
@@ -128,28 +124,30 @@ int main(int argc, char **argv)
              << endl
 #endif
              << " Usage: " << argv[0] << " [options] <inputfile>" << endl << endl
-             << " -b   -- disable bounded model checking (BMC) heuristic" << endl
-             << " -c   -- perform RSCTL model checking" << endl
+			 << " TASKS:" << endl	 
+             << "  -c   -- perform RSCTL model checking" << endl
              //<< " -f K -- generate SMT input for the depth K" << endl
-             << " -p   -- show progress (where possible)" << endl
-             << " -P   -- print parsed system" << endl
-             << " -r   -- print reactions" << endl
-             << " -s   -- print the set of all the reachable states" << endl
-             << " -t   -- print the set of all the reachable states with their successors" << endl
-             << " -x   -- use partitioned transition relation (may use less memory)" << endl
-             << " -z   -- use reordering of the BDD variables" << endl
-             << " -v   -- verbose (can be used more than once to increase verbosity)" << endl
+             << "  -P   -- print parsed system" << endl
+             << "  -r   -- print reactions" << endl
+             << "  -s   -- print the set of all the reachable states" << endl
+             << "  -t   -- print the set of all the reachable states with their successors" << endl
+			 << endl << " OTHER:" << endl 
+	         << "  -b   -- disable bounded model checking (BMC) heuristic" << endl
+             << "  -x   -- use partitioned transition relation (may use less memory)" << endl
+             << "  -z   -- use reordering of the BDD variables" << endl
+             << "  -v   -- verbose (can be used more than once to increase verbosity)" << endl
+             << "  -p   -- show progress (where possible)" << endl
              << endl
              << " Benchmarking options:" << endl
-             << " -m   -- measure and display time and memory usage" << endl
-             << " -B   -- display an easy to parse summary (enables -m)" << endl
+             << "  -m   -- measure and display time and memory usage" << endl
+             << "  -B   -- display an easy to parse summary (enables -m)" << endl
              << endl;
         return 100;
     }
 
     if (!(reach_states || reach_states_succ || rstl_model_checking || show_reactions || print_parsed_sys))
     {
-        FERROR("No task specified: -c, -f, -P, -r, or -s needs to be used");
+        FERROR("No task specified: -c, -P, -r, or -s needs to be used");
     }
 
     if (opts->verbose > 0) 
@@ -163,6 +161,17 @@ int main(int argc, char **argv)
     {
         FERROR("Parse error");
     }
+	
+	//
+	// Here we retrieve the reaction system from the parser
+	//
+	// We decide which RS will be used at the parser level.
+	// This decision depends on whether we use concentrations,
+	// context automaton, etc.
+	//
+	auto rs = *driver.getReactionSystem();
+	
+    rs.setOptions(opts); // these need to be passed to the driver
 
     if (show_reactions)
         rs.showReactions();
@@ -184,9 +193,14 @@ int main(int argc, char **argv)
         if (rstl_model_checking)
         {
             if (bmc)
-                mc.checkRSCTL(driver.getFormRSCTL());
-            else
-                mc.checkRSCTLfull(driver.getFormRSCTL());
+			{
+				cout << "Using BDD-based Bounded Model Checking" << endl;
+				mc.checkRSCTL(driver.getFormRSCTL());	
+			}
+            else 
+			{
+				mc.checkRSCTLfull(driver.getFormRSCTL());	
+			}
         }
     }
 
@@ -197,7 +211,7 @@ int main(int argc, char **argv)
              << "Verification time: " << opts->ver_time << " sec" << endl
              << "Encoding memory: " << opts->enc_mem << " MB" << endl
              << "Memory (total): " << opts->ver_mem << " MB" << endl
-             << "TOTAL time: " << opts->enc_time+opts->ver_time << " sec" << endl;
+             << "TOTAL time: " << opts->enc_time + opts->ver_time << " sec" << endl;
         if (benchmarking)
         {
             cout << std::setprecision(4)
diff --git a/mc.cc b/mc.cc
index e3670a3..850e56f 100644
--- a/mc.cc
+++ b/mc.cc
@@ -151,7 +151,7 @@ bool ModelChecker::checkReach(const RctSys::Entities testState)
 
 BDD ModelChecker::getStatesRSCTL(const FormRSCTL *form)
 {
-    assert(reach != NULL);
+    assert(reach != nullptr);
     Oper oper = form->getOper();
     if (oper == RSCTL_PV)
     {
@@ -364,7 +364,7 @@ bool ModelChecker::checkRSCTLfull(FormRSCTL *form)
     if (opts->measure)
         opts->ver_time = cpuTime();
 
-    assert(form != NULL);
+    assert(form != nullptr);
 
     bool result = false;
 
