lazar 0.9.3 → 1.0.0

data/lib/validation.rb

@@ -1,108 +1,25 @@
 module OpenTox
 
-  class Validation
-
-    field :model_id, type: BSON::ObjectId
-    field :prediction_dataset_id, type: BSON::ObjectId
-    field :crossvalidation_id, type: BSON::ObjectId
-    field :test_dataset_id, type: BSON::ObjectId
-    field :nr_instances, type: Integer
-    field :nr_unpredicted, type: Integer
-    field :predictions, type: Array
-
-    def prediction_dataset
-      Dataset.find prediction_dataset_id
-    end
-
-    def test_dataset
-      Dataset.find test_dataset_id
-    end
-
-    def model
-      Model::Lazar.find model_id
-    end
-
-    def self.create model, training_set, test_set, crossvalidation=nil
-      
-      atts = model.attributes.dup # do not modify attributes from original model
-      atts["_id"] = BSON::ObjectId.new
-      atts[:training_dataset_id] = training_set.id
-      validation_model = model.class.create training_set, atts
-      validation_model.save
-      cids = test_set.compound_ids
-
-      test_set_without_activities = Dataset.new(:compound_ids => cids.uniq) # remove duplicates and make sure that activities cannot be used
-      prediction_dataset = validation_model.predict test_set_without_activities
-      predictions = []
-      nr_unpredicted = 0
-      activities = test_set.data_entries.collect{|de| de.first}
-      prediction_dataset.data_entries.each_with_index do |de,i|
-        if de[0] #and de[1] 
-          cid = prediction_dataset.compound_ids[i]
-          rows = cids.each_index.select{|r| cids[r] == cid }
-          activities = rows.collect{|r| test_set.data_entries[r][0]}
-          prediction = de.first
-          confidence = de[1]
-          predictions << [prediction_dataset.compound_ids[i], activities, prediction, de[1]]
-        else
-          nr_unpredicted += 1
-        end
+  module Validation
+
+    class Validation
+      include OpenTox
+      include Mongoid::Document
+      include Mongoid::Timestamps
+      store_in collection: "validations"
+      field :name, type: String
+      field :model_id, type: BSON::ObjectId
+      field :nr_instances, type: Integer, default: 0
+      field :nr_unpredicted, type: Integer, default: 0
+      field :predictions, type: Hash, default: {}
+      field :finished_at, type: Time 
+
+      def model
+        Model::Lazar.find model_id
       end
-      validation = self.new(
-        :model_id => validation_model.id,
-        :prediction_dataset_id => prediction_dataset.id,
-        :test_dataset_id => test_set.id,
-        :nr_instances => test_set.compound_ids.size,
-        :nr_unpredicted => nr_unpredicted,
-        :predictions => predictions#.sort{|a,b| p a; b[3] <=> a[3]} # sort according to confidence
-      )
-      validation.crossvalidation_id = crossvalidation.id if crossvalidation
-      validation.save
-      validation
-    end
-
-  end
-
-  class ClassificationValidation < Validation
-  end
 
-  class RegressionValidation < Validation
-
-    def statistics
-      rmse = 0
-      weighted_rmse = 0
-      rse = 0
-      weighted_rse = 0
-      mae = 0
-      weighted_mae = 0
-      confidence_sum = 0
-      predictions.each do |pred|
-        compound_id,activity,prediction,confidence = pred
-        if activity and prediction
-          error = Math.log10(prediction)-Math.log10(activity.median)
-          rmse += error**2
-          weighted_rmse += confidence*error**2
-          mae += error.abs
-          weighted_mae += confidence*error.abs
-          confidence_sum += confidence
-        else
-          warnings << "No training activities for #{Compound.find(compound_id).smiles} in training dataset #{model.training_dataset_id}."
-          $logger.debug "No training activities for #{Compound.find(compound_id).smiles} in training dataset #{model.training_dataset_id}."
-        end
-      end
-      x = predictions.collect{|p| p[1].median}
-      y = predictions.collect{|p| p[2]}
-      R.assign "measurement", x
-      R.assign "prediction", y
-      R.eval "r <- cor(-log(measurement),-log(prediction),use='complete')"
-      r = R.eval("r").to_ruby
-
-      mae = mae/predictions.size
-      weighted_mae = weighted_mae/confidence_sum
-      rmse = Math.sqrt(rmse/predictions.size)
-      weighted_rmse = Math.sqrt(weighted_rmse/confidence_sum)
-      { "R^2" => r**2, "RMSE" => rmse, "MAE" => mae }
     end
+
   end
 
