WIP: more sanity checks

Author: danv61

vcell-core/src/main/java/cbit/vcell/mapping/ReactionRuleSpec.java

@@ -1339,12 +1339,14 @@ public boolean checkOnRate(SiteAttributesSpec sasOne, SiteAttributesSpec sasTwo)
 		}
 		double kon = Double.parseDouble(lp.getExpression().infix());
 // TODO: check all scaling
-		double kon_scale = 1660000.0 * kon;			// Kon also needs some conversion (TODO: why?)
+		double kon_scale = 1660000.0 * kon;			// Kon also needs some conversion (micromolar -> particles)
 		double D_scale = D * 1000000.0;				// D is in um^2/s, convert to nm^2/s
 
-		double rhs1 = 4.0*Math.PI*R*D_scale;
+		double kD = 4.0*Math.PI*R*D_scale;
 
-		boolean check = (kon_scale < rhs1);
+		// double kOnIntrinsic = (rescalekon * kD) / (kD - rescalekon); cannot be negative,
+		// hence kD must be > kon_scale
+		boolean check = (kon_scale < kD);
 		return check;
 	}
 

vcell-core/src/main/java/cbit/vcell/mapping/SpeciesContextSpec.java

@@ -1504,6 +1504,11 @@ public void gatherIssues(IssueContext issueContext, List<Issue> issueVector){
                     return;
                 }
 
+                // TODO: diameter of each site must be smaller than partition size on x, y, z
+
+                // TODO: diffusion speed * dt must be smaller than the partition size on x, y, z so that the particle
+                //  won't be able to jump outside the current partition or its neighboring partitions
+
                 // rate rules and assignment rules are not permitted
                 // normally it is not possible to create RateRule or AssignmentRule using the vcell UI, the Protocols subpanels are disabled
                 // we check this just in case the user is very crafty and finds a way