@@ -378,7 +378,7 @@ bool ModelChecker::checkRSCTLfull(FormRSCTL *form)
     form->encodeActions(srs);
     VERB("Contexts encoded");
 
-    assert(reach == NULL);
+    assert(reach == nullptr);
 
     reach = new BDD(*initStates);
     BDD reach_p = cuddMgr->bddZero();
@@ -437,7 +437,7 @@ bool ModelChecker::checkRSCTLbmc(FormRSCTL *form)
     if (opts->measure)
         opts->ver_time = cpuTime();
 
-    assert(form != NULL);
+    assert(form != nullptr);
 
     if (!form->isERSCTL())
     {
@@ -456,7 +456,7 @@ bool ModelChecker::checkRSCTLbmc(FormRSCTL *form)
     form->encodeActions(srs);
     VERB("Contexts encoded");
 
-    assert(reach == NULL);
+    assert(reach == nullptr);
 
     reach = new BDD(*initStates);
     BDD reach_p = cuddMgr->bddZero();
@@ -499,6 +499,6 @@ bool ModelChecker::checkRSCTLbmc(FormRSCTL *form)
 void ModelChecker::cleanup(void)
 {
     delete reach;
-    reach = NULL;
+    reach = nullptr;
 }
 
diff --git a/mc.hh b/mc.hh
index 20ff756..35f1e7f 100644
--- a/mc.hh
+++ b/mc.hh
@@ -59,10 +59,10 @@ public:
         pv_succ_E = srs->getEncPVsucc_E();
         pv_act_E = srs->getEncPVact_E();
         trp = srs->getEncPartTrans();
-        if (trp == NULL) trp_size = 0;
+        if (trp == nullptr) trp_size = 0;
         else trp_size = trp->size();
         trm = srs->getEncMonoTrans();
-        reach = NULL;
+        reach = nullptr;
     }
 
     void printReach(void);
diff --git a/memtime.hh b/memtime.hh
index df3a089..1bcef66 100644
--- a/memtime.hh
+++ b/memtime.hh
@@ -40,7 +40,7 @@ static inline int memReadStat(void)
     pid_t pid = getpid();
     sprintf(name, "/proc/%d/statm", pid);
     FILE* in = fopen(name, "rb");
-    if (in == NULL)
+    if (in == nullptr)
     {
         return 0;
     }
diff --git a/rs.cc b/rs.cc
index d2b327f..d3dde71 100644
--- a/rs.cc
+++ b/rs.cc
@@ -24,7 +24,7 @@ void RctSys::addEntity(std::string name)
 
         VERB_L2("Adding entity: " << name << " index=" << new_entity_id);
 
-        entities_ids.push_back(name);
+        entities_ids.push_back(name);		
         entities_names[name] = new_entity_id;
     }
 }
@@ -166,7 +166,6 @@ void RctSys::printSystem(void)
     showInitialStates();
     showActionEntities();
     showReactions();
-
 }
 
 bool CtxAut::hasState(std::string name)
@@ -177,6 +176,15 @@ bool CtxAut::hasState(std::string name)
         return true;
 }
 
+CtxAut::State CtxAut::getStateID(std::string name)
+{
+    if (!hasState(name))
+    {
+        FERROR("No such state: " << name);
+    }
+    return states_names[name];
+}
+
 void CtxAut::addState(std::string name)
 {
     if (!hasState(name))
@@ -190,12 +198,20 @@ void CtxAut::addState(std::string name)
     }
 }
 
-void CtxAut::pushContextEntity(std::string entityName) 
+void CtxAut::pushContextEntity(RctSys::Entity entity_id) 
 {
-	
+	tmpEntities.insert(entity_id);
 }
 
 void CtxAut::addTransition(std::string srcStateName, std::string dstStateName) 
 {
-		
+    VERB_L3("Saving transition");
+	
+	Transition new_transition;
+	
+	new_transition.src_state = getStateID(srcStateName);
+	new_transition.ctx = tmpEntities; 
+	tmpEntities.clear();
+	new_transition.dst_state = getStateID(dstStateName);
 }
+
diff --git a/rs.hh b/rs.hh
index d127e1e..97fc22b 100644
--- a/rs.hh
+++ b/rs.hh
@@ -95,12 +95,6 @@ class RctSys
 	    void printSystem(void);
 };
 
-class RctSysWithCtxAut : private RctSys
-{
-	friend class CtxAut;
-	
-};
-
 // Context Automaton
 class CtxAut
 {
@@ -113,14 +107,13 @@ class CtxAut
 			RctSys::Entities ctx;
 			State dst_state;
 		};
+		
 		bool hasState(std::string name);
 		void addState(std::string stateName);
+		State getStateID(std::string name);
 		void addTransition(std::string srcStateName, std::string dstStateName);
-		void pushContextEntity(std::string entityName);	
-	    void setOptions(Options *opts)
-	    {
-	        this->opts = opts;
-	    }
+		void pushContextEntity(RctSys::Entity entity_id);	
+	    void setOptions(Options *opts) { this->opts = opts; }
 		
 	private:
 	    Options *opts;
@@ -129,5 +122,11 @@ class CtxAut
 		RctSys::Entities tmpEntities;	
 };
 