 end

data/scripts/mg2mmol.rb

@@ -0,0 +1,17 @@
+#!/usr/bin/env ruby
+require_relative '../lazar/lib/lazar'
+include OpenTox
+newfile = ARGV[0].sub(/.csv/,"_mmol.csv") 
+p newfile
+CSV.open(newfile, "wb") do |csv|
+  CSV.read(ARGV[0]).each do |line|
+    smi,mg = line
+    if mg.numeric?
+      c = Compound.from_smiles smi
+      mmol = c.mg_to_mmol mg.to_f
+      csv << [smi, mmol]
+    else
+      csv << [smi, mg.gsub(/mg/,'mmol')]
+    end
+  end
+end

data/scripts/mirror-enm2test.rb

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+require_relative '../lib/lazar'
+include OpenTox
+Import::Enanomapper.mirror File.join(File.dirname(__FILE__),"..","test","data","enm")

data/scripts/mmol2-log10.rb

@@ -0,0 +1,32 @@
+#!/usr/bin/env ruby
+require_relative '../lib/lazar'
+include OpenTox
+
+newfile = ARGV[0].sub(/.csv/,"_log10.csv")
+p newfile
+CSV.open(newfile, "wb") do |csv|
+  i = 1
+  CSV.read(ARGV[0]).each do |line|
+    type,mmol = line
+    if i == 1
+      @type = type
+      csv << ["SMILES", "-log10(#{mmol})"]
+    else
+      if mmol.numeric?
+        if @type =~ /smiles/i
+          c = Compound.from_smiles type
+        elsif @type =~ /inchi/i
+          c = Compound.from_inchi type
+          type = c.smiles
+        else
+          p "Unknown type '#{type}' at line 1."
+        end
+        mmol = -Math.log10(mmol.to_f)
+        csv << [type, mmol]
+      else
+        p "Line #{i}: '#{mmol}' is not a numeric value."
+      end
+    end
+    i += 1
+  end
+end

data/test/compound.rb

@@ -2,19 +2,16 @@ require_relative "setup.rb"
 
 class CompoundTest < MiniTest::Test
 
-  def test_0_compound_from_smiles
+  def test_compound_from_smiles
     c = OpenTox::Compound.from_smiles "F[B-](F)(F)F.[Na+]"
     assert_equal "InChI=1S/BF4.Na/c2-1(3,4)5;/q-1;+1", c.inchi.chomp
     assert_equal "F[B-](F)(F)F.[Na+]", c.smiles, "A failure here might be caused by a compound webservice running on 64bit architectures using an outdated version of OpenBabel. Please install OpenBabel version 2.3.2 or higher." # seems to be fixed in 2.3.2
   end
 
-  def test_1_compound_from_smiles
+  def test_compound_from_smiles
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C#N"
     assert_equal "InChI=1S/C6H9NO/c1-5(4-7)3-6(2)8/h5H,3H2,1-2H3", c.inchi
     assert_equal "CC(C#N)CC(=O)C", c.smiles
-  end
-
-  def test_2_compound_from_smiles
     c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
     assert_equal "InChI=1S/C6H5N2.BF4/c7-8-6-4-2-1-3-5-6;2-1(3,4)5/h1-5H;/q+1;-1", c.inchi
     assert_equal "F[B-](F)(F)F.N#[N+]c1ccccc1", c.smiles
@@ -79,16 +76,6 @@ print c.sdf
     assert_equal 9, c.fingerprint("FP4").size
   end
 
-  def test_neighbors
-    d = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
-    d.compounds.each do |c|
-      refute_nil c.fingerprint("MP2D")
-    end
-    c = d.compounds[371]
-    n = c.fingerprint_neighbors({:type => "FP4", :min_sim => 0.7, :training_dataset_id => d.id })
-    assert n.size >= 18, "Neighbors size (#{n.size}) should be larger than 17"
-  end
-
   def test_openbabel_segfault
     inchi = "InChI=1S/C19H27NO7/c1-11-9-19(12(2)27-19)17(23)26-14-6-8-20(4)7-5-13(15(14)21)10-25-16(22)18(11,3)24/h5,11-12,14,24H,6-10H2,1-4H3/b13-5-/t11-,12-,14-,18-,19?/m1/s1"
 
