y_petri 2.1.50 → 2.1.51

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 7c7445c48f5803b021e7d1689f51d0eae2adfff2
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data/lib/y_petri/agent/petri_net_related.rb

@@ -78,21 +78,33 @@ module YPetri::Agent::PetriNetRelated
   # world. Rate closure has to be supplied as a block.
   # 
   def TT( *ordered, **named, &block )
-    fail ArgumentError, "Timed transition constructor requires a block " +
-      "defining the rate function!" unless block
-    world.Transition.send( :new, *ordered, **named.update( rate: block ) )
+    if named.has? :rate then
+      fail ArgumentError, "Block must not be given if :rate named argument " +
+        "is given!" if block
+    else
+      fail ArgumentError, "Timed transition constructor requires either " +
+        "a :rate argument, or a block!" unless block
+      named.update rate: block
+    end
+    world.Transition.send( :new, *ordered, **named )
   end
 
   # Timed stoichiometric transition constructor, that expects stoichiometry
   # given directly as hash-collected arguments. Two special keys allowed are
   # +:name+ (alias +:ɴ) and +:domain+. (Key +:codomain+ is not allowed.)
   # 
-  def TS **stoichiometry, &block
-    args = { s: stoichiometry }
-    args.update name: stoichiometry.delete( :name ) if
-      stoichiometry.has? :name, syn!: :ɴn
-    args.update domain: stoichiometry.delete( :domain ) if
-      stoichiometry.has? :domain
+  def TS *domain, **stoichiometry, &block
+    nn = stoichiometry
+    args = { s: nn }
+    args.update name: nn.delete( :name ) if nn.has? :name, syn!: :ɴ
+    if domain.empty? then
+      args.update domain: nn.delete( :domain ) if nn.has? :domain
+    else
+      fail ArgumentError, "There must not be any ordered arguments if " +
+        "named argument :domain is given!" unless domain.empty?
+      args.update domain: domain
+    end
+    args.update rate: nn.delete( :rate ) if nn.has? :rate, syn!: :rate_closure
     TT **args, &block
   end
 
@@ -105,8 +117,7 @@ module YPetri::Agent::PetriNetRelated
       "defining the assignment function!" unless block
     world.Transition.send( :new,
                            codomain: codomain,
-                           assignment: true,
-                           action: block,
+                           assignment: block,
                            **nn )
   end
 

data/lib/y_petri/transition.rb

@@ -277,9 +277,7 @@ class YPetri::Transition
   # 
   def to_s
     "#<Transition: %s>" %
-      "#{name.nil? ? '' : '%s ' % name }(#{type}%s)%s" %
-      [ "#{assignment_action? ? ' Assign.' : ''}",
-        "#{name.nil? ? ' id:%s' % object_id : ''}" ]
+      "#{'%s ' % name if name}(#{type})#{' id:%s' % object_id unless name}"
   end
 
   def place id

data/lib/y_petri/version.rb

@@ -1,4 +1,4 @@
 module YPetri
-  VERSION = "2.1.50"
+  VERSION = "2.1.51"
   DEBUG = false
 end

