Revert back rates as members instead of methds in secretion and molecular

Author: asmelko

addons/dFBA/src/dfba_intracellular.cpp

@@ -192,7 +192,7 @@ int dFBAIntracellular::update_phenotype_parameters(PhysiCell::Phenotype& phenoty
         // how to rescale FBA exchanges into net_export_rates
         float scaling = 1;
         flux *= scaling;
-        phenotype.secretion.net_export_rates()[ex_strut.density_index] = flux;
+        phenotype.secretion.net_export_rates[ex_strut.density_index] = flux;
     }
 
     float delta_vol = 1;

addons/libRoadrunner/src/librr_intracellular.cpp

@@ -389,24 +389,24 @@ int RoadRunnerIntracellular::update_phenotype_parameters(PhysiCell::Phenotype& p
             if (elm.first.substr(0,3) == "sur")
             {
                 //std::cout << sub_index << std::endl;
-                //std::cout << "Before sur1 : " << phenotype.secretion.uptake_rates()[sub_index] << std::endl;
-                phenotype.secretion.uptake_rates()[1] = phenotype.intracellular->get_parameter_value(elm.second);
-                //std::cout << "After sur1 : " << phenotype.secretion.uptake_rates()[sub_index] << std::endl;
+                //std::cout << "Before sur1 : " << phenotype.secretion.uptake_rates[sub_index] << std::endl;
+                phenotype.secretion.uptake_rates[1] = phenotype.intracellular->get_parameter_value(elm.second);
+                //std::cout << "After sur1 : " << phenotype.secretion.uptake_rates[sub_index] << std::endl;
             }
             //secretion rate
             else if (elm.first.substr(0,3) == "ssr")
             {
-                phenotype.secretion.secretion_rates()[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
+                phenotype.secretion.secretion_rates[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
             }
             //secretion density
             else if (elm.first.substr(0,3) == "ssd")
             {
-                phenotype.secretion.saturation_densities()[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
+                phenotype.secretion.saturation_densities[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
             }
             //net export rate
             else if (elm.first.substr(0,3) == "ser")
             {
-                phenotype.secretion.net_export_rates()[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
+                phenotype.secretion.net_export_rates[sub_index] = phenotype.intracellular->get_parameter_value(elm.second);
             }
             else
             {

core/PhysiCell_cell.cpp

@@ -598,9 +598,9 @@ Cell* Cell::divide( )
 	// if these are not actively tracked, they are zero anyway 
 	for ( int n = 0 ; n < phenotype.molecular.pMicroenvironment->number_of_densities() ; n++ )
 	{
-		phenotype.molecular.internalized_total_substrates()[n] *= 0.5; 
-		child->phenotype.molecular.internalized_total_substrates()[n] = 
-			phenotype.molecular.internalized_total_substrates()[n];
+		phenotype.molecular.internalized_total_substrates[n] *= 0.5; 
+		child->phenotype.molecular.internalized_total_substrates[n] = 
+			phenotype.molecular.internalized_total_substrates[n];
 	}
 
 	// The following is already performed by create_cell(). JULY 2017 ***
@@ -858,9 +858,9 @@ void Cell::turn_off_reactions(double dt)
 
 	for(int i=0;i< phenotype.secretion.pMicroenvironment->number_of_densities();i++)
 	{
-		phenotype.secretion.uptake_rates()[i] = 0.0;  
-		phenotype.secretion.secretion_rates()[i] = 0.0; 
-		phenotype.secretion.net_export_rates()[i] = 0.0; 
+		phenotype.secretion.uptake_rates[i] = 0.0;  
+		phenotype.secretion.secretion_rates[i] = 0.0; 
+		phenotype.secretion.net_export_rates[i] = 0.0; 
 	}
 	set_internal_uptake_constants(dt);
 