@@ -107,25 +94,6 @@ print c.sdf
     end
   end
 
-  def test_fingerprint_neighbors
-    types = ["FP2", "FP3", "FP4", "MACCS"]
-    min_sim = 0.7
-    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
-    [
-      "CC(=O)CC(C)C#N",
-      "CC(=O)CC(C)C",
-      "C(=O)CC(C)C#N",
-    ].each do |smi|
-      c = OpenTox::Compound.from_smiles smi
-      types.each do |type|
-        neighbors = c.fingerprint_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
-        unless type == "FP2" and smi == "CC(=O)CC(C)C#N" or smi == "C(=O)CC(C)C#N" and (type == "FP2" or type == "MACCS")
-          refute_empty neighbors
-        end
-      end
-    end
-  end
-
   def test_mna
     c = OpenTox::Compound.from_smiles "N#[N+]C1=CC=CC=C1.F[B-](F)(F)F"
     assert_equal 18, c.fingerprint("MNA").size
@@ -138,72 +106,14 @@ print c.sdf
     assert 7, c.fingerprint("MP2D").uniq.size
   end
 
-  def test_fingerprint_count_neighbors
-    types = ["MP2D", "MNA"]
-    min_sim = 0.0
-    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
-    [
-      "CC(=O)CC(C)C#N",
-      "CC(=O)CC(C)C",
-      "C(=O)CC(C)C#N",
-    ].each do |smi|
-      c = OpenTox::Compound.from_smiles smi
-      types.each do |type|
-        neighbors = c.fingerprint_count_neighbors({:type => type, :training_dataset_id => training_dataset.id, :min_sim => min_sim})
-        if type == "FP4"
-          fp4_neighbors = c.neighbors
-          neighbors.each do |n|
-            assert_includes fp4_neighbors, n
-          end
-        end
-      end
-    end
-  end
-
-  def test_fingerprint_db_neighbors
-    #skip
-    training_dataset = Dataset.from_csv_file File.join(DATA_DIR,"EPAFHM.csv")
-    [
-      "CC(=O)CC(C)C#N",
-      "CC(=O)CC(C)C",
-      "C(=O)CC(C)C#N",
-    ].each do |smi|
-      c = OpenTox::Compound.from_smiles smi
-      t = Time.now
-      neighbors = c.db_neighbors(:training_dataset_id => training_dataset.id, :min_sim => 0.2)
-      p Time.now - t
-      t = Time.now
-      neighbors2 = c.fingerprint_neighbors({:type => "MP2D", :training_dataset_id => training_dataset.id, :min_sim => 0.2})
-      p Time.now - t
-      p neighbors.size
-      p neighbors2.size
-      #p neighbors
-      #p neighbors2
-      #p neighbors2 - neighbors
-      #assert_equal neighbors, neighbors2
-    end
-  end
-
   def test_molecular_weight
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C"
     assert_equal 100.15888, c.molecular_weight
   end
 
-  def test_mg_conversions
-    # TODO fix!
-    skip
-    c = OpenTox::Compound.from_smiles "O"
-    mw = c.molecular_weight
-    assert_equal 18.01528, mw
-    assert_equal 0.8105107141417474, c.logmmol_to_mg(4.34688225631145, mw)
-    assert_equal 9007.64, c.mmol_to_mg(500, mw)
-    assert_equal 2437.9999984148976, c.logmg_to_mg(3.387033701)
-  end
-
   def test_physchem
     c = OpenTox::Compound.from_smiles "CC(=O)CC(C)C"
-    assert_equal PhysChem::OBDESCRIPTORS.size, c.physchem.size
-    assert_equal PhysChem::OBDESCRIPTORS.size, c.physchem(PhysChem.openbabel_descriptors).size
-    assert_equal PhysChem::unique_descriptors.size, c.physchem(PhysChem.unique_descriptors).size
+    properties = c.calculate_properties(PhysChem.openbabel_descriptors)
+    assert_equal PhysChem::OPENBABEL.size, properties.size
   end
 end