data/test/examples/example_IV.rb

@@ -0,0 +1,135 @@
+#encoding: utf-8
+
+require 'y_petri' and include YPetri
+# require 'mathn'
+
+Pieces_per_microM = 100_000
+set_step 10
+set_sampling 30
+set_target_time 30 * 60
+
+# === Places (all in µM)
+
+AMP = Place m!: 8695.0
+ADP = Place m!: 6521.0
+ATP = Place m!: 3152.0
+DeoxyCytidine = Place m!: 5.0
+DeoxyCTP = Place m!: 20.0
+DeoxyGMP = Place m!: 20.0
+UMP_UDP_pool = Place m!: 2737.0
+DeoxyUMP_DeoxyUDP_pool = Place m!: 10.0
+DeoxyTMP = Place m!: 50.0
+DeoxyTDP_DeoxyTTP_pool = Place m!: 100.0
+Thymidine = Place m!: 10.0
+
+TK1 = Place m!: 100_000 / Pieces_per_microM
+TYMS = Place m!: 100_000 / Pieces_per_microM
+RNR = Place m!: 100_000 / Pieces_per_microM
+TMPK = Place m!: 100_000 / Pieces_per_microM
+
+# === Molecular masses
+
+TK1_kDa = 24.8
+TYMS_kDa = 66.0
+RNR_kDa = 140.0
+TMPK_kDa = 50.0
+
+# === Enzyme specific activities
+
+TK1_a = 5.40
+TYMS_a = 3.80
+RNR_a = 1.00
+TMPK_a = 0.83
+
+# === Clamps (all in µM)
+
+clamp AMP: 8695.0, ADP: 6521.0, ATP: 3152.0
+clamp DeoxyCytidine: 5.0, DeoxyCTP: 20.0, DeoxyGMP: 20.0
+clamp Thymidine: 20
+clamp UMP_UDP_pool: 2737.0
+
+# === Function closures
+
+Vmax_per_min_per_enz_molecule =
+  lambda { |spec_act_microM_per_min_per_mg, kDa|
+             spec_act_microM_per_min_per_mg * kDa }
+Vmax_per_min =
+  lambda { |spec_act, kDa, enz_molecules_per_cell|
+           Vmax_per_min_per_enz_molecule.( spec_act, kDa ) *
+             enz_molecules_per_cell }
+Vmax_per_s =
+  lambda { |spec_act, kDa, enz_mol_per_cell|
+           Vmax_per_min.( spec_act, kDa, enz_mol_per_cell ) / 60 }
+Km_reduced =
+  lambda { |km, ki_hash={}|
+           ki_hash.map { |c, ki| c / ki }.reduce( 1, :+ ) * km }
+Occupancy =
+  lambda { |c, km, compet_inh_w_Ki_hash={}|
+           c / ( c + Km_reduced.( km, compet_inh_w_Ki_hash ) ) }
+MM_with_inh_microM_per_second =
+  lambda { |c, spec_act, kDa, enz_mol_per_cell, km, ki_hash={}|
+            Vmax_per_s.( spec_act, kDa, enz_mol_per_cell ) *
+              Occupancy.( c, km, ki_hash ) }
+MMi = MM_with_inh_microM_per_second
+
+# === Michaelis constants (all in µM)
+
+TK1_Thymidine_Km = 5.0
+TYMS_DeoxyUMP_Km = 2.0
+RNR_UDP_Km = 1.0
+DNA_creation_speed = 3_000_000_000.0 / ( 12 * 3600 ) / 4 / Pieces_per_microM
+TMPK_DeoxyTMP_Km = 12.0
+
+# === Transitions
+
+Transition name: :TK1_Thymidine_DeoxyTMP,
+           domain: [ Thymidine, TK1, DeoxyTDP_DeoxyTTP_pool, DeoxyCTP,
+                     DeoxyCytidine, AMP, ADP, ATP ],
+           stoichiometry: { Thymidine: -1, DeoxyTMP: 1 },
+           rate: proc { |c, e, pool1, ci2, ci3, master1, master2, master3|
+                        ci1 = pool1 * master3 / ( master2 + master3 )
+                        MMi.( c, TK1_a, TK1_kDa, e, TK1_Thymidine_Km,
+                              ci1 => 13.5, ci2 => 0.8, ci3 => 40.0 ) }
+
+Transition name: :TYMS_DeoxyUMP_DeoxyTMP,
+           domain: [ DeoxyUMP_DeoxyUDP_pool, TYMS, AMP, ADP, ATP ],
+           stoichiometry: { DeoxyUMP_DeoxyUDP_pool: -1, DeoxyTMP: 1 },
+           rate: proc { |pool, e, mono, di, tri|
+                        c = pool * di / ( mono + di )
+                        MMi.( c, TYMS_a, TYMS_kDa, e, TYMS_DeoxyUMP_Km ) }
+
+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, mono, di, tri|
+                        c = pool * di / ( mono + di )
+                        MMi.( c, RNR_a, RNR_kDa, e, RNR_UDP_Km ) }
+
+Transition name: :DNA_polymerase_consumption_of_DeoxyTTP,
+           stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1 },
+           rate: proc { DNA_creation_speed / 4 }
+
+Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
+           domain: [ DeoxyTMP, TMPK, DeoxyTDP_DeoxyTTP_pool, DeoxyGMP, AMP, ADP, ATP ],
+           stoichiometry: { DeoxyTMP: -1, TMPK: 0, DeoxyTDP_DeoxyTTP_pool: 1 },
+           rate: proc { |c, e, pool, ci4, mono, di, tri|
+                        ci1 = di
+                        ci2 = pool * di / ( di + tri )
+                        ci3 = pool * tri / ( di + tri )
+                        MMi.( c, TMPK_a, TMPK_kDa, e, TMPK_DeoxyTMP_Km,
+                              ci1 => 250.0, ci2 => 30.0, ci3 => 750, ci4 => 117 ) }
+
+Transition name: :PhosphataseI,
+           stoichiometry: { DeoxyTMP: -1, Thymidine: 1 },
+           rate: 0.04
+
+Transition name: :PhosphataseII,
+           stoichiometry: { DeoxyTDP_DeoxyTTP_pool: -1, DeoxyTMP: 1 },
+           rate: 0.01
+
+# === Transitions
+
+net.visualize
+run!
+recording.plot
+recording.flux.plot