-#endif
+class RctSysWithCtxAut : public RctSys
+{
+	// friend class CtxAut;
+	
+	CtxAut ctx_aut;
+};
 
+#endif
diff --git a/rsin_driver.cc b/rsin_driver.cc
index 8c8862a..ac76c39 100644
--- a/rsin_driver.cc
+++ b/rsin_driver.cc
@@ -1,15 +1,31 @@
 #include "rsin_driver.hh"
 #include "rsin_parser.hh"
 
+rsin_driver::rsin_driver(void)
+: trace_scanning(false), trace_parsing(false)
+{
+	initialise();
+}
+
 rsin_driver::rsin_driver(RctSys *rs)
 : trace_scanning(false), trace_parsing(false)
 {
-    this->rsctlform = NULL;
-    this->rs = rs;
+	initialise();
+	this->rs = rs;
+}
+
+void rsin_driver::initialise(void)
+{
+    this->rs = nullptr;
+    this->rsctlform = nullptr;
+	opts = nullptr;
+	use_ctx_aut = false;
+	use_concentrations = false;
 }
 
 rsin_driver::~rsin_driver ()
 {
+	// placeholder
 }
 
 int rsin_driver::parse(const std::string &f)
@@ -33,10 +49,9 @@ void rsin_driver::error(const std::string &m)
     std::cerr << m << std::endl;
 }
 
-
 FormRSCTL *rsin_driver::getFormRSCTL(void)
 {
-    if (rsctlform == NULL)
+    if (rsctlform == nullptr)
     {
         FERROR("RSCTL formula was not supplied!");
     }
@@ -44,3 +59,40 @@ FormRSCTL *rsin_driver::getFormRSCTL(void)
     return rsctlform;
 }
 
+//
+// Checks if we are not too late to be setting any options
+//
+void rsin_driver::ensureOptionsAllowed(void)
+{
+	if (rs != nullptr)
+	{
+		FERROR("Options cannot be set/modified after the reaction system is initialised")
+	}
+}
+
+void rsin_driver::ensureReactionSystemReady(void)
+{
+	if (rs == nullptr)
+		setupReactionSystem();
+}
+
+void rsin_driver::setupReactionSystem(void)
+{
+	assert(rs == nullptr);
+	if (use_ctx_aut)
+	{
+		rs = new RctSysWithCtxAut;
+	}
+	else
+	{
+		rs = new RctSys;
+	}
+	rs->setOptions(opts);
+}
+
+RctSys *rsin_driver::getReactionSystem(void)
+{
+	ensureReactionSystemReady();
+	assert(rs != nullptr);
+	return rs;
+}
diff --git a/rsin_driver.hh b/rsin_driver.hh
index f6acabc..7d8eec5 100644
--- a/rsin_driver.hh
+++ b/rsin_driver.hh
@@ -5,6 +5,7 @@
 #include "rsin_parser.hh"
 #include "rs.hh"
 #include "formrsctl.hh"
+#include "options.hh"
 
 // Tell Flex the lexer's prototype ...
 #define YY_DECL                                  \
@@ -19,12 +20,20 @@ YY_DECL;
 class rsin_driver
 {
 public:
+    rsin_driver(void);
     rsin_driver(RctSys *rs);
     virtual ~rsin_driver();
 
     //std::map<std::string, int> variables;
     RctSys *rs;
     FormRSCTL *rsctlform;
+    Options *opts;
+	
+	//
+	// options in configuration file
+	//
+	bool use_ctx_aut;
+	bool use_concentrations;
 
     // Handling the scanner
     void scan_begin();
@@ -35,14 +44,26 @@ public:
     std::string file;
     bool trace_parsing;
 
-    void addFormRSCTL(FormRSCTL *f) { rsctlform = f; }
+	void setOptions(Options *opts) 		{ this->opts = opts; };
+    void addFormRSCTL(FormRSCTL *f) 	{ rsctlform = f; };
     FormRSCTL *getFormRSCTL(void);
 
+	void ensureOptionsAllowed(void);
+	void useContextAutomaton(void)		{ ensureOptionsAllowed(); use_ctx_aut = true; };
+	void useConcentrations(void)		{ ensureOptionsAllowed(); use_concentrations = true; };
+	
+	void ensureReactionSystemReady(void);
+	void setupReactionSystem(void);
+	
+	RctSys *getReactionSystem(void);
+
     // Error handling.
     void error(const yy::location &l, const std::string &m);
     void error(const std::string &m);
+	
+private:
+	void initialise(void);
 };
 
