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Diffstat (limited to 'lib/kazius-alerts.rb~')
| -rw-r--r-- | lib/kazius-alerts.rb~ | 99 |
1 files changed, 0 insertions, 99 deletions
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 |