diff --git a/Classifier/__init__.py b/Classifier/__init__.py new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/Classifier/__init__.py @@ -0,0 +1 @@ + diff --git a/Classifier/dict/index_v1.json b/Classifier/dict/index_v1.json index ed24a5c..4622696 100644 --- a/Classifier/dict/index_v1.json +++ b/Classifier/dict/index_v1.json @@ -1 +1,6720 @@ -{"Pathway": {"Alkaloids": 0, "Amino acids and Peptides": 1, "Carbohydrates": 2, "Fatty acids": 3, "Polyketides": 4, "Shikimates and Phenylpropanoids": 5, "Terpenoids": 6}, "Superclass": {"Alkylresorsinols": 0, "Amino acid glycosides": 1, "Aminosugars and aminoglycosides": 2, "Anthranilic acid alkaloids": 3, "Apocarotenoids": 4, "Aromatic polyketides": 5, "Carotenoids (C40)": 6, "Carotenoids (C45)": 7, "Carotenoids (C50)": 8, "Chromanes": 9, "Coumarins": 10, "Cyclic polyketides": 11, "Diarylheptanoids": 12, "Diazotetronic acids and derivatives": 13, "Diphenyl ethers (DPEs)": 14, "Diterpenoids": 15, "Docosanoids": 16, "Eicosanoids": 17, "Fatty Acids and Conjugates": 18, "Fatty acyl glycosides": 19, "Fatty acyls": 20, "Fatty amides": 21, "Fatty esters": 22, "Flavonoids": 23, "Fluorenes": 24, "Glycerolipids": 25, "Glycerophospholipids": 26, "Guanidine alkaloids": 27, "Histidine alkaloids": 28, "Isoflavonoids": 29, "Lignans": 30, "Linear polyketides": 31, "Lysine alkaloids": 32, "Macrolides": 33, "Meroterpenoids": 34, "Miscellaneous alkaloids": 35, "Miscellaneous polyketides": 36, "Mitomycin derivatives": 37, "Monoterpenoids": 38, "Mycosporine derivatives": 39, "Naphthalenes": 40, "Nicotinic acid alkaloids": 41, "Nucleosides": 42, "Octadecanoids": 43, "Oligopeptides": 44, "Ornithine alkaloids": 45, "Peptide alkaloids": 46, "Phenanthrenoids": 47, "Phenolic acids (C6-C1)": 48, "Phenylethanoids (C6-C2)": 49, "Phenylpropanoids (C6-C3)": 50, "Phloroglucinols": 51, "Polycyclic aromatic polyketides": 52, "Polyethers": 53, "Polyols": 54, "Polyprenols": 55, "Proline alkaloids": 56, "Pseudoalkaloids": 57, "Pseudoalkaloids (transamidation)": 58, "Saccharides": 59, "Serine alkaloids": 60, "Sesquiterpenoids": 61, "Sesterterpenoids": 62, "Small peptides": 63, "Spingolipids": 64, "Steroids": 65, "Stilbenoids": 66, "Styrylpyrones": 67, "Terphenyls": 68, "Tetramate alkaloids": 69, "Triterpenoids": 70, "Tropolones": 71, "Tryptophan alkaloids": 72, "Tyrosine alkaloids": 73, "Xanthones": 74, "\u03b2-lactams": 75, "\u03b3-lactam-\u03b2-lactones": 76}, "Class": {"12-oxophytodienoic acid metabolites": 0, "2-arylbenzofurans": 1, "2-pyrone derivatives": 2, "3-Decalinoyltetramic acids": 3, "3-Spirotetramic acids": 4, "3-acyl tetramic acids": 5, "3-oligoenoyltetramic acids": 6, "4-pyrone derivatives": 7, "Abeoabietane diterpenoids": 8, "Abeolupane triterpenoids": 9, "Abeotaxane diterpenoids": 10, "Abietane diterpenoids": 11, "Acetate-derived alkaloids": 12, "Acetogenins": 13, "Acidic glycosphingolipids": 14, "Acorane sesquiterpenoids": 15, "Acridone alkaloids": 16, "Actinomycins": 17, "Acutumine alkaloids": 18, "Acyclic guanidine alkaloids": 19, "Acyclic monoterpenoids": 20, "Acyclic triterpenoids": 21, "Acyl phloroglucinols": 22, "Adianane triterpenoids": 23, "Aeruginosins": 24, "Aflatoxins": 25, "Africanane sesquiterpenoids": 26, "Agarofuran sesquiterpenoids": 27, "Ahp-containing cyclodepsipeptides": 28, "Alliacane sesquiterpenoids": 29, "Allohimachalane sesquiterpenoids": 30, "Amarylidaceae alkaloids": 31, "Amino cyclitols": 32, "Amino fatty acids": 33, "Aminoacids": 34, "Aminoglycosides": 35, "Aminosugars": 36, "Amphilectane diterpenoids": 37, "Anabaenopeptins": 38, "Androstane steroids": 39, "Angucyclines": 40, "Ansa macrolides": 41, "Ansa peptide alkaloids": 42, "Anthocyanidins": 43, "Anthracyclines": 44, "Anthranillic acid derivatives": 45, "Anthraquinones and anthrones": 46, "Antimycins": 47, "Aphidicolane diterpenoids": 48, "Aplysiatoxins": 49, "Apocarotenoids (C30, \u03a8-\u03a8)": 50, "Apocarotenoids (\u03a8-)": 51, "Apocarotenoids (\u03b2-)": 52, "Apocarotenoids(\u03b5-)": 53, "Aporphine alkaloids": 54, "Apotirucallane triterpenoids": 55, "Aristolane sesquiterpenoids": 56, "Aromadendrane sesquiterpenoids": 57, "Aromatic polyketides with side chains": 58, "Arteminisin": 59, "Arylnaphthalene and aryltetralin lignans": 60, "Asbestinane diterpenoids": 61, "Ascarosides": 62, "Ascomycins and Rapamycins": 63, "Asperane sesterterpenoids": 64, "Aspidosperma type": 65, "Aspidosperma-Iboga hybrid type (Vinca alkaloids)": 66, "Asteriscane sesquiterpenoids": 67, "Atisane diterpenoids": 68, "Aurones": 69, "Avermectins": 70, "Azaphilones": 71, "Azo and Azoxy alkaloids": 72, "Baccharane triterpenoids": 73, "Bactoprenols": 74, "Bafilomycins": 75, "Bagremycins": 76, "Bauerane triterpenoids": 77, "Benastatins and derivatives": 78, "Benzodiazepine alkaloids": 79, "Benzophenones": 80, "Benzoquinones": 81, "Bergamotane sesquiterpenoids": 82, "Betaestacin-type sesterterpenoids": 83, "Betalain alkaloids": 