y_petri 2.0.7 → 2.0.14.p1

data/test/acceptance/simulation_with_physical_units_test.rb

@@ -0,0 +1,153 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+describe "Use of TimedSimulation with units" do
+  before do
+    require 'sy'
+
+    @m = YPetri::Manipulator.new
+
+    # === General assumptions
+    Cytoplasm_volume = 5.0e-11.l
+    Pieces_per_concentration = SY::Nᴀ * Cytoplasm_volume
+
+    # === Simulation settings
+    @m.set_step 60.s
+    @m.set_target_time 10.min
+    @m.set_sampling 120.s
+
+    # === Places
+    AMP = @m.Place m!: 8695.0.µM
+    ADP = @m.Place m!: 6521.0.µM
+    ATP = @m.Place m!: 3152.0.µM
+    Deoxycytidine = @m.Place m!: 0.5.µM
+    DeoxyCTP = @m.Place m!: 1.0.µM
+    DeoxyGMP = @m.Place m!: 1.0.µM
+    U12P = @m.Place m!: 2737.0.µM
+    DeoxyU12P = @m.Place m!: 0.0.µM
+    DeoxyTMP = @m.Place m!: 3.3.µM
+    DeoxyT23P = @m.Place m!: 5.0.µM
+    Thymidine = @m.Place m!: 0.5.µM
+    TK1 = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
+    TYMS = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
+    RNR = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
+    TMPK = @m.Place m!: 100_000.unit.( SY::MoleAmount ) / Cytoplasm_volume
+
+    # === Enzyme molecular masses
+    TK1_m = 24.8.kDa
+    TYMS_m = 66.0.kDa
+    RNR_m = 140.0.kDa
+    TMPK_m = 50.0.kDa
+
+    # === Specific activities of the enzymes
+    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
+
+    # === Clamps
+    @m.clamp AMP: 8695.0.µM, ADP: 6521.0.µM, ATP: 3152.0.µM
+    @m.clamp Deoxycytidine: 0.5.µM, DeoxyCTP: 1.0.µM, DeoxyGMP: 1.0.µM
+    @m.clamp Thymidine: 0.5.µM
+    @m.clamp U12P: 2737.0.µM
+
+    # === Function closures
+
+    # Vmax of an enzyme.
+    # 
+    Vmax_enzyme = lambda { |specific_activity, mass, enzyme_conc|
+      specific_activity * mass * enzyme_conc.( SY::Molecularity )
+    }
+
+    # Michaelis constant reduced for competitive inhibitors.
+    # 
+    Km_reduced = lambda { |km, ki_hash={}|
+      ki_hash.map { |concentration, ci_Ki|
+        concentration / ci_Ki }
+        .reduce( 1, :+ ) * km
+    }
+
+    # Occupancy of enzyme active sites at given concentration of reactants
+    # and competitive inhibitors.
+    # 
+    Occupancy = lambda { |ʀ_conc, ʀ_Km, cɪ_Kɪ={}|
+      ʀ_conc / ( ʀ_conc + Km_reduced.( ʀ_Km, cɪ_Kɪ ) )
+    }
+
+    # Michaelis and Menten equation with competitive inhibitors.
+    # 
+    MMi = MM_equation_with_inhibitors = lambda {
+      |ʀ_conc, ᴇ_specific_activity, ᴇ_mass, ᴇ_conc, ʀ_Km, cɪ_Kɪ={}|
+      Vmax_enzyme.( ᴇ_specific_activity, ᴇ_mass, ᴇ_conc ) *
+        Occupancy.( ʀ_conc, ʀ_Km, cɪ_Kɪ )
+    }
+
+    # === Michaelis constants of the enzymes involved.
+
+    TK1_Thymidine_Km = 5.0.µM
+    TYMS_DeoxyUMP_Km = 2.0.µM
+    RNR_UDP_Km = 1.0.µM
+    TMPK_DeoxyTMP_Km = 12.0.µM
+
+    # === DNA synthesis speed.
+
+    DNA_creation_speed = 3_000_000_000.unit.( SY::MoleAmount ) / 12.h / Cytoplasm_volume
+
+    # === Transitions
+
+    # Synthesis of TMP by TK1.
+    # 
+    TK1_Thymidine_DeoxyTMP = @m.Transition s: { Thymidine: -1, DeoxyTMP: 1 },
+      domain: [ Thymidine, TK1, DeoxyT23P, DeoxyCTP, Deoxycytidine, AMP, ADP, ATP ],
+        rate: proc { |rc, e, pool1, ci2, ci3, master1, master2, master3|
+                ci1 = pool1 * master3 / ( master2 + master3 )
+                MMi.( rc, TK1_a, TK1_m, e, TK1_Thymidine_Km,
+                      ci1 => 13.5.µM, ci2 => 0.8.µM, ci3 => 40.0.µM )
+              }
+
+    # Methylation of DeoxyUMP into TMP by TYMS.
+    TYMS_DeoxyUMP_DeoxyTMP = @m.Transition s: { DeoxyU12P: -1, DeoxyTMP: 1 },
+      domain: [ DeoxyU12P, TYMS, AMP, ADP, ATP ],
+        rate: proc { |pool, e, master1, master2, master3|
+                rc = pool * master2 / ( master1 + master2 )
+                MMi.( rc, TYMS_a, TYMS_m, e, TYMS_DeoxyUMP_Km )
+              }
+
+    # Reduction of UDP into DeoxyUDP by RNR.
+    RNR_UDP_DeoxyUDP = @m.Transition s: { U12P: -1, DeoxyU12P: 1 },
+      domain: [ U12P, RNR, DeoxyU12P, AMP, ADP, ATP ],
+        rate: proc { |pool, e, master1, master2, master3|
+                rc = pool * master2 / ( master1 + master2 )
+                MMi.( rc, RNR_a, RNR_m, e, RNR_UDP_Km )
+              }
+
+    # Consumption of TTP by DNA synthesis.
+    DeoxyTTP_to_DNA = @m.Transition s: { DeoxyT23P: -1 },
+        rate: proc { DNA_creation_speed / 4 }
+
+    # Phosphorylation of TMP into TDP-TTP pool.
+    TMPK_DeoxyTMP_DeoxyTDP = @m.Transition s: { DeoxyTMP: -1, TMPK: 0, DeoxyT23P: 1 },
+      domain: [ DeoxyTMP, TMPK, ADP, DeoxyT23P, DeoxyGMP, AMP, ATP ],
+        rate: proc { |rc, e, ci1, pool, ci4, master1, master3|
+                master2 = ci1
+                ci2 = pool * master2 / ( master2 + master3 )
+                ci3 = pool * master3 / ( master2 + master3 )
+                MMi.( rc, TMPK_a, TMPK_m, e, TMPK_DeoxyTMP_Km,
+                      ci1 => 250.0.µM, ci2 => 30.0.µM, ci3 => 750.µM, ci4 => 117.µM )
+              }
+  end
+
+  it "should work" do
+    # === Simulation execution
+    @m.run!
+    # === Plotting of the results
+    @m.plot_state
+    sleep 20
+  end
+end