data/test/examples/example_VI_gillespie.rb

@@ -0,0 +1,21 @@
+#! /usr/bin/ruby
+# encoding: utf-8
+
+require 'y_petri' and include YPetri
+
+A = Place m!: 10
+B = Place m!: 10
+AB = Place m!: 0
+AB_association = TS A: -1, B: -1, AB: 1, rate: 0.1
+AB_dissociation = TS AB: -1, A: 1, B: 1, rate: 0.1
+A2B = TS A: -1, B: 1, rate: 0.05
+B2A = TS A: 1, B: -1, rate: 0.07
+
+set_step 1
+set_target_time 50
+set_sampling 1
+set_simulation_method :gillespie
+
+run!
+print_recording
+plot_state

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: y_petri
 version: !ruby/object:Gem::Version
-  version: 2.1.50
+  version: 2.1.51
 platform: ruby
 authors:
 - boris
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-31 00:00:00.000000000 Z
+date: 2013-09-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: y_support
@@ -175,10 +175,10 @@ files:
 - test/agent_test.rb
 - test/examples/demonstrator.rb
 - test/examples/demonstrator_2.rb
-- test/examples/demonstrator_3.rb
 - test/examples/demonstrator_4.rb
 - test/examples/example_2.rb
-- test/examples/gillespie.rb
+- test/examples/example_IV.rb
+- test/examples/example_VI_gillespie.rb
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb
@@ -223,10 +223,10 @@ test_files:
 - test/agent_test.rb
 - test/examples/demonstrator.rb
 - test/examples/demonstrator_2.rb
-- test/examples/demonstrator_3.rb
 - test/examples/demonstrator_4.rb
 - test/examples/example_2.rb
-- test/examples/gillespie.rb
+- test/examples/example_IV.rb
+- test/examples/example_VI_gillespie.rb
 - test/examples/manual_examples.rb
 - test/net_test.rb
 - test/place_test.rb