84, "Beyerane diterpenoids": 85, "Biaryl type diarylheptanoids": 86, "Bicyclic guanidine alkaloids": 87, "Bicyclogermacrane sesquiterpenoids": 88, "Bicyclohumulane sesquiterpenoids": 89, "Bisabolane sesquiterpenoids": 90, "Bisnaphthalenes": 91, "Bleomycins": 92, "Boromycins": 93, "Botryane sesquiterpenoids": 94, "Bourbonane sesquiterpenoids": 95, "Branched fatty acids": 96, "Brasilane sesquiterpenoids": 97, "Breviane diterpenoids": 98, "Briarane diterpenoids": 99, "Bryostatins": 100, "Bufadienolides": 101, "CDP-Glycerols": 102, "Cadinane sesquiterpenoids": 103, "Camphane monoterpenoids": 104, "Campherenane sesquiterpenoids": 105, "Cannabinoids": 106, "Capnellane sesquiterpenoids": 107, "Capsaicins and Capsaicinoids": 108, "Carabrane sesquiterpenoids": 109, "Carane monoterpenoids": 110, "Carbapenems": 111, "Carbazole alkaloids": 112, "Carbocyclic fatty acids": 113, "Carboline alkaloids": 114, "Cardenolides": 115, "Carotenoids (C40, \u03a7-\u03a7)": 116, "Carotenoids (C40, \u03a7-\u03a8)": 117, "Carotenoids (C40, \u03a8-\u03a8)": 118, "Carotenoids (C40, \u03b2-\u03a7)": 119, "Carotenoids (C40, \u03b2-\u03a8)": 120, "Carotenoids (C40, \u03b2-\u03b2)": 121, "Carotenoids (C40, \u03b2-\u03b3)": 122, "Carotenoids (C40, \u03b2-\u03b5)": 123, "Carotenoids (C40, \u03b2-\u03ba)": 124, "Carotenoids (C40, \u03b2-\u03c0)": 125, "Carotenoids (C40, \u03b3-\u03a8)": 126, "Carotenoids (C40, \u03b3-\u03b5)": 127, "Carotenoids (C40, \u03b5-\u03a8)": 128, "Carotenoids (C40, \u03b5-\u03b5)": 129, "Carotenoids (C40, \u03ba-\u03a7)": 130, "Carotenoids (C40, \u03ba-\u03ba)": 131, "Carotenoids (C40, \u03c0-\u03a7)": 132, "Carotenoids (C40, \u03c0-\u03a8)": 133, "Carotenoids (C40, \u03c0-\u03c0)": 134, "Carotenoids (C45, \u03a8-\u03a8)": 135, "Carotenoids (C45, \u03b2-\u03a8)": 136, "Carotenoids (C45, \u03b5-\u03a8)": 137, "Carotenoids (C50, \u03a8-\u03a8)": 138, "Carotenoids (C50, \u03b2-\u03a8)": 139, "Carotenoids (C50, \u03b2-\u03b2)": 140, "Carotenoids (C50, \u03b3-\u03b3)": 141, "Carotenoids (C50, \u03b5-\u03b5)": 142, "Caryolane sesquiterpenoids": 143, "Caryophyllane sesquiterpenoids": 144, "Casbane diterpenoids": 145, "Cassane diterpenoids": 146, "Catechols with side chains": 147, "Cedrane and Isocedrane sesquiterpenoids": 148, "Cembrane diterpenoids": 149, "Cephalosporins": 150, "Cephalotaxus alkaloids": 151, "Cephamycins": 152, "Ceramides": 153, "Cericerane sesterterpenoids": 154, "Chalcones": 155, "Chamigrane sesquiterpenoids": 156, "Cheilanthane sesterterpenoids": 157, "Chiloscyphane sesquiterpenoids": 158, "Cholane steroids": 159, "Cholestane steroids": 160, "Chromones": 161, "Cinnamic acid amides": 162, "Cinnamic acids and derivatives": 163, "Cinnamoyl phenols": 164, "Clavams": 165, "Clavulones": 166, "Cleistanthane diterpenoids": 167, "Clovane sesquiterpenoids": 168, "Colensane and Clerodane diterpenoids": 169, "Coloratane sesquiterpenoids": 170, "Copaane sesquiterpenoids": 171, "Copacamphane sesquiterpenoids": 172, "Corynanthe type": 173, "Coumarinolignans": 174, "Coumaronochromones": 175, "Coumestan": 176, "Cryptophycins": 177, "Cubebane sesquiterpenoids": 178, "Cucurbitane triterpenoids": 179, "Cuparane sesquiterpenoids": 180, "Cyano esters": 181, "Cyanogenic glycosides": 182, "Cyathane diterpenoids": 183, "Cyclic peptides": 184, "Cyclitols": 185, "Cycloabietane diterpenoids": 186, "Cycloamphilectane diterpenoids": 187, "Cycloapotirucallane triterpenoids": 188, "Cycloartane triterpenoids": 189, "Cyclobisabolane sesquiterpenoids": 190, "Cycloeudesmane sesquiterpenoids": 191, "Cyclofarnesane sesquiterpenoids": 192, "Cyclogermacrane sesquiterpenoids": 193, "Cyclolaurane sesquiterpenoids": 194, "Cyclonerane sesquiterpenoids": 195, "Cyclophytane diterpenoids": 196, "Cyclopiane diterpenoids": 197, "Cyclopiazonic acid-tpye tetramate alkaloids": 198, "Cytochalasan alkaloids": 199, "Cytosporins": 200, "DKXanthenes and derivatives": 201, "Dactylomelane diterpenoids": 202, "Dammarane and Protostane triterpenoids": 203, "Daphnane diterpenoids": 204, "Daucane sesquiterpenoids": 205, "Decalins with 2-pyrones": 206, "Decalins with side chains": 207, "Decipiane diterpenoids": 208, "Depsides": 209, "Depsidones": 210, "Depsipeptides": 211, "Devadarane diterpenoids": 212, "Diacylglycerols": 213, "Dialkylresorcinols": 214, "Diarylether type diarylheptanoids": 215, "Dibenzocyclooctadienes lignans": 216, "Dibenzylbutane lignans": 217, "Dibenzylbutyrolactone lignans": 218, "Dicarboxylic acids": 219, "Dihydroflavonols": 220, "Dimeric phloroglucinols": 221, "Dipeptides": 222, "Disaccharides": 223, "Docosa-1,2-dioxolanes": 224, "Dolabellane diterpenoids": 225, "Dolastane diterpenoids": 226, "Dolichols": 227, "Drimane sesquiterpenoids": 228, "Duclauxin and derivatives": 229, "Dunniane sesquiterpenoids": 230, "Ecdysteroids": 231, "Eicosa-1,2-dioxolanes": 232, "Elemane sesquiterpenoids": 233, "Elfamycins": 234, "Enediynes": 235, "Epothilones": 