data/test/acceptance/token_game_test.rb

@@ -0,0 +1,36 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+describe "Token game" do
+  before do
+    @m = YPetri::Manipulator.new
+    @m.Place name: "A"
+    @m.Place name: "B"
+    @m.Place name: "C", marking: 7.77
+    @m.Transition name: "A2B", stoichiometry: { A: -1, B: 1 }
+    @m.Transition name: "C_decay", stoichiometry: { C: -1 }, rate: 0.05
+  end
+
+  it "should work" do
+    @m.place( :A ).marking = 2
+    @m.place( :B ).marking = 5
+    @m.places.map( &:name ).must_equal [:A, :B, :C]
+    @m.places.map( &:marking ).must_equal [2, 5, 7.77]
+    @m.transition( :A2B ).arcs.must_equal [ @m.place( :A ), @m.place( :B ) ]
+    @m.transition( :A2B ).fire!
+    @m.places.map( &:marking ).must_equal [1, 6, 7.77]
+    @m.transition( :A2B ).fire!
+    @m.place( :A ).marking.must_equal 0
+    @m.place( :B ).marking.must_equal 7
+    2.times do @m.transition( :C_decay ).fire! 1 end
+    @m.transition( :C_decay ).fire! 0.1
+    200.times do @m.transition( :C_decay ).fire! 1 end
+    assert_in_delta @m.place( :C ).marking, 0.00024, 0.00001
+  end
+end

data/test/acceptance/visualization_test.rb

@@ -0,0 +1,25 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+describe "Graphviz visualization" do
+  before do
+    @m = YPetri::Manipulator.new
+    @m.Place name: :A, m!: 1
+    @m.Place name: :B, m!: 1.5
+    @m.Place name: :C, m!: 2
+    @m.Place name: :D, m!: 2.5
+    @m.Transition name: :A_pump, s: { A: -1 }, rate: proc { 0.005 }
+    @m.Transition name: :B_decay, s: { B: -1 }, rate: 0.05
+    @m.Transition name: :C_guard, assignment: true, codomain: :C, action: -> { 2 }
+  end
+
+  it "should work" do
+    @m.net.visualize
+  end
+end

