kazius-alerts 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: fd5c89372096f5368e0a985fd5aa755be37784ea
+  data.tar.gz: 2d4e65adeff7ed18b4bad037cd67f83c3d1884b9
+SHA512:
+  metadata.gz: 627e56312fa5e7bf364c18e447efc2ec96327d9ff67625bb62e64fcd7d8a7e0bab1f2bb38924fb2b99a34c9d73c5e5ae1c2518ec2aa5047a73c1c40f9dfe2359
+  data.tar.gz: 4bcb57fdb14ec488fd19488cb28c1fbbb3aac68e9e35b32bb17fd42bf516819af824896f78cb69e0b50b9435c048356edaffeef2315bc4754401379de6801ada

data/kazius-alerts.gemspec

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+Gem::Specification.new do |s|
+  s.name        = "kazius-alerts"
+  s.version     = "0.0.1"
+  s.authors     = ["Christoph Helma"]
+  s.email       = ["helma@in-silico.ch"]
+  s.homepage    = "http://github.com/opentox/kazius-alerts"
+  s.summary     = %q{Kazius structural alerts}
+  s.license     = 'GPL-3.0'
+
+  s.rubyforge_project = "kazius-alerts"
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.require_paths = ["lib"]
+end

data/lib/kazius-alerts.rb

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+re 'openbabel'
+
+class KaziusAlerts
+
+  SMARTS = [ # name, smarts, excluded smarts
+    ["specific arom nitro", 'O=N(~O)a', 'O=N(O)c[$(aS(=O)=O),$(aaS(=O)=O),$(aaaS(=O)=O),$(aC((F)F)F),$(aaC((F)F)F),$(aaaC((F)F)F)]'],
+    ["specific arom amine", 'a[NH2]', '[NH2]a[$(a[$(C((F)F)F),$(S(=O)=O),$(C(=O)O)]),$(aa[$(C((F)F)F),$(S(=O)=O),$(C(=O)O)]),$(aaa[$(C((F)F)F),$(S(=O)=O),$(C(=O)O)])]'],
+    ["aromatic nitroso", 'a[N;X2]=O'],
+    ["alkyl nitrite", 'CO[N;X2]=O'],
+    ["nitrosamine", 'N[N;X2]=O'],
+    ["epoxide", 'O1[c,C]-[c,C]1'],
+    ["aziridine", 'C1NC1'],
+    ["azide", 'N=[N+]=[N-]'],
+    ["diazo", 'C=[N+]=[N-]'],
+    ["triazene", 'N=N-N'],
+    ["aromatic azo", 'c[N;X2]!@;=[N,X2]c', '[$([N;X2]([$(acS((=O)=O)),$(aacS((=O)=O)),$(aaacS((=O)=O)),$(aaaacS((=O)=O))])=[N;X2][$(acS((=O)=O)),$(aacS((=O)=O)),$(aaacS((=O)=O)),$(aaaacS((=O)=O))])]'],
+    ["unsubstituted heteroatom-bonded heteroatom", '[OH,NH2][N,O]', 'O=N(O)[O-]'],
+    ["aromatic", '[OH]Na'],
+    ["aliphatic halide", '[Cl,Br,I]C'],
+    ["carboxylic acid halide", '[Cl,Br,I]C=O'],
+    ["nitrogen or sulphur mustard", '[N,S]!@[C;X4]!@[CH2][Cl,Br,I]'],
+    ["bay region in PAHs", '[cH]1[cH]ccc2c1c3c(cc2)cc[cH][cH]3'],
+    ["k-region in PAHs", '[cH]1cccc2c1[cH][cH]c3c2ccc[cH]3'],
+    ["polycyclic aromatic system", '[$(a13~a~a~a~a2~a1~a(~a~a~a3)~a~a~a2),$(a1~a~a~a2~a1~a~a3~a(~a2)~a~a~a3),$(a1~a~a~a2~a1~a~a~a3~a2~a~a~a3),$(a1~a~a~a~a2~a1~a3~a(~a2)~a~a~a~a3),$(a1~a~a~a~a2~a1~a~a3~a(~a2)~a~a~a3),$(a1~a~a~a~a2~a1~a~a3~a(~a2)~a~a~a~a3),$(a1~a~a~a~a2~a1~a~a~a3~a2~a~a~a3),$(a1~a~a~a~a2~a1~a~a~a3~a2~a~a~a~a3),$(a13~a~a~a~a2~a1~a(~a~a~a3)~a~a2)]'], # smarts error of original smarts fixed
+    ["sulphonate bonded carbon", '[$([C,c]OS((=O)=O)O!@[c,C]),$([c,C]S((=O)=O)O!@[c,C])]'],
+    ["aliphatic N-nitro", 'O=N(~O)N'],
+    ["alpha,beta unsaturated aldehyde", '[$(O=[CH]C=C),$(O=[CH]C=O)]', '[$(O=[CH]C([N,O,S])=C),$(O=[CH]C=C[N,O,S]),$(O=[CH]C=Ca)]'],
+    ["diazonium", '[N;v4]#N'],
+    ["beta-propriolactone", 'O=C1CCO1'],
+    ["alpha,beta unsaturated alkoxy group", '[CH]=[CH]O'],
+    ["1-aryl-2-monoalkyl hydrazine", '[NH;!R][NH;!R]a'],
+    ["aromatic methylamine", '[CH3][NH]a', '[CH3][NH]a[$(a[$(C((F)F)F),$(S=O),$(C(=O)O)]),$(aa[$(C((F)F)F),$(S=O),$(C(=O)O)]),$(aaa[$(C((F)F)F),$(S=O),$(C(=O)O)])]'],
+    ["ester derivative of aromatic hydroxylamine", 'aN([$([OH]),$(O*=O)])[$([#1]),$(C(=O)[CH3]),$([CH3]),$([OH]),$(O*=O)]'],
+    ["polycyclic planar system", '[$([X2,X3]13~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3
+](~[X2,X3]~[X2,X3]~[X2,X3]3)~[X2,X3]~[X2,X3]~[X2,X3]2),$([X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,
+X3]1~[X2,X3]~[X2,X3]3~[X2,X3](~[X2,X3]2)~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]~[X2,X3]~[
+X2,X3]2~[X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]3~[X2,X3]2~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]
