simulation_test.rb in y_petri-2.3.4

- old
+ new

@@ -2,11 +2,11 @@
 # encoding: utf-8
 
 require 'minitest/autorun'
 require_relative '../../lib/y_petri'     # tested component itself
 # require 'y_petri'
-# require 'sy'
+require 'sy'
 
 describe "Simplified dTTP pathway used for demo with Dr. Chang" do
   before do
     @m = YPetri::Agent.new
     Cytoplasm_volume_in_litres = 5.0e-11
@@ -40,78 +40,84 @@
     TMPK_a = 0.83
     @m.clamp AMP: 8695.0, ADP: 6521.0, ATP: 3152.0
     @m.clamp Deoxycytidine: 0.5, DeoxyCTP: 1.0, DeoxyGMP: 1.0
     @m.clamp Thymidine: 0.5
     @m.clamp UMP_UDP_pool: 2737.0
+
     # Functions
     Vmax_per_minute_per_enzyme_molecule =
-      lambda { |enzyme_specific_activity_in_micromol_per_minute_per_mg,
-                enzyme_molecular_mass_in_kDa|
-                  enzyme_specific_activity_in_micromol_per_minute_per_mg *
-                    enzyme_molecular_mass_in_kDa }
+      -> specific_activity_µmol_per_min_per_mg, mol_mass_in_kDa {
+        specific_activity_µmol_per_min_per_mg * mol_mass_in_kDa
+    }
+
     Vmax_per_minute =
-      lambda { |specific_activity, kDa, enzyme_molecules_per_cell|
-               Vmax_per_minute_per_enzyme_molecule.( specific_activity, kDa ) *
-                 enzyme_molecules_per_cell }
+      -> specific_activity, kDa, enzyme_molecules_per_cell {
+        Vmax_per_minute_per_enzyme_molecule.( specific_activity, kDa ) *
+        enzyme_molecules_per_cell
+    }
+
     Vmax_per_second =
-      lambda { |specific_activity, kDa, enzyme_molecules_per_cell|
-               Vmax_per_minute.( specific_activity,
-                                 kDa,
-                                 enzyme_molecules_per_cell ) / 60 }
+      -> specific_activity, kDa, enzyme_molecules_per_cell {
+        Vmax_per_minute.( specific_activity, kDa, enzyme_molecules_per_cell ) / 60
+    }
+
     Km_reduced =
-      lambda { |km, ki_hash={}|
-               ki_hash.map { |concentration, ci_Ki|
-                             concentration / ci_Ki
-                           }.reduce( 1, :+ ) * km }
+      -> km, ki_hash=Hash.new {
+        ki_hash.map { |conc, ci_Ki| conc / ci_Ki }.reduce( 1, :+ ) * km
+    }
+
     Occupancy =
-      lambda { |concentration, reactant_Km, compet_inh_w_Ki_hash={}|
-               concentration / ( concentration +
-                                 Km_reduced.( reactant_Km,
-                                              compet_inh_w_Ki_hash ) ) }
+      -> conc, reactant_Km, compet_inh_w_Ki_hash=Hash.new {
+        conc / ( conc + Km_reduced.( reactant_Km, compet_inh_w_Ki_hash ) )
+    }
+
     MM_with_inh_micromolars_per_second =
-      lambda { |reactant_concentration,
-                enzyme_specific_activity,
-                enzyme_mass_in_kDa,
-                enzyme_molecules_per_cell,
-                reactant_Km,
-                competitive_inh_w_Ki_hash={}|
-                Vmax_per_second.( enzyme_specific_activity,
-                                  enzyme_mass_in_kDa,
-                                  enzyme_molecules_per_cell ) *
-                  Occupancy.( reactant_concentration,
+      -> reactant_conc, enz_spec_activity, enz_mass_in_kDa,
+         enz_molecules_per_cell, reactant_Km, compet_inh_w_Ki_hash=Hash.new {
+      Vmax_per_second.( enz_spec_activity,
+                        enz_mass_in_kDa,
+                        enz_molecules_per_cell ) *
+                  Occupancy.( reactant_conc,
                               reactant_Km,
-                              competitive_inh_w_Ki_hash ) }
+                              compet_inh_w_Ki_hash )
+    }
+
     MMi = MM_with_inh_micromolars_per_second
     TK1_Thymidine_Km = 5.0
     TYMS_DeoxyUMP_Km = 2.0
     RNR_UDP_Km = 1.0
-    DNA_creation_speed = 3_000_000_000 / ( 12 * 3600 )
+    DNA_creation_speed = 3_000_000_000 / ( 12 * 3600 ) / Pieces_per_micromolar
     TMPK_DeoxyTMP_Km = 12.0
 
     # transitions
     @m.Transition name: :TK1_Thymidine_DeoxyTMP,
-                  domain: [ Thymidine, TK1, DeoxyTDP_DeoxyTTP_pool, DeoxyCTP, Deoxycytidine, AMP, ADP, ATP ],
+                  domain: [ Thymidine, TK1, DeoxyTDP_DeoxyTTP_pool,
+                            DeoxyCTP, Deoxycytidine, AMP, ADP, ATP ],
                   stoichiometry: { Thymidine: -1, DeoxyTMP: 1 },
                   rate: proc { |rc, e, pool1, ci2, ci3, master1, master2, master3|
                                ci1 = pool1 * master3 / ( master2 + master3 )
                                MMi.( rc, TK1_a, TK1_kDa, e, TK1_Thymidine_Km,
                                      ci1 => 13.5, ci2 => 0.8, ci3 => 40.0 ) }
+
     @m.Transition name: :TYMS_DeoxyUMP_DeoxyTMP,
                   domain: [ DeoxyUMP_DeoxyUDP_pool, TYMS, AMP, ADP, ATP ],
                   stoichiometry: { DeoxyUMP_DeoxyUDP_pool: -1, DeoxyTMP: 1 },
                   rate: proc { |pool, e, master1, master2, master3|
                           rc = pool * master2 / ( master1 + master2 )
                           MMi.( rc, TYMS_a, TYMS_kDa, e, TYMS_DeoxyUMP_Km ) }
+
     @m.Transition name: :RNR_UDP_DeoxyUDP,
                   domain: [ UMP_UDP_pool, RNR, DeoxyUMP_DeoxyUDP_pool, AMP, ADP, ATP ],
                   stoichiometry: { UMP_UDP_pool: -1, DeoxyUMP_DeoxyUDP_pool: 1 },
                   rate: proc { |pool, e, master1, master2, master3|
                                rc = pool * master2 / ( master1 + master2 )
                                MMi.( rc, RNR_a, RNR_kDa, e, RNR_UDP_Km ) }
+
     @m.Transition name: :DNA_polymerase_consumption_of_DeoxyTTP,
                   stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1 },
                   rate: proc { DNA_creation_speed / 4 }
+
     @m.Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
                   domain: [ DeoxyTMP, TMPK, ADP,
                             DeoxyTDP_DeoxyTTP_pool,
                             DeoxyGMP, AMP, ATP ],
                   stoichiometry: { DeoxyTMP: -1, TMPK: 0, DeoxyTDP_DeoxyTTP_pool: 1 },
@@ -119,9 +125,10 @@
                                master2 = ci1
                                ci2 = pool * master2 / ( master2 + master3 )
                                ci3 = pool * master3 / ( master2 + master3 )
                                MMi.( rc, TMPK_a, TMPK_kDa, e, TMPK_DeoxyTMP_Km,
                                      ci1 => 250.0, ci2 => 30.0, ci3 => 750, ci4 => 117 ) }
+
   end
 
   it "should work" do
     @m.run!
     @m.plot_state