data/test/acceptance_tests.rb

@@ -0,0 +1,14 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+require_relative 'acceptance/token_game_test'
+require_relative 'acceptance/basic_usage_test'
+require_relative 'acceptance/simulation_test'
+require_relative 'acceptance/visualization_test'
+require_relative 'acceptance/simulation_with_physical_units_test'

data/test/manipulator_test.rb

@@ -0,0 +1,100 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+describe ::YPetri::Manipulator do
+  before do
+    @m = ::YPetri::Manipulator.new
+  end
+  
+  it "has net basic points" do
+    # --- net point related assets ---
+    @m.net_point_reset
+    @m.net_point_set @m.workspace.net( :Top )
+    @m.net.must_equal @m.workspace.Net::Top
+    # --- simulation point related assets ---
+    @m.simulation_point.reset
+    @m.simulation.must_equal nil
+    @m.simulation_point.key.must_equal nil
+    # --- cc point related assets ---
+    @m.cc_point.reset
+    @m.cc_point.set :Base
+    @m.cc.must_equal @m.workspace.clamp_collection
+    @m.cc.wont_equal :Base
+    @m.cc_point.key.must_equal :Base
+    # --- imc point related assets ---
+    @m.imc_point.reset
+    @m.imc_point.set :Base
+    @m.imc.must_equal @m.workspace.initial_marking_collection
+    @m.imc.wont_equal :Base
+    @m.imc_point.key.must_equal :Base
+    # --- ssc point related assets ---
+    @m.ssc_point.reset
+    @m.ssc_point.set :Base
+    @m.ssc.must_equal @m.workspace.simulation_settings_collection
+    @m.ssc.wont_equal :Base
+    @m.ssc_point.key.must_equal :Base
+  end
+
+  it "has basic selections" do
+    @m.net_selection.clear
+    @m.simulation_selection.clear
+    @m.cc_selection.clear
+    @m.imc_selection.clear
+    @m.ssc_selection.clear
+    @m.net_selection.get.must_equal []
+    @m.simulation_selection.get.must_equal []
+    @m.ssc_selection.get.must_equal []
+    @m.cc_selection.get.must_equal []
+    @m.imc_selection.get.must_equal []
+  end
+
+  it "presents some methods from workspace" do
+    [ @m.places, @m.transitions, @m.nets, @m.simulations ].map( &:size )
+      .must_equal [ 0, 0, 1, 0 ]
+    [ @m.clamp_collections,
+      @m.initial_marking_collections,
+      @m.simulation_settings_collections ].map( &:size ).must_equal [ 1, 1, 1 ]
+    [ @m.clamp_collections,
+      @m.initial_marking_collections,
+      @m.simulation_settings_collections ]
+    .map( &:keys ).must_equal [[:Base]] * 3
+    @m.pp.must_equal []
+    @m.tt.must_equal []
+    @m.nn.must_equal [ :Top ]       # ie. :Top net spanning whole workspace
+  end
+  
+  describe "slightly more complicated case" do
+    before do
+      @p = @m.Place ɴ: "P", default_marking: 1
+      @q = @m.Place ɴ: "Q", default_marking: 1
+      @decay_t = @m.Transition ɴ: "Tp", s: { P: -1 }, rate: 0.1
+      @constant_flux_t = @m.Transition ɴ: "Tq", s: { Q: 1 }, rate: -> { 0.02 }
+      @m.initial_marking @p => 1.2
+      @m.initial_marking @q => 2
+      @m.set_step 0.01
+      @m.set_sampling 1
+      @m.set_time 30
+    end
+    
+    it "works" do
+      @m.run!
+      @m.simulation.places.must_equal [ @p, @q ]
+      @m.simulation.transitions.must_equal [ @decay_t, @constant_flux_t ]
+      @m.simulation.SR_tt.must_equal [ :Tp, :Tq ]
+      @m.simulation.sparse_stoichiometry_vector( :Tp )
+        .must_equal Matrix.column_vector( [-1, 0] )
+      @m.simulation.stoichiometry_matrix_for( @m.transitions ).column_size
+        .must_equal 2
+      @m.simulation.stoichiometry_matrix_for( @m.transitions ).row_size
+        .must_equal 2
+      @m.simulation.flux_vector.row_size.must_equal 2
+      # @m.plot_recording
+    end
+  end
+end