+~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3]3~[X2,X3](~[X2,X3]2)~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3]~[X2,X3]3~[X2,X3](~[X2,X3]2)~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3]~[X2,X3]3~[X2,X3](~[X2,X3]2)~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]3~[X2,X3]2~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3]~[X2,X3]~[X2,X3]3~[X2,X3]2~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]3),$([X2,X3]13~[X2,X3]~[X2,X3]~[X2,X3]~[X2,X3]2~[X2,X3]1~[X2,X3](~[X2,X3]~[X2,X3]~[X2,X3]3)~[X2,X3]~[X2,X3]2)]', '[S]1-*~*-[N,O,S]-*~*-1'] # smarts error of original smarts fixed
+  ]
+
+  CONFIDENCES = {
+    "specific arom nitro" => 0.81,
+    "specific arom amine" => 0.79,
+    "nitrosamine" => 0.90,
+    "epoxide" => 0.85,
+    "aliphatic halide" => 0.79,
+    "polycyclic aromatic system" => 0.90,
+    "other SAs" => 0.81
+  }
+
+  def self.predict smiles
+    smi2mol = OpenBabel::OBConversion.new
+    smi2mol.set_in_format("smi")
+    mol = OpenBabel::OBMol.new
+    smi2mol.read_string(mol, smiles)
+
+    matches = []
+    prediction = false
+    error_product = 1
+
+    smarts_pattern = OpenBabel::OBSmartsPattern.new
+    SMARTS.each do |sma|
+      if sma[2]
+        smarts_pattern.init sma[1]
+        if smarts_pattern.match(mol)
+          smarts_pattern.init sma[2]
+          matches << sma if !smarts_pattern.match(mol)
+        end
+      else
+        smarts_pattern.init sma[1]
+        matches << sma if smarts_pattern.match(mol)
+      end
+
+    matches.each { |m| error_product *= error(m) }
+
+    prediction = true if matches.size > 0
+    {:prediction => prediction, :error_product => error_product, :matches => matches}
+  end
+
+  def self.error(alert)
+    if CONFIDENCES[alert[0]]
+      return 1 - CONFIDENCES[alert[0]]
+    else
+      return 1 - CONFIDENCES["other SAs"]
+    end
+  end
+
+end
+
+class ConsensusMutagenicity
+
+  def self.predict smiles
+    sa_prediction = KaziusAlerts.predict smiles
+    lazar_prediction = Lazar.predict smiles
+    confidence = 0
+    if sa_prediction[:prediction] == false && lazar_mutagenicity.prediction == 0
+      confidence = 0.85
+    elsif sa_prediction[:prediction] == true && lazar_mutagenicity.prediction == 1
+      confidence = 0.85 * ( 1 - sa_prediction[:error_product] )
+    elsif sa_prediction[:prediction] == false && lazar_mutagenicity.prediction == 1
+      confidence = 0.11
+    elsif sa_prediction[:prediction] == true && lazar_mutagenicity.prediction == 0
+      confidence = ( 1 - sa_prediction[:error_product] ) - 0.57
+    end
+    {:prediction => prediction, :confidence => confidence}
+  end
+
+end
+

data/test/kazius-alerts.rb

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+require 'minitest/autorun'
+#require 'kazius-alerts'
+require_relative '../lib/kazius-alerts.rb'
+
+class KaziusAlertsTest < MiniTest::Test
+
+  def test_alerts_size
+    assert_equal 29, KaziusAlerts::SMARTS.size
+  end
+
+  def test_kazius_alerts_prediction
+    prediction = KaziusAlerts.predict("c1ccccc1NN")
+    assert prediction[:prediction]
+    assert_equal [["unsubstituted heteroatom-bonded heteroatom", "[OH,NH2][N,O]", "O=N(O)[O-]"]], prediction[:matches]
+  end
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: kazius-alerts
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Christoph Helma
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2017-09-12 00:00:00.000000000 Z
+dependencies: []
+description: 
+email:
+- helma@in-silico.ch
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- kazius-alerts.gemspec
+- lib/kazius-alerts.rb
+- test/kazius-alerts.rb
+homepage: http://github.com/opentox/kazius-alerts
+licenses:
+- GPL-3.0
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: kazius-alerts
+rubygems_version: 2.6.11
+signing_key: 
+specification_version: 4
+summary: Kazius structural alerts
+test_files:
+- test/kazius-alerts.rb