data/test/data/EPAFHM.medi_log10.csv

@@ -0,0 +1,92 @@
+STRUCTURE_SMILES,-log10(LC50_mmol)
+C1=CC(C=O)=CC(OC)=C1OCCCCCC,1.9469215565165803
+C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O,0.575118363368933
+C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2,2.114073660198569
+CC1=C(NC=O)C=CC=C1Cl,0.5606673061697374
+CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1,2.490797477668897
+C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C,1.2732727909734278
+CCCSCCSCCC,1.3746875490383261
+CCCSCCCCSCCC,1.8386319977650252
+CCCSCCCCSCCC,1.7328282715969863
+ClCCOC(=O)NC1CCCCC1,0.7695510786217261
+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,-0.31806333496276157
+OC1=C(C=C(C=C1)[N+](=O)[O-])[N+](=O)[O-],1.2276782932770802
+NC(=O)OCC,-1.7693773260761385
+[O-]C(C1=CC=CC=C1O)=O.[Na+],-1.0969100130080565
+C1=CC=CC=C1C(=O)N,-0.7371926427047373
+CC[N+](CC)(CC)CC1(=CC=CC=C1).[Cl-],0.1505805862031006
+CN(C)N,0.8827287043442358
+CC(C(C(NC([O-])=N1)=O)(C1=O)CC)CCC.[Na+],0.7011469235902933
+N1C(=O)C(CC)(CCC(C)C)C(=O)NC1=O,0.42365864979420714
+O=C1C2=C(N=CN2C)N(C(=O)N1C)C,0.10902040301031106
+C1=CC=C2C(=C1)C(=O)C(C)=CC2=O,3.1944991418415998
+OC1=C(Cl)C(Cl)=C(Cl)C=C1Cl,2.3526170298853804
+OC1=CC(C)=C(Cl)C=C1,1.4156687756324693
+O=S(O)(O)=O.C1(=CC=CC=C1CC(N)C).C2=CC=CC=C2CC(N)C,1.106793246940152
+O(CC)CC,-1.5378190950732742
+NC1=CC=CC=C1,-0.05307844348341968
+O=C(OC1=C2C(=CC=C1)C=CC=C2)NC,1.3615107430453628
+CCO,-2.503790683057181
+C1(=NC=CC=C1C2CCCN2C).OS(O)(=O)=O,1.275724130399211
+C1(O)=CC=CC=C1C(=O)N,0.13312218566250114
+CCCCCC=O,0.7569619513137056
+O=C1OC2=CC=CC=C2C(O)=C1CC3=C(O)C4=CC=CC=C4OC3=O,1.8181564120552274
+C1(C=O)=CC=C(OC2=CC=CC=C2)C=C1,1.6345120151091004
+CO,-2.962369335670021
+OC(C)C,-2.1583624920952498
+CC(=O)C,-2.089905111439398
+ClC(Cl)Cl,0.22767829327708025
+CS(=O)C,-2.6384892569546374
+ClC(C(Cl)(Cl)Cl)(Cl)Cl,2.221848749616356
+OC1=C(C=C(C(=C1CC2=C(C(=CC(=C2Cl)Cl)Cl)O)Cl)Cl)Cl,4.287350298372789
+C1=CC(=CC=C1N)C(=O)CC,0.009217308196862182
+OCCC,-1.8790958795000727
+CCCCO,-1.3673559210260189
+CCCCCO,-0.72916478969277
+C1=CC=CC=C1,0.6478174818886375
+CC(Cl)(Cl)Cl,0.4497716469449059
+[S-]C1=NC(C(C(C)CCC)(CC)C(N1)=O)=O.[Na+],1.0039263455147247
+CC#N,-1.6031443726201824
+CC=O,0.11520463605101904
+ClCCl,-0.5899496013257077
+IC(I)I,2.129596094720973
+[N+](C)(C)(C)C.[Cl-],-0.6253124509616739
+CC(C)(C)O,-1.9370161074648142
+C(F)(F)(F)CO,-0.07554696139253074
+CC(=O)C(C)(C)C,0.06098022355133353
+ClC(C(Cl)Cl)(Cl)Cl,1.4294570601181025
+CC1(C)NC(=O)NC1=O,-2.110589710299249
+CCC(O)(C)CC,-0.8182258936139555
+C#CC(O)(C)CC,-1.0934216851622351
+C1CCCC(C#C)(O)C1,-0.31386722036915343
+CCCCOCCOP(=O)(OCCOCCCC)OCCOCCCC,1.5512936800949202
+CCCCOCCOP(=O)(OCCOCCCC)OCCOCCCC,1.7423214251308154
+OCC(C)C,-1.2855573090077739
+CC(Cl)CCl,-0.04921802267018165
+NCC(N)C,-1.1335389083702174
+CC(O)CC,-1.6946051989335686
+CCC(=O)C,-1.6503075231319364
+OC(C)CN,-1.526339277389844
+ClC(CCl)Cl,0.21324857785443882
+ClC(=CCl)Cl,0.4736607226101559
+CC(=O)OC,-0.6830470382388496
+ClC(C(Cl)Cl)Cl,0.9172146296835499
+C1(C)(C)CCCC(C)=C1C=CC(C)=O,1.576754126063192
+ClC1=C(O)C(Cl)=CC(=C1)C(C2=CC(Cl)=C(O)C(=C2)Cl)(C)C,2.4400933749638876
+C(C1C=CC(=CC=1)O)(CC)(C)C,1.8013429130455774
+C1CC(CCC1(N)C)C(C)(N)C,0.41680122603137726
+ClC(Cl)C1=C(Cl)C=CC=C1Cl,2.374687549038326
+C1=CC=C2C=CC=C3C2=C1CC3,1.9507819773298183
+CC1=CNC2=C1C=CC=C2,1.1713401034646802
+C1=CC=CC=C1OC(=O)C2=CC=CC=C2C(=O)OC3=CC=CC=C3,3.600326278518962
+CCOC(=O)C1=CC=CC=C1C(=O)OCC,0.8446639625349383
+C1=CC=C(C(=O)OCCCC)C(=C1)C(=O)OCCCC,2.444905551421681
+O=C1C2=C(C=CC=C2)N=NN1CSP(=S)(OC)OC,3.694648630553376
+C1=CC=CC=C1NC(=O)C2=C(O)C=CC=C2,1.7328282715969863
+Cl\C(Cl)=C(Cl)/C(Cl)=C(Cl)\Cl,3.462180904926726
+OC1=C(C(=C(C(=C1Cl)Cl)Cl)Cl)Cl,3.040005161671584
+OC1=C(C=C(C=C1Cl)Cl)Cl,1.6055483191737838
+OC1=CC(C(F)(F)F)=C([N+]([O-])=O)C=C1,1.3555614105321614
+C1(N)=CC=CC=C1C(=O)N,-0.4623979978989561
+C1(N)=CC=CC=C1C(=O)N,-0.3979400086720376
+OC1=C([N+]([O-])=O)C=CC=C1,-0.06069784035361165