data/test/net_test.rb

@@ -0,0 +1,171 @@
+#! /usr/bin/ruby
+# -*- coding: utf-8 -*-
+
+require 'minitest/spec'
+require 'minitest/autorun'
+require_relative '../lib/y_petri'     # tested component itself
+# require 'y_petri'
+# require 'sy'
+
+describe YPetri::Net do
+  before do
+    @tç = tç = Class.new YPetri::Transition
+    @pç = pç = Class.new YPetri::Place
+    @nç = nç = Class.new YPetri::Net
+    [ tç, pç, nç ].each { |ç|
+      ç.namespace!.class_exec {
+        define_method :Place do pç end
+        define_method :Transition do tç end
+        define_method :Net do nç end
+        private :Place, :Transition, :Net
+      }
+    }
+    @p1 = pç.new ɴ: "A", quantum: 0.1, marking: 1.1
+    @p2 = pç.new ɴ: "B", quantum: 0.1, marking: 2.2
+    @p3 = pç.new ɴ: "C", quantum: 0.1, marking: 3.3
+    @net = nç.new
+    [@p1, @p2, @p3].each { |p| @net.include_place! p }
+    @p_not_included = pç.new ɴ: "X", marking: 0
+  end
+
+  describe "net of 3 places and no transitions" do
+    before do
+      @p1.m = 1.1
+      @p2.m = 2.2
+      @p3.m = 3.3
+    end
+
+    it "should expose its elements" do
+      assert_equal [@p1, @p2, @p3], @net.places
+      assert_equal [:A, :B, :C], @net.pp
+      assert_equal [], @net.transitions
+    end
+
+    it "should expose transition groups" do
+      assert_equal [], @net.transitions_with_rate
+      assert_equal [], @net.rateless_transitions
+      assert_equal [], @net.transitions_without_rate
+      assert_equal [], @net.stoichiometric_transitions
+      assert_equal [], @net.nonstoichiometric_transitions
+    end
+
+    it "should tell its qualities" do
+      assert_equal true, @net.functional?
+      assert_equal true, @net.timed?
+      assert @net.include?( @p1 ) && !@net.include?( YPetri::Place.new )
+    end
+
+    it "should have 'standard equipment' methods" do
+      assert @net == @net.dup
+      assert @net.inspect.start_with? "#<Net:"
+      assert @net.include?( @p1 )
+      assert ! @net.include?( @p_not_included )
+      begin
+        @net.exclude_place! @p_not_included
+        @net.include_transition! YPetri::Transition.new( s: { @p_not_included => -1 } )
+        flunk "Attempt to include illegal transition fails to raise"
+      rescue; end
+    end
+
+    describe "plus 1 stoichio. transition with rate" do
+      before do
+        @t1 = @tç.new!( ɴ: "T1",
+                        s: { @p1 => 1, @p2 => -1, @p3 => -1 },
+                        rate: 0.01 )
+        @net.include_transition! @t1
+      end
+
+      it "should expose its elements" do
+        assert_equal [@t1], @net.transitions
+        assert_equal [:T1], @net.tt
+      end
+
+      it "should expose transition groups" do
+        assert_equal true, @t1.has_rate?
+        assert_equal [@t1], @net.transitions_with_rate
+        assert_equal [], @net.rateless_transitions
+        assert_equal [@t1], @net.stoichiometric_transitions
+        assert_equal [], @net.nonstoichiometric_transitions
+      end
+
+      it "should tell its qualities" do
+        assert_equal true, @net.functional?
+        assert_equal true, @net.timed?
+        assert @net.include?( @t1 )
+      end
+
+      it "should have #place & #transition for safe access to the said elements" do
+        @net.send( :place, @p1 ).must_equal @p1
+        @net.send( :transition, @t1 ).must_equal @t1
+      end
+
+      it "has #new_simulation & #new_timed_simulation constructors" do
+        @net.must_respond_to :new_simulation
+        @net.must_respond_to :new_timed_simulation
+      end
+
+      it "should have other methods" do
+        assert_equal [1.1, 2.2, 3.3], [@p1, @p2, @p3].map( &:marking ).map{ |n| n.round 6 }
+        assert_equal 2.2 * 3.3 * 0.01, @t1.rate_closure.call( @p2.marking, @p3.marking )
+        assert_equal [ @p2, @p3 ], @t1.domain
+        @t1.fire! 1
+        assert_equal [1.1726, 2.1274, 3.2274], [@p1, @p2, @p3].map( &:marking ).map{ |n| n.round 6 }
+      end
+
+      describe "plus 1 more nameless timeless functionless transition" do
+        before do
+          @t2 = @tç.new s: { @p2 => -1, @p3 => 1 }
+          @net.include_transition! @t2
+        end
+
+        it "should expose its elements" do
+          assert_equal [@t1, @t2], @net.transitions
+          assert_equal [:T1, nil], @net.tt
+          @net.tap{ |n| n.exclude_transition! @t1 }.exclude_transition! @t2
+          @net.tap{ |n| n.exclude_place! @p3 }.pp.must_equal [:A, :B]
+        end
+
+        it "should expose transition groups" do
+          assert_equal [], @net.timeless_nonstoichiometric_transitions
+          assert_equal [], @net.timeless_nonstoichiometric_tt
+          assert_equal [@t2], @net.timeless_stoichiometric_transitions
+          assert_equal [nil], @net.timeless_stoichiometric_tt
+          assert_equal [], @net.timed_nonstoichiometric_transitions_without_rate
+          assert_equal [], @net.timed_rateless_nonstoichiometric_transitions
+          assert_equal [], @net.timed_nonstoichiometric_tt_without_rate
+          assert_equal [], @net.timed_rateless_nonstoichiometric_tt
+          assert_equal [], @net.timed_nonstoichiometric_transitions_without_rate
+          assert_equal [], @net.timed_rateless_nonstoichiometric_transitions
+          assert_equal [], @net.timed_nonstoichiometric_tt_without_rate
+          assert_equal [], @net.timed_rateless_nonstoichiometric_tt
+          assert_equal [], @net.nonstoichiometric_transitions_with_rate
+          assert_equal [], @net.nonstoichiometric_tt_with_rate
+          assert_equal [@t1], @net.stoichiometric_transitions_with_rate
+          assert_equal [:T1], @net.stoichiometric_tt_with_rate
+          assert_equal [], @net.assignment_transitions
+          assert_equal [], @net.assignment_tt
+          assert_equal [@t1, @t2], @net.stoichiometric_transitions
+          assert_equal [:T1, nil], @net.stoichiometric_tt
+          assert_equal [], @net.nonstoichiometric_transitions
+          assert_equal [], @net.nonstoichiometric_tt
+          assert_equal [@t1], @net.timed_transitions
+          assert_equal [:T1], @net.timed_tt
+          assert_equal [@t2], @net.timeless_transitions
+          assert_equal [nil], @net.timeless_tt
+          assert_equal [@t1], @net.transitions_with_rate
+          assert_equal [:T1], @net.tt_with_rate
+          assert_equal [@t2], @net.rateless_transitions
+          assert_equal [nil], @net.rateless_tt
+        end
+
+        it "should tell its qualities" do
+          assert_equal false, @net.functional?
+          assert_equal false, @net.timed?
+          @net.exclude_transition! @t2
+          assert_equal true, @net.functional?
+          assert_equal true, @net.timed?
+        end
+      end
+    end
+  end
+end