236, "Epoxy fatty acids": 237, "Epoxyeicosatrienoic acids": 238, "Eremane diterpenoids": 239, "Eremophilane sesquiterpenoids": 240, "Ergostane steroids": 241, "Ergot alkaloids": 242, "Ericamycins": 243, "Erythromycins": 244, "Erythroxylane diterpenoids": 245, "Estrane steroids": 246, "Eudesmane sesquiterpenoids": 247, "Eunicellane diterpenoids": 248, "Farnesane sesquiterpenoids": 249, "Fasamycins and derivatives": 250, "Fatty acid estolides": 251, "Fatty acyl CoAs": 252, "Fatty acyl carnitines": 253, "Fatty acyl glycosides of mono- and disaccharides": 254, "Fatty acyl homoserine lactones": 255, "Fatty alcohols": 256, "Fatty aldehydes": 257, "Fatty ethers": 258, "Fatty nitriles": 259, "Fenchane monoterpenoids": 260, "Fernane and Arborinane triterpenoids": 261, "Filicane triterpenoids": 262, "Flavan-3-ols": 263, "Flavandiols (Leucoanthocyanidins)": 264, "Flavanones": 265, "Flavans": 266, "Flavones": 267, "Flavonolignans": 268, "Flavonols": 269, "Flavonostilbenes": 270, "Friedelane triterpenoids": 271, "Fukinane sesquiterpenoids": 272, "Fungal DPEs": 273, "Fungal cyclic polyketides (Miscellaneous)": 274, "Furanoabietane diterpenoids": 275, "Furanoid lignans": 276, "Furans": 277, "Furocoumarins": 278, "Furofuranoid lignans": 279, "Furostane steroids": 280, "Fusicoccane diterpenoids": 281, "Fusidane triterpenoids": 282, "Gallotannins": 283, "Gammacerane triterpenoids": 284, "Germacrane sesquiterpenoids": 285, "Gersemiane diterpenoids": 286, "Gibberellins": 287, "Glucosinolates": 288, "Glutinane triterpenoids": 289, "Glycerophosphates": 290, "Glycerophosphocholines": 291, "Glycerophosphoethanolamines": 292, "Glycerophosphoglycerols": 293, "Glycerophosphoglycerophosphates": 294, "Glycerophosphoglycerophosphoglycerols": 295, "Glycerophosphoinositol phosphates": 296, "Glycerophosphoinositolglycans": 297, "Glycerophosphoinositols": 298, "Glycerophosphoserines": 299, "Glycosyldiacylglycerols": 300, "Glycosylglycerophospholipids": 301, "Glycosylmonoacylglycerols": 302, "Gorgonane sesquiterpenoids": 303, "Grayanotoxane diterpenoids": 304, "Griseofulvins": 305, "Guaiane sesquiterpenoids": 306, "Guanacastane diterpenoids": 307, "Gymnomitrane sesquiterpenoids": 308, "Halimane diterpenoids": 309, "Halogenated hydrocarbons": 310, "Hamigerane sesquiterpenoids": 311, "Hapalindole alkaloids": 312, "Hasubanan alkaloids": 313, "Hepoxilins": 314, "Herbertane sesquiterpenoids": 315, "Heterocyclic fatty acids": 316, "Himachalane sesquiterpenoids": 317, "Hirsutane sesquiterpenoids": 318, "Homoerythrina alkaloids": 319, "Homofarnesane sesquiterpenoids": 320, "Hopane and Moretane triterpenoids": 321, "Humbertiane sesquiterpenoids": 322, "Humulane sesquiterpenoids": 323, "Hydrocarbons": 324, "Hydroperoxy fatty acids": 325, "Hydroxy fatty acids": 326, "Hydroxy-hydroperoxyeicosapentaenoic acids": 327, "Hydroxy-hydroperoxyeicosatetraenoic acids": 328, "Hydroxy-hydroperoxyeicosatrienoic acids": 329, "Iboga type": 330, "Icetexane diterpenoids": 331, "Illudalane sesquiterpenoids": 332, "Illudane sesquiterpenoids": 333, "Imidazole alkaloids": 334, "Indole diketopiperazine alkaloids (L-Trp, L-Ala)": 335, "Indole diketopiperazine alkaloids (L-Trp, L-Pro)": 336, "Indole diketopiperazine alkaloids (L-Trp, L-Trp)": 337, "Indole-Diterpenoid alkaloids (Penitrems)": 338, "Indolizidine alkaloids": 339, "Ingenane diterpenoids": 340, "Iphionane sesquiterpenoids": 341, "Iridoids monoterpenoids": 342, "Irregular monoterpenoids": 343, "Isariotin alkaloids": 344, "Ishwarane sesquiterpenoids": 345, "Isoaurones": 346, "Isocomane sesquiterpenoids": 347, "Isocoumarins": 348, "Isodaucane sesquiterpenoids": 349, "Isoflavanones": 350, "Isoflavones": 351, "Isofurans": 352, "Isoindole alkaloids": 353, "Isolactarane sesquiterpenoids": 354, "Isoprostanes": 355, "Isoquinoline alkaloids": 356, "Ivaxillarane sesquiterpenoids": 357, "Jasmonic acids": 358, "Jatrophane diterpenoids": 359, "Jatropholane diterpenoids": 360, "Kaurane and Phyllocladane diterpenoids": 361, "Kavalactones and derivatives": 362, "Kempane diterpenoids": 363, "Labdane diterpenoids": 364, "Lactam bearing macrolide lactones": 365, "Lactarane sesquiterpenoids": 366, "Lactones": 367, "Ladder polyethers": 368, "Lanostane, Tirucallane and Euphane triterpenoids": 369, "Lathyrane diterpenoids": 370, "Laurane sesquiterpenoids": 371, "Leukotrienes": 372, "Levuglandins": 373, "Limonoids": 374, "Linear diarylheptanoids": 375, "Linear peptides": 376, "Linear polyenes": 377, "Linear sesterterpenoids": 378, "Linear tetronates": 379, "Lipopeptides": 380, "Lipoxins": 381, "Lippifoliane sesquiterpenoids": 382, "Lobane diterpenoids": 383, "Long-Chain Bicyclic Phosphotriester": 384, "Longibornane sesquiterpenoids": 385, "Longifolane sesquiterpenoids": 386, "Longipinane sesquiterpenoids": 387, "Luminacins and derivatives": 388, "Lupane triterpenoids": 389, "Macrocyclic tetramic acids": 390, "Macrolide lactams": 