 #endif
 
-
diff --git a/rsin_parser.ll b/rsin_parser.ll
index 5c8249a..8f72e39 100644
--- a/rsin_parser.ll
+++ b/rsin_parser.ll
@@ -38,6 +38,9 @@ blank [ \t]
   typedef yy::rsin_parser::token token;
 %}
 
+"options"				return token::OPTIONS;
+"use-context-automaton"	return token::USE_CTX_AUT;
+"use-concentrations"	return token::USE_CONCENTRATIONS;
 "reactions"             return token::REACTIONS;
 "initial-contexts"      return token::INITIALCONTEXTS;
 "context-entities"      return token::CONTEXTENTITIES;
diff --git a/rsin_parser.yy b/rsin_parser.yy
index 08722df..6fa3950 100644
--- a/rsin_parser.yy
+++ b/rsin_parser.yy
@@ -44,6 +44,7 @@ class rsin_driver;
 #include "rsin_driver.hh"
 }
 
+%token OPTIONS USE_CTX_AUT USE_CONCENTRATIONS
 %token REACTIONS INITIALCONTEXTS CONTEXTENTITIES RSCTLFORM
 %token CONTEXTAUTOMATON STATES TRANSITIONS
 %token LCB RCB LRB RRB LSB RSB LAB RAB COL SEMICOL COMMA RARR
@@ -75,6 +76,7 @@ class rsin_driver;
 %start system;
 
 system: 
+	| OPTIONS LCB options RCB system
     | REACTIONS LCB reactions RCB system
     | INITIALCONTEXTS LCB initstates RCB system
     | CONTEXTENTITIES LCB actionentities RCB system
@@ -84,6 +86,14 @@ system:
     }
     ;
 
+options:
+	| options option SEMICOL
+	;
+
+option:
+	| USE_CTX_AUT { } 
+	;
+
 /* 
  * -------------------------
  *         REACTIONS 
@@ -95,7 +105,7 @@ reactions:
 
 reaction:
     | LCB reactionConditions RARR LCB reactionProducts RCB RCB {
-        driver.rs->commitReaction();
+        driver.getReactionSystem()->commitReaction();
     }
     ;
 
@@ -109,7 +119,7 @@ reactants:
     ;
 
 reactant: IDENTIFIER {
-        driver.rs->pushReactant(*$1);
+        driver.getReactionSystem()->pushReactant(*$1);
         free($1);
     }
     ;
@@ -121,7 +131,7 @@ inhibitors:
 
 inhibitor:
     | IDENTIFIER {
-        driver.rs->pushInhibitor(*$1);
+        driver.getReactionSystem()->pushInhibitor(*$1);
         free($1);
     }
     ;
@@ -132,7 +142,7 @@ reactionProducts:
     ;
 
 reactionProduct: IDENTIFIER {
-        driver.rs->pushProduct(*$1);
+        driver.getReactionSystem()->pushProduct(*$1);
         free($1);
     }
     ;
@@ -141,10 +151,10 @@ reactionProduct: IDENTIFIER {
 
 initstates:
     LCB initstate RCB {
-        driver.rs->commitInitState();
+        driver.getReactionSystem()->commitInitState();
     }
     | initstates COMMA LCB initstate RCB {
-        driver.rs->commitInitState();
+        driver.getReactionSystem()->commitInitState();
     }
     ;
 
@@ -154,7 +164,7 @@ initstate:
     ;
 
 entity: IDENTIFIER {
-        driver.rs->pushStateEntity(*$1);
+        driver.getReactionSystem()->pushStateEntity(*$1);
         free($1);
     }
     ;
@@ -167,7 +177,7 @@ actionentities:
     ;
 
 actentity: IDENTIFIER {
-        driver.rs->addActionEntity(*$1);
+        driver.getReactionSystem()->addActionEntity(*$1);
         free($1);
     }
     ;
diff --git a/symrs.cc b/symrs.cc
index e2eca69..4af9b45 100644
--- a/symrs.cc
+++ b/symrs.cc
@@ -318,7 +318,7 @@ void SymRS::encodeInitStates(void)
 
 #ifndef NDEBUG
     if (opts->part_tr_rel)
-        assert(partTrans != NULL);
+        assert(partTrans != nullptr);
 #endif
 		
     initStates = new BDD(BDD_FALSE);
diff --git a/symrs.hh b/symrs.hh
index 2b2cc66..f20dc76 100644
--- a/symrs.hh
+++ b/symrs.hh
@@ -122,8 +122,8 @@ public:
         totalReactions = rs->getReactionsSize();
         totalActions = rs->getActionsSize();
 
-        partTrans = NULL;
-        monoTrans = NULL;
+        partTrans = nullptr;
+        monoTrans = nullptr;
 
         encode();
     }