data/test/examples/demonstrator_3.rb

@@ -1,150 +0,0 @@
-#encoding: utf-8
-
-require 'y_petri'
-include YPetri
-require 'sy'
-require 'mathn'
-
-# === General assumptions
-
-Cell_diameter = 10.µm
-Cytoplasm_volume = ( 4 / 3 * Math::PI * ( Cell_diameter / 2 ) ** 3 ).( SY::LitreVolume )
-# Cytoplasm_volume = 5.0e-11.l         # of an average cell
-# How many molecules are there in the average cell per micromolar.
-Pieces_per_µM = ( 1.µM * Cytoplasm_volume ).in( :unit )
-
-# === Simulation settings
-
-set_step 60.s.in( :s )
-set_target_time 20.min.in( :s )
-set_sampling 120.s.in( :s )
-
-# === Places (all in µM)
-
-AMP = Place m!: 8695.0
-ADP = Place m!: 6521.0
-ATP = Place m!: 3152.0
-DeoxyCytidine = Place m!: 0.5
-DeoxyCTP = Place m!: 1.0
-DeoxyGMP = Place m!: 1.0
-U12P = Place m!: 2737.0
-DeoxyU12P = Place m!: 0.0
-DeoxyTMP = Place m!: 3.3
-DeoxyT23P = Place m!: 5.0
-Thymidine = Place m!: 0.5
-TK1 = Place m!: 100_000 / Pieces_per_µM
-TYMS = Place m!: 100_000 / Pieces_per_µM
-RNR = Place m!: 100_000 / Pieces_per_µM
-TMPK = Place m!: 100_000 / Pieces_per_µM
-
-# === Molecular masses
-
-TK1_m = 24.8.kDa
-TYMS_m = 66.0.kDa
-RNR_m = 140.0.kDa
-TMPK_m = 50.0.kDa
-
-# === Enzyme specific activities
-
-TK1_a = 5.40.µmol.min⁻¹.mg⁻¹
-TYMS_a = 3.80.µmol.min⁻¹.mg⁻¹
-RNR_a = 1.00.µmol.min⁻¹.mg⁻¹
-TMPK_a = 0.83.µmol.min⁻¹.mg⁻¹
-
-# === Enzyme kcat
-
-TK1_k_cat = ( TK1_a * TK1_m ).( SY::Amount / SY::Time ).in :s⁻¹
-TYMS_k_cat = ( TYMS_a * TYMS_m ).( SY::Amount / SY::Time ).in :s⁻¹
-RNR_k_cat = ( RNR_a * RNR_m ).( SY::Amount / SY::Time ).in :s⁻¹
-TMPK_k_cat = ( TMPK_a * TMPK_m ).( SY::Amount / SY::Time ).in :s⁻¹
-
-# === Clamps (all in µM)
-
-clamp AMP: 8695.0, ADP: 6521.0, ATP: 3152.0
-clamp DeoxyCytidine: 0.5, DeoxyCTP: 1.0, DeoxyGMP: 1.0
-clamp Thymidine: 0.5
-clamp U12P: 2737.0
-
-# === Function closures
-
-# Vmax of an enzyme.
-# 
-Vmax = -> enzyme_µM, k_cat do enzyme_µM * k_cat end
-
-# Michaelis constant reduced for competitive inhibitors.
-# 
-Km_reduced = -> reactant_Km, hash_Ki=Hash.new do
-  hash_Ki.map { |compet_inhibitor_concentration, compet_inhibitor_Ki|
-    compet_inhibitor_concentration / compet_inhibitor_Ki
-  }.reduce( 1, :+ ) * reactant_Km
-end
-
-# Occupancy fraction of the Michaelis-Menten equation.
-# 
-Occupancy = -> reactant_µM, reactant_Km, hash_Ki=Hash.new do
-  reactant_µM / ( reactant_µM + Km_reduced.( reactant_Km, hash_Ki ) )
-end
-
-# Michaelis-Menten equation with competitive inhibitors.
-# 
-MMi = -> reactant_µM, reactant_Km, enzyme_µM, k_cat, hash_Ki=Hash.new do
-  Vmax.( enzyme_µM, k_cat ) * Occupancy.( reactant_µM, reactant_Km, hash_Ki )
-end
-
-# === Michaelis constants (all in µM)
-
-TK1_Thymidine_Km = 5.0
-TYMS_DeoxyUMP_Km = 2.0
-RNR_UDP_Km = 1.0
