Add secret help option (--help-rates) to show meaning of reaction rate constants.

diff --git a/ss.cpp b/ss.cpp
index 2839ce9..5610564 100644 (file)
--- a/ss.cpp
+++ b/ss.cpp
@@ -918,6 +918,7 @@ void importEpitope_Potts(RunParameters_SS &r, Species_parray &species, Rxn_parra
         if (r.rate_p != 0.0) for (it = Tgen.begin(); it != end; ++it) {   // p
             AAKillingReaction* rx = new AAKillingReaction(r.rate_p / r.vol);
             rx->T = *it;  rx->V = V;
+            rx->name = (*it)->name + " + V --(p)--> " + (*it)->name;
             reactions.push_back(rx);    update_rxn_dependents(reactions);
         }
         if (r.rate_a != 0.0) {   // a
@@ -1049,6 +1050,27 @@ void usage()
 ;   std::cout.flush();
 }
 
+void usage_rates()
+{
+    std::cout <<
+"Reactions and their rate constants:\n"
+"\n"
+"Killing        rate_p         T[i] + V -> T[i]\n"
+"CTLActivation  rate_a         N + V -> T[1] + V\n"
+"Elementary     rate_r         T[i] -> 2 T[i+1]\n"
+"Elementary     rate_r         T[const_ND-1] -> 0\n"
+"Elementary     rate_d         T[i] -> 0\n"
+"Elementary     rate_b         N -> 2 N\n"
+"Elementary     rate_e         N -> 0\n"
+"Elementary     rate_w         0 -> N\n"
+"CTLActivation  rate_aprime    M + V -> T[1]\n"
+"Elementary     rate_g         T[i] -> M\n"
+"Elementary     rate_h         M -> 0\n"
+"Virus          rate_s         V -> V + V'\n"
+"VirusDeath     rate_u         V -> 0\n"
+;   std::cout.flush();
+}
+
 /*
  * Command line rules:
  *
@@ -1128,6 +1150,7 @@ int main(int argc, char *argv[]) {
         else if (strcmp(argv[i],"-flush_each")==0) { r.flushOften = true; }
 
         else if (strcmp(argv[i],"-h")==0 || strcmp(argv[i],"--help")==0)   { usage(); return 0;    }
+        else if (strcmp(argv[i],"--help-rates")==0)   { usage_rates(); return 0;    }
 
         else printf("Unrecognized argument! '%s'\n",argv[i]);