gemspec added, backup files removed

3 files changed, 14 insertions, 114 deletions

diff --git a/kazius-alerts.gemspec b/kazius-alerts.gemspec
new file mode 100644
index 0000000..ec938f3
--- /dev/null
+++ b/kazius-alerts.gemspec
@@ -0,0 +1,14 @@
+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
diff --git a/lib/kazius-alerts.rb~ b/lib/kazius-alerts.rb~
deleted file mode 100644
index ccc888c..0000000
--- a/lib/kazius-alerts.rb~
+++ /dev/null
@@ -1,99 +0,0 @@
-require '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 = OBConversion.new
-    smi2mol.set_in_format("smi")
-    mol = OBMol.new
-    smi2mol.read_string(mol, smiles)
-
-    matches = []
-    prediction = false
-    error_product = 1
-
-    SMARTS.each do |sma|
-      if sma[2]
-        matches << sma if mol.matches_smarts?(sma[1]) && !mol.matches_smarts?(sma[2])
-      else
-        matches << sma if mol.matches_smarts?(sma[1])
-      end
-    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
diff --git a/test/kazius-alerts.rb~ b/test/kazius-alerts.rb~
deleted file mode 100644
index e0e0acf..0000000
--- a/test/kazius-alerts.rb~
+++ /dev/null
@@ -1,15 +0,0 @@
-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
-    assert_equal 29, KaziusAlerts::SMARTS.size
-  end
-
-end