391, "Macrolide lactones": 392, "Macrotetrolides": 393, "Malabaricane triterpenoids": 394, "Mangicol-type sesterterpenoids": 395, "Marasmane sesquiterpenoids": 396, "Maresins": 397, "Marine-bacterial DPEs": 398, "Megastigmanes": 399, "Melithiazole and Myxothiazole derivatives": 400, "Menthane monoterpenoids": 401, "Merohemiterpenoids": 402, "Meromonoterpenoids": 403, "Merosesquiterpenoids": 404, "Meroterpenoids with 5- or 6-membered ring": 405, "Meroterpenoids with bridged ring": 406, "Methoxy fatty acids": 407, "Methyl xanthones": 408, "Microcolins and mirabimids": 409, "Microcystins": 410, "Microginins": 411, "Minor lignans": 412, "Miscellaneous alkaloids": 413, "Miscellaneous apocarotenoids": 414, "Miscellaneous meroterpenoids": 415, "Miscellaneous polyketides": 416, "Mitomycins": 417, "Monacolins and Monacolin derivatives": 418, "Monoacylglycerols": 419, "Monoalkylresorcinols": 420, "Monocarbocyclic sesterterpenoids": 421, "Monocyclic guanidine alkaloids": 422, "Monocyclic monoterpenoids": 423, "Monocyclic \u03b2-lactams": 424, "Monomeric stilbenes": 425, "Monosaccharides": 426, "Morphinan alkaloids": 427, "Mulinane diterpenoids": 428, "Multiflorane triterpenoids": 429, "Mycolic acids": 430, "Mycosporine and Mycosporine-like amino acids": 431, "Myrsinane diterpenoids": 432, "N-acyl amines": 433, "N-acyl ethanolamines (endocannabinoids)": 434, "Nagilactone diterpenoids": 435, "Naphthalenes and derivatives": 436, "Naphthalenones": 437, "Naphthoquinones": 438, "Nardosinane sesquiterpenoids": 439, "Neoflavonoids": 440, "Neohopane triterpenoids": 441, "Neolignans": 442, "Neurofurans": 443, "Neuroprostanes": 444, "Neutral glycosphingolipids": 445, "Nitro fatty acids": 446, "Nonadrides": 447, "Norcembrane diterpenoids": 448, "Noreremophilane sesquiterpenoids": 449, "Noreudesmane sesquiterpenoids": 450, "Norkaurane diterpenoids": 451, "Norlabdane diterpenoids": 452, "Norpimarane and Norisopimarane diterpenoids": 453, "Norsesterterpenoids": 454, "Oblogolides": 455, "Obtusane diterpenoids": 456, "Oleanane triterpenoids": 457, "Oligomeric phloroglucinols (phlorotannins)": 458, "Oligomeric stibenes": 459, "Oligomycins": 460, "Onocerane triterpenoids": 461, "Open-chain polyketides": 462, "Open-chained neoflavonoids": 463, "Ophiobolane sesterterpenoids": 464, "Oplopane sesquiterpenoids": 465, "Oppositane sesquiterpenoids": 466, "Orthosomycins": 467, "Other Docosanoids": 468, "Other Eicosanoids": 469, "Other Octadecanoids": 470, "Other indole diketopiperazine alkaloids": 471, "Other polyketide meroterpenoids": 472, "Oxa-Bridged Macrolides": 473, "Oxasqualenoids": 474, "Oxazole alkaloids": 475, "Oxidized glycerophospholipids": 476, "Oxo fatty acids": 477, "Oxygenated hydrocarbons": 478, "Pachydictyane diterpenoids": 479, "Pachysanane triterpenoids": 480, "Pacifigorgiane sesquiterpenoids": 481, "Panasinsane sesquiterpenoids": 482, "Paraconic acids and derivatives": 483, "Paraliane diterpenoids": 484, "Parguerane diterpenoids": 485, "Patchoulane sesquiterpenoids": 486, "Paulomycins and derivatives": 487, "Penicillins": 488, "Pentacyclic guanidine alkaloids": 489, "Pentalenane sesquiterpenoids": 490, "Pepluane diterpenoids": 491, "Peptaibols": 492, "Perforane sesquiterpenoids": 493, "Phenalens": 494, "Phenanthrenes": 495, "Phenazine alkaloids": 496, "Phenethylisoquinoline alkaloids": 497, "Phenoxazine alkaloids": 498, "Phenylalanine-derived alkaloids": 499, "Phenylethanoids": 500, "Phenylethylamines": 501, "Phloroglucinol-terpene hybrids": 502, "Phoslactomycins or Phosphazomycins": 503, "Phosphosphingolipids": 504, "Phthalide derivatives": 505, "Phytane diterpenoids": 506, "Phytofurans": 507, "Phytoprostanes": 508, "Picrotoxane sesquiterpenoids": 509, "Pimarane and Isopimarane diterpenoids": 510, "Pimprinine alkaloids": 511, "Pinane monoterpenoids": 512, "Pinguisane sesquiterpenoids": 513, "Piperidine alkaloids": 514, "Plant xanthones": 515, "Platensimycin and Platencins": 516, "Podocarpane diterpenoids": 517, "Polyamines": 518, "Polyene macrolides": 519, "Polyesters": 520, "Polyether ionophores": 521, "Polypodane triterpenoids": 522, "Polyprenol derivatives": 523, "Polyprenylated cyclic polyketides (Hop meroterpenoids)": 524, "Polysaccharides": 525, "Pradimicins": 526, "Pregnane steroids": 527, "Premyrsinane diterpenoids": 528, "Prenyl quinone meroterpenoids": 529, "Prenylated,geranylated phloroglucinols": 530, "Prenylbisabolane diterpenoids": 531, "Prenyleudesmane diterpenoids": 532, "Presilphiperfolane and Probotryane sesquiterpenoids": 533, "Prezizaane sesquiterpenoids": 534, "Primary amides": 535, "Proanthocyanins": 536, "Prodigiosins": 537, "Prostaglandins": 538, "Protoberberine alkaloids": 539, "Protoilludane sesquiterpenoids": 540, "Protopine alkaloids": 541, "Pseudoguaiane sesquiterpenoids": 542, "Pseudopterane diterpenoids": 543, "Pterocarpan": 544, "Pulvinones": 545, "Purine alkaloids": 546, "Purine nucleos(t)ides": 