data/test/place_test.rb

@@ -66,18 +66,19 @@ describe YPetri::Place do
   end
 
   it "should have guard mechanics" do
-    @p.guards.size.must_equal 2 # working automatic guard construction
+    @p.guards.size.must_equal 3 # working automatic guard construction
     g1, g2 = @p.guards
-    g1.assertion.must_include "number"
-    g2.assertion.must_include "complex"
+    [g1.assertion, g2.assertion].tap { |u, v|
+      assert u.include?( "number" ) || u.include?( "Numeric" )
+      assert v.include?( "complex" ) || v.include?( "Complex" )
+    }
     begin; g1.validate 11.1; g2.validate 11.1; @p.guard.( 11.1 ); :nothing_raised
     rescue; :error end.must_equal :nothing_raised
     -> { g2.validate Complex( 1, 1 ) }.must_raise YPetri::GuardError
     @p.marking "must be in 0..10" do |m| fail unless ( 0..10 ) === m end
-    @p.guards.size.must_equal 3
+    @p.guards.size.must_equal 4
     g = @p.federated_guard_closure
     -> { g.( 11.1 ) }.must_raise YPetri::GuardError
-    @p.marking = -1.11
-    -> { @p.guard! }.must_raise YPetri::GuardError
+    -> { @p.marking = -1.11 }.must_raise YPetri::GuardError
   end
 end