@@ -994,8 +994,8 @@ void Cell::copy_data(Cell* copy_me)
 	// expected_phenotype = copy_me-> expected_phenotype; //it is taken care in set_phenotype
 	for ( int i = 0 ; i < copy_me->phenotype.molecular.pMicroenvironment->number_of_densities() ; i++ )
 	{
-		phenotype.molecular.internalized_total_substrates()[i] = 
-			copy_me->phenotype.molecular.internalized_total_substrates()[i];
+		phenotype.molecular.internalized_total_substrates[i] = 
+			copy_me->phenotype.molecular.internalized_total_substrates[i];
 	}
 
 	return; 
@@ -1476,13 +1476,13 @@ void Cell::ingest_cell( Cell* pCell_to_eat )
 
 		for ( int i = 0 ; i < pCell_to_eat->phenotype.molecular.pMicroenvironment->number_of_densities() ; i++ )
 		{
-			pCell_to_eat->phenotype.molecular.internalized_total_substrates()[i] *= 
+			pCell_to_eat->phenotype.molecular.internalized_total_substrates[i] *= 
 				pCell_to_eat->custom_data["fraction_transferred_when_ingested"]; //
 
-			phenotype.molecular.internalized_total_substrates()[i] += 
-				pCell_to_eat->phenotype.molecular.internalized_total_substrates()[i];
+			phenotype.molecular.internalized_total_substrates[i] += 
+				pCell_to_eat->phenotype.molecular.internalized_total_substrates[i];
 
-			pCell_to_eat->phenotype.molecular.internalized_total_substrates()[i] = 0.0;
+			pCell_to_eat->phenotype.molecular.internalized_total_substrates[i] = 0.0;
 		}
 
 		// conserved quantitites in custom data during phagocytosis
@@ -1647,10 +1647,10 @@ void Cell::fuse_cell( Cell* pCell_to_fuse )
 		// absorb the internalized substrates 
 		for ( int i = 0 ; i < pCell_to_fuse->phenotype.molecular.pMicroenvironment->number_of_densities() ; i++ )
 		{
-			phenotype.molecular.internalized_total_substrates()[i] += 
-				pCell_to_fuse->phenotype.molecular.internalized_total_substrates()[i];
+			phenotype.molecular.internalized_total_substrates[i] += 
+				pCell_to_fuse->phenotype.molecular.internalized_total_substrates[i];
 
-			pCell_to_fuse->phenotype.molecular.internalized_total_substrates()[i] = 0.0;
+			pCell_to_fuse->phenotype.molecular.internalized_total_substrates[i] = 0.0;
 		}
 
 		// set target volume(s)
@@ -2135,10 +2135,10 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 			// secretion  
 			for (int i = 0; i < number_of_substrates; i++ )
 			{
-				pCD->phenotype.secretion.secretion_rates()[i] = 0.0; 
-				pCD->phenotype.secretion.uptake_rates()[i] = 0.0; 
-				pCD->phenotype.secretion.net_export_rates()[i] = 0.0; 
-				pCD->phenotype.secretion.saturation_densities()[i] = 0.0; 
+				pCD->phenotype.secretion.secretion_rates[i] = 0.0; 
+				pCD->phenotype.secretion.uptake_rates[i] = 0.0; 
+				pCD->phenotype.secretion.net_export_rates[i] = 0.0; 
+				pCD->phenotype.secretion.saturation_densities[i] = 0.0; 
 			}
 
 			// interaction 
@@ -2975,22 +2975,22 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
 			// secretion rate
 			pugi::xml_node node_sec1 = node_sec.child( "secretion_rate" ); 
 			if( node_sec1 )
-			{ pS->secretion_rates()[index] = xml_get_my_double_value( node_sec1 ); }
+			{ pS->secretion_rates[index] = xml_get_my_double_value( node_sec1 ); }
 
 			// secretion target 
 			node_sec1 = node_sec.child( "secretion_target" ); 
 			if( node_sec1 )
-			{ pS->saturation_densities()[index] = xml_get_my_double_value( node_sec1 ); }
+			{ pS->saturation_densities[index] = xml_get_my_double_value( node_sec1 ); }
 
 			// uptake rate 
 			node_sec1 = node_sec.child( "uptake_rate" ); 
 			if( node_sec1 )
-			{ pS->uptake_rates()[index] = xml_get_my_double_value( node_sec1 ); }
+			{ pS->uptake_rates[index] = xml_get_my_double_value( node_sec1 ); }
 
 			// net export rate 
 			node_sec1 = node_sec.child( "net_export_rate" ); 
 			if( node_sec1 )
-			{ pS->net_export_rates()[index] = xml_get_my_double_value( node_sec1 ); }
+			{ pS->net_export_rates[index] = xml_get_my_double_value( node_sec1 ); }
 
 			node_sec = node_sec.next_sibling( "substrate" ); 
 		}