547, "Pyranocoumarins": 548, "Pyrazine and Piperazine alkaloids": 549, "Pyridine alkaloids": 550, "Pyrimidine nucleos(t)ides": 551, "Pyrrocidine tetramate alkaloids": 552, "Pyrrole alkaloids": 553, "Pyrrolidine alkaloids": 554, "Pyrrolizidine alkaloids": 555, "Pyrroloindole alkaloids": 556, "Pyrroloquinoline alkaloids": 557, "Quadrane 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"Pathway": [ + 4 + ] + }, + "15": { + "Pathway": [ + 6 + ] + }, + "34": { + "Pathway": [ + 4, + 6 + ] + }, + "5": { + "Pathway": [ + 4 + ] + }, + "0": { + "Pathway": [ + 4 + ] + }, + "52": { + "Pathway": [ + 4 + ] + }, + "51": { + "Pathway": [ + 4, + 6 + ] + }, + "74": { + "Pathway": [ + 4, + 5 + ] + }, + "40": { + "Pathway": [ + 4 + ] + }, + "53": { + "Pathway": [ + 4, + 6 + ] + }, + "71": { + "Pathway": [ + 4, + 5 + ] + }, + "48": { + "Pathway": [ + 5 + ] + }, + "14": { + "Pathway": [ + 4, + 5 + ] + }, + "50": { + "Pathway": [ + 1, + 5 + ] + }, + "49": { + "Pathway": [ + 5 + ] + }, + "39": { + "Pathway": [ + 1, + 5 + ] + }, + "30": { + "Pathway": [ + 5 + ] + }, + "10": { + "Pathway": [ + 5 + ] + }, + "67": { + "Pathway": [ + 5 + ] + }, + "12": { + "Pathway": [ + 5 + ] + }, + "68": { + "Pathway": [ + 5 + ] + }, + "13": { + "Pathway": [ + 5 + ] + }, + "24": { + "Pathway": [ + 5 + ] + }, + "23": { + "Pathway": [ + 5 + ] + }, + "66": { + "Pathway": [ + 5 + ] + }, + "29": { + "Pathway": [ + 5 + ] + }, + "38": { + "Pathway": [ + 6 + ] + }, + "61": { + "Pathway": [ + 6 + ] + }, + "62": { + "Pathway": [ + 6 + ] + }, + "70": { + "Pathway": [ + 6 + ] + }, + "65": { + "Pathway": [ + 6 + ] + }, + "6": { + "Pathway": [ + 6 + ] + }, + "7": { + "Pathway": [ + 6 + ] + }, + "8": { + "Pathway": [ + 6 + ] + }, + "4": { + "Pathway": [ + 6 + ] + }, + "55": { + "Pathway": [ + 6 + ] + }, + "45": { + "Pathway": [ + 0 + ] + }, + "32": { + "Pathway": [ + 0 + ] + }, + "41": { + "Pathway": [ + 0 + ] + }, + "73": { + "Pathway": [ + 0 + ] + }, + "72": { + "Pathway": [ + 0, + 6 + ] + }, + "56": { + "Pathway": [ + 0 + ] + }, + "3": { + "Pathway": [ + 0 + ] + }, + "28": { + "Pathway": [ + 0 + ] + }, + "27": { + "Pathway": [ + 0 + ] + }, + "57": { + "Pathway": [ + 0, + 6 + ] + }, + "46": { + "Pathway": [ + 0, + 1 + ] + }, + "69": { + "Pathway": [ + 0, + 1 + ] + }, + "44": { + "Pathway": [ + 1, + 4 + ] + }, + "63": { + "Pathway": [ + 1 + ] + }, + "75": { + "Pathway": [ + 1 + ] + }, + "76": { + "Pathway": [ + 1 + ] + }, + "1": { + "Pathway": [ + 1 + ] + }, + "59": { + "Pathway": [ + 2 + ] + }, + "54": { + "Pathway": [ + 2 + ] + }, + "2": { + "Pathway": [ + 2 + ] + }, + "42": { + "Pathway": [ + 2 + ] + }, + "35": { + "Pathway": [ + 0 + ] + }, + "36": { + "Pathway": [ + 4 + ] + }, + "37": { + "Pathway": [ + 0 + ] + }, + "58": { + "Pathway": [ + 0 + ] + }, + "60": { + "Pathway": [ + 0 + ] + }, + "47": { + "Pathway": [ + 5 + ] + } + } +} diff --git a/Classifier/prediction_voting.py b/Classifier/prediction_voting.py index 7fa2166..89a1dcb 100644 --- a/Classifier/prediction_voting.py +++ b/Classifier/prediction_voting.py @@ -1,101 +1,74 @@ - -import itertools import numpy as np -def vote_classification(n_path, - n_class, - n_super, - pred_class, - pred_super, - path_from_class, - path_from_superclass, isglycoside, ontology_dictionary): - class_result = [] - superclass_result = [] - pathway_result = [] - - index = ontology_dictionary - - index_class = list(index['Class'].keys()) - index_superclass = list(index['Superclass'].keys()) - index_pathway = list(index['Pathway'].keys()) - - path_for_vote = n_path+path_from_class+path_from_superclass - path = list(set([ k for k in path_for_vote if path_for_vote.count(k) ==3])) - - if path == []: - path = list(set([ k for k in path_for_vote if path_for_vote.count(k) ==2])) - if len(path)>1: - path = list(set([ k for k in path_for_vote if path_for_vote.count(k) ==2])) - if path == []: - for w in n_path: - pathway_result.append(index_pathway[w]) - return pathway_result,superclass_result,class_result,isglycoside - - - else: #path != [] - if set(n_path) & set(path) != set(): - if set(path) & set(path_from_superclass) != set(): - n_super = [ l for l in n_super if set(path)& set(index['Super_hierarchy'][str(l)]['Pathway']) != set()] - if n_super == []: - n_class = [ m for m in n_class if set(path) & set(index['Class_hierarchy'][str(m)]['Pathway']) != set() ] - n_super = [index['Class_hierarchy'][str(n)]['Superclass'] for n in n_class] - n_super = list(set(itertools.chain.from_iterable(n_super))) - - elif len(n_super) > 1: #super != [] - n_class = [ u for u in n_class if set(path) & set(index['Class_hierarchy'][str(u)]['Pathway']) != set() ] - if n_class != []: - n_super = [index['Class_hierarchy'][str(v)]['Superclass'] for v in n_class] - n_path = [index['Class_hierarchy'][str(v)]['Pathway'] for v in n_class] - n_path = list(set(itertools.chain.from_iterable(n_path))) - n_super = list(set(itertools.chain.from_iterable(n_super))) - - elif len(path)==1: - n_super = [np.argmax(pred_super)] - n_class = [ m for m in [np.argmax(pred_class)] if set(n_super) & set(index['Class_hierarchy'][str(m)]['Superclass']) != set() ] - - - else: - n_class = [ o for o in n_class if set(n_super) & set(index['Class_hierarchy'][str(o)]['Superclass'])!