-TMPK_DeoxyTMP_Km = 12.0
-
-# === DNA synthesis speed
-
-S_phase_duration = 12.h
-Genome_size = 3_000_000_000          # of bases
-DNA_creation_speed = Genome_size / S_phase_duration.in( :s ) # in base.s⁻¹
-
-# === Transitions
-
-Transition name: :TK1_Thymidine_DeoxyTMP,
-           domain: [ Thymidine, TK1, DeoxyT23P, DeoxyCTP, DeoxyCytidine, AMP, ADP, ATP ],
-           stoichiometry: { Thymidine: -1, DeoxyTMP: 1 },
-           rate: proc { |reactant, enzyme, pool, inhibitor_2, inhibitor_3, mono, di, tri|
-             inhibitor_1 = pool * tri / ( di + tri ) # conc. of DeoxyTTP
-             MMi.( reactant, TK1_Thymidine_Km, enzyme, TK1_k_cat,
-                   inhibitor_1 => 13.5, inhibitor_2 => 0.8, inhibitor_3 => 40.0 )
-           }
-
-Transition name: :TYMS_DeoxyUMP_DeoxyTMP,
-           domain: [ DeoxyU12P, TYMS, AMP, ADP, ATP ],
-           stoichiometry: { DeoxyU12P: -1, DeoxyTMP: 1 },
-           rate: proc { |pool, enzyme, mono, di, tri|
-             reactant = pool * di / ( mono + di ) # conc. of DeoxyUMP
-             MMi.( reactant, TYMS_DeoxyUMP_Km, enzyme, TYMS_k_cat )
-           }
-
-Transition name: :RNR_UDP_DeoxyUDP,
-           domain: [ U12P, RNR, DeoxyU12P, AMP, ADP, ATP ],
-           stoichiometry: { U12P: -1, DeoxyU12P: 1 },
-           rate: proc { |pool, enzyme, mono, di, tri|
-             reactant = pool * di / ( mono + di )
-             MMi.( reactant, RNR_UDP_Km, enzyme, RNR_k_cat )
-           }
-
-Transition name: :DNA_polymerase_consumption_of_DeoxyTTP,
-           stoichiometry: { DeoxyT23P: -1 },
-           rate: proc { DNA_creation_speed / 4 }
-
-Transition name: :TMPK_DeoxyTMP_DeoxyTDP,
-           domain: [ DeoxyTMP, TMPK, DeoxyT23P, DeoxyGMP, AMP, ADP, ATP ],
-           stoichiometry: { DeoxyTMP: -1, DeoxyT23P: 1 },
-           rate: proc { |reactant, enzyme, pool, inhibitor_4, mono, di, tri|
-             inhibitor_1 = di
-             inhibitor_2 = pool * di / ( di + tri ) # conc. of DeoxyTDP
-             inhibitor_3 = pool * tri / ( di + tri ) # conc. of DeoxyTTP
-             MMi.( reactant, TMPK_DeoxyTMP_Km, enzyme, TMPK_k_cat )
-           }
-
-# execution
-run!
-plot_recording

data/test/examples/gillespie.rb

@@ -1,26 +0,0 @@
-#! /usr/bin/ruby
-# encoding: utf-8
-
-require 'y_petri'
-require 'sy'
-require 'mathn'
-include YPetri
-
-A = Place m!: 10
-B = Place m!: 10
-AB = Place m!: 0
-AB_association = Transition s: { A: -1, B: -1, AB: 1 }, rate: 0.1
-AB_dissociation = Transition s: { AB: -1, A: 1, B: 1 }, rate: 0.1
-A2B = Transition s: { A: -1, B: 1 }, rate: 0.05
-B2A = Transition s: { A: 1, B: -1 }, rate: 0.07
-
-set_step 1
-set_target_time 50
-set_sampling 1
-set_simulation_method :gillespie
-
-run!
-
-print_recording
-
-plot_state