data/test/data/EPAFHM.mini_log10.csv

@@ -0,0 +1,16 @@
+STRUCTURE_SMILES,-log10(LC50_mmol)
+C1=CC(C=O)=CC(OC)=C1OCCCCCC,1.9469215565165803
+C1(OC)=C([N+]([O-])=O)C(C=O)=CC(Br)=C1O,0.575118363368933
+C1=CC(Cl)=CC=C1OC2=C([N+](=O)[O-])C=CC=C2,2.114073660198569
+CC1=C(NC=O)C=CC=C1Cl,0.5606673061697374
+CCCCOC(=O)C1=CC=CC(C(=O)OCCCC)=C1,2.490797477668897
+C(C1=CC=CC=C1)(C2=CC=CC=C2)(O)C#C,1.2732727909734278
+CCCSCCSCCC,1.3746875490383261
+CCCSCCCCSCCC,1.8386319977650252
+ClCCOC(=O)NC1CCCCC1,0.7695510786217261
+O=C1C(C2=CC=CC=C2)(C(=O)NC(=O)N1)CC,-0.31806333496276157
+OC1=C(C=C(C=C1)[N+](=O)[O-])[N+](=O)[O-],1.2276782932770802
+NC(=O)OCC,-1.7693773260761385
+[O-]C(C1=CC=CC=C1O)=O.[Na+],-1.0969100130080565
+C1=CC=CC=C1C(=O)N,-0.7371926427047373
+CC[N+](CC)(CC)CC1(=CC=CC=C1).[Cl-],0.1505805862031006