=set() ] - if n_class == []: - n_class = [ m for m in [np.argmax(pred_class)] if set(n_super) & set(index['Class_hierarchy'][str(m)]['Superclass']) != set() ] - else: - n_class = [ p for p in n_class if set(path) & set(index['Class_hierarchy'][str(p)]['Pathway']) !=set() ] - n_super = [index['Class_hierarchy'][str(q)]['Superclass'] for q in n_class] - - n_super = list(set(itertools.chain.from_iterable(n_super))) + +# TODO this can be vastly simplified again + + +def vote_classification(n_path, n_class, n_super, + pred_class, pred_super, + path_from_class, path_from_superclass, + index): + """ + Classify the obtained classes + + @param n_path: predicted pathways above noise + @param n_class: predicted classes above noise + @param n_super: predicted superclasses above noise + @param pred_class: predicted classes (all) + @param pred_super: predicted superclasses (all) + @param path_from_class: pathways extracted from classes + @param path_from_superclass: pathways extracted from superclasses + @param index: the "ontology" + @return: pathway_result, superclass_result, class_result => the classified results ids + """ + + pathways_for_vote = list(n_path) + list(path_from_class) + list(path_from_superclass) + + # Select pathways with at least 3 counts + + path = {k for k in pathways_for_vote if pathways_for_vote.count(k) == 3} + + if not path: # if path is empty, we select pathways with only 2 counts + path = {k for k in pathways_for_vote if pathways_for_vote.count(k) == 2} + + if not path: # if path is still empty + # Add all the pathways we already know about, the rest is empty + return n_path, [], [] + + if path & set(n_path): # we have at least some of n_path in our path + if path & set(path_from_superclass): # we have at least some of the path from superclass in path + n_super = [i for i in n_super if path & set(index['Super_hierarchy'][str(i)]['Pathway'])] + n_class = [i for i in n_class if path & set(index['Class_hierarchy'][str(i)]['Pathway'])] + + if not n_super: # n_super is empty + n_super = list({index['Class_hierarchy'][str(n)]['Superclass'] for n in n_class}) + + elif len(n_super) > 1: # super != [] + if n_class: # n_class is not empty + n_super = list({j for i in n_class for j in index['Class_hierarchy'][str(i)]['Superclass']}) + n_path = list({j for i in n_class for j in index['Class_hierarchy'][str(i)]['Pathway']}) + elif len(path) == 1: + n_super = [np.argmax(pred_super)] + best_candidate_class_index = np.argmax(pred_class) + if set(n_super) & set(index['Class_hierarchy'][str(best_candidate_class_index)]['Superclass']): + n_class = [best_candidate_class_index] + + else: # we have only one n_super + # now our classes are only the classes from our best superclass + n_class = [i for i in n_class if set(n_super) & set(index['Class_hierarchy'][str(i)]['Superclass'])] + if not n_class: # n_class is empty, we take the predicted class with the highest score + best_candidate_class_index = np.argmax(pred_class) + if set(n_super) & set(index['Class_hierarchy'][str(best_candidate_class_index)]['Superclass']): + n_class = [best_candidate_class_index] else: - n_super = [ l for l in n_super if set(path) & set(index['Super_hierarchy'][str(l)]['Pathway']) != set()] - if n_super == []: - n_class = [ m for m in n_class if set(path) & set(index['Class_hierarchy'][str(m)]['Pathway']) != set()] - n_super = [index['Class_hierarchy'][str(n)]['Superclass'] for n in n_class] - n_path = [index['Class_hierarchy'][str(v)]['Pathway'] for v in n_class] - n_path = list(set(itertools.chain.from_iterable(n_path))) - n_super = list(set(itertools.chain.from_iterable(n_super))) - - - elif len(n_super) > 1: #super != [] - n_class = [ u for u in n_class if set(path) & set(index['Class_hierarchy'][str(u)]['Pathway']) != set()] - n_super = [index['Class_hierarchy'][str(v)]['Superclass'] for v in n_class] - n_path = [index['Class_hierarchy'][str(v)]['Pathway'] for v in n_class] - n_path = list(set(itertools.chain.from_iterable(n_path))) - n_super = list(set(itertools.chain.from_iterable(n_super))) - - - else: - n_class = [ o for o in n_class if set(path) & set(index['Class_hierarchy'][str(o)]['Pathway']) != set() ] - n_super = [index['Class_hierarchy'][str(v)]['Superclass'] for v in n_class] - n_path = [index['Class_hierarchy'][str(v)]['Pathway'] for v in n_class] - n_path = list(set(itertools.chain.from_iterable(n_path))) - n_super = list(set(itertools.chain.from_iterable(n_super))) - - for r in path: - pathway_result.append(index_pathway[r]) - for s in n_super: - superclass_result.append(index_superclass[s]) - for t in n_class: - class_result.append(index_class[t]) - - return pathway_result,superclass_result,class_result,isglycoside #three class results and glycoside checker result (True/False) - + n_class = [p for p in n_class if path & set(index['Class_hierarchy'][str(p)]['Pathway'])] + n_super = list({index['Class_hierarchy'][str(q)]['Superclass'] for q in n_class}) + + else: + # Select all the classes that are part of our selected pathways + n_class = [m for m in n_class if set(path) & set(index['Class_hierarchy'][str(m)]['Pathway'])] + n_super = list({index['Class_hierarchy'][str(n)]['Superclass'] for n in n_class}) + n_path = list({index['Class_hierarchy'][str(v)]['Pathway'] for v in n_class}) + return path, n_super, n_class # We have to check if we want path or n_path here! diff --git a/app.py b/app.py index a629d54..2ebcb7b 100644 --- a/app.py +++ b/app.py @@ -4,22 +4,15 @@ import dash_bootstrap_components as dbc import dash_html_components as html import dash_table -import plotly.express as px from dash.dependencies import Input, Output -import os -from zipfile import ZipFile import urllib.parse from flask import Flask, request import json -import pandas as pd import requests -import numpy as np import urllib.parse -import sys -sys.path.insert(0, "Classifier") -import fingerprint_handler -import prediction_voting +from classification import classify_structure +from models import ClassifyEntity server = Flask(__name__) app = dash.Dash(__name__, server=server, external_stylesheets=[dbc.themes.BOOTSTRAP]) @@ -27,10 +20,6 @@ server = app.server - -from models import ClassifyEntity - - ontology_dictionary = json.loads(open("Classifier/dict/index_v1.json").read()) NAVBAR = dbc.Navbar( @@ -42,11 +31,14 @@ dbc.Nav( [ dbc.NavItem(dbc.NavLink("NP Classifier", href="#")), - dbc.NavItem(dbc.NavLink("Report Feedback", href="https://docs.google.com/forms/d/e/1FAIpQLSf1-sw-P0SQGokyeaOpEmLda0UPJW93qkrI8rfp7D46fHVi6g/viewform?usp=sf_link")), - dbc.NavItem(dbc.NavLink("Preprint Publication", href="https://chemrxiv.org/articles/preprint/NPClassifier_A_Deep_Neural_Network-Based_Structural_Classification_Tool_for_Natural_Products/12885494/1")), - dbc.NavItem(dbc.NavLink("API", href="https://ccms-ucsd.github.io/GNPSDocumentation/api/#structure-np-classifier")), + dbc.NavItem(dbc.NavLink("Report Feedback", + href="https://docs.google.com/forms/d/e/1FAIpQLSf1-sw-P0SQGokyeaOpEmLda0UPJW93qkrI8rfp7D46fHVi6g/viewform?usp=sf_link")), + dbc.NavItem(dbc.NavLink("Preprint Publication", + href="https://chemrxiv.org/articles/preprint/NPClassifier_A_Deep_Neural_Network-Based_Structural_Classification_Tool_for_Natural_Products/12885494/1")), + dbc.NavItem(dbc.NavLink("API", + href="https://ccms-ucsd.github.io/GNPSDocumentation/api/#structure-np-classifier")), ], - navbar=True) + navbar=True) ], color="light", dark=False, @@ -83,7 +75,7 @@ BODY = dbc.Container( [ - dbc.Row([dbc.Col(dbc.Card(DASHBOARD)),], style={"marginTop": 30}), + dbc.Row([dbc.Col(dbc.Card(DASHBOARD)), ], style={"marginTop": 30}), ], className="mt-12", ) @@ -101,44 +93,34 @@ def display_page(pathname): else: return "CC1C(O)CC2C1C(OC1OC(COC(C)=O)C(O)C(O)C1O)OC=C2C(O)=O" -# This function will rerun at any + +# This function will rerun at any @app.callback( [Output('classification_table', 'children'), Output('structure', 'children')], [Input('smiles_string', 'value')], ) def handle_smiles(smiles_string): classification_dict = _process_full_classification(smiles_string) - #isglycoside, class_results, superclass_results, pathway_results, path_from_class, path_from_superclass, n_path, fp1, fp2 = classify_structure(smiles_string) output_list = [] for result in classification_dict["pathway_results"]: - output_dict = {} - output_dict["type"] = "pathway" - output_dict["entry"] = result + output_dict = {"type": "pathway", "entry": result} output_list.append(output_dict) - for result in classification_dict["superclass_results"]: - output_dict = {} - output_dict["type"] = "superclass" - output_dict["entry"] = result + output_dict = {"type": "superclass", "entry": result} output_list.append(output_dict) - for result in classification_dict["class_results"]: - output_dict = {} - output_dict["type"] = "class" - output_dict["entry"] = result + output_dict = {"type": "class", "entry": result} output_list.append(output_dict) if classification_dict["isglycoside"]: - output_dict = {} - output_dict["type"] = "is glycoside" - output_dict["entry"] = "glycoside" + output_dict = {"type": "is glycoside", "entry": "glycoside"} output_list.append(output_dict) - #Creating Table + # Creating Table white_list_columns = ["type", "entry"] table_fig = dash_table.DataTable( columns=[ @@ -153,16 +135,18 @@ def handle_smiles(smiles_string): selected_columns=[], selected_rows=[], page_action="native", - page_current= 0, - page_size= 10, + page_current=0, + page_size=10, ) # Creating Structure Image - img_obj = html.Img(id='image', src="https://gnps-structure.ucsd.edu/structureimg?smiles={}".format(urllib.parse.quote(smiles_string))) + img_obj = html.Img(id='image', src="https://gnps-structure.ucsd.edu/structureimg?smiles={}".format( + urllib.parse.quote(smiles_string))) return [table_fig, img_obj] -# This function will rerun at any + +# This function will rerun at any @app.callback( [Output('usage_summary', 'children')], [Input('url', 'pathname')], @@ -172,84 +156,6 @@ def usage_summary(pathname): return ["Total Unique SMILES Classified - {}".format(number_entries)] -def classify_structure(smiles): - isglycoside = fingerprint_handler._isglycoside(smiles) - - fp = fingerprint_handler.calculate_fingerprint(smiles, 2) - - fp1 = fp[0].tolist()[0] - fp2 = fp[1].tolist()[0] - - query_dict = {} - query_dict["input_3"] = fp1 - query_dict["input_4"] = fp2 - - # Handling SUPERCLASS - fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/SUPERCLASS:predict" - payload = json.dumps({"instances": [ query_dict ]}) - - headers = {"content-type": "application/json"} - json_response = requests.post(fp_pred_url, data=payload, headers=headers) - - pred_super = np.asarray(json.loads(json_response.text)['predictions'])[0] - n_super = list(np.where(pred_super>=0.3)[0]) - - path_from_superclass = [] - for j in n_super: - path_from_superclass += ontology_dictionary['Super_hierarchy'][str(j)]['Pathway'] - path_from_superclass = list(set(path_from_superclass)) - - query_dict = {} - query_dict["input_3"] = fp1 - query_dict["input_4"] = fp2 - - # Handling CLASS - fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/CLASS:predict" - payload = json.dumps({"instances": [ query_dict ]}) - - headers = {"content-type": "application/json"} - json_response = requests.post(fp_pred_url, data=payload, headers=headers) - - pred_class = np.asarray(json.loads(json_response.text)['predictions'])[0] - n_class = list(np.where(pred_class>=0.1)[0]) - - path_from_class = [] - for j in n_class: - path_from_class += ontology_dictionary['Class_hierarchy'][str(j)]['Pathway'] - path_from_class = list(set(path_from_class)) - - query_dict = {} - query_dict["input_1"] = fp1 - query_dict["input_2"] = fp2 - - # Handling PATHWAY - fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/PATHWAY:predict" - payload = json.dumps({"instances": [ query_dict ]}) - - headers = {"content-type": "application/json"} - json_response = requests.post(fp_pred_url, data=payload, headers=headers) - - pred_path = np.asarray(json.loads(json_response.text)['predictions'])[0] - n_path = list(np.where(pred_path>=0.5)[0]) - - class_result = [] - superclass_result = [] - pathway_result = [] - - # Voting on Answer - pathway_result, superclass_result, class_result, isglycoside = prediction_voting.vote_classification(n_path, - n_class, - n_super, - pred_class, - pred_super, - path_from_class, - path_from_superclass, - isglycoside, - ontology_dictionary) - - return isglycoside, class_result, superclass_result, pathway_result, path_from_class, path_from_superclass, n_path, fp1, fp2 - - def _process_full_classification(smiles_string): try: db_record = ClassifyEntity.get(ClassifyEntity.smiles == smiles_string) @@ -257,27 +163,29 @@ def _process_full_classification(smiles_string): except: pass - isglycoside, class_results, superclass_results, pathway_results, path_from_class, path_from_superclass, n_path, fp1, fp2 = classify_structure(smiles_string) + class_result, superclass_result, pathway_result, fp1, fp2, isglycoside = classify_structure(smiles_string, ontology_dictionary) + + # Next version of the API response could just output *_result directly - respond_dict = {} - respond_dict["class_results"] = class_results - respond_dict["superclass_results"] = superclass_results - respond_dict["pathway_results"] = pathway_results - respond_dict["isglycoside"] = isglycoside - - respond_dict["fp1"] = fp1 - respond_dict["fp2"] = fp2 + respond_dict = {"class_results": list(class_result.values()), + "superclass_results": list(superclass_result.values()), + "pathway_results": list(pathway_result.values()), + "class_results_ids": [int(i) for i in class_result.keys()], + "superclass_results_ids": [int(i) for i in superclass_result.keys()], + "pathway_results_ids": [int(i) for i in pathway_result.keys()], + "isglycoside": isglycoside, + "fp1": fp1, "fp2": fp2} # Lets save the result here, we should also check if its changed, and if so, we overwrite try: # Save it out ClassifyEntity.create( - smiles=smiles_string, - classification_json=json.dumps(respond_dict) - ) + smiles=smiles_string, + classification_json=json.dumps(respond_dict) + ) except: pass - + return respond_dict @@ -288,6 +196,7 @@ def classify(): return json.dumps(respond_dict) + # This gets you the model metadata @server.route("/model/metadata") def metadata(): @@ -295,7 +204,8 @@ def metadata(): all_metadata = {} pathway_metadata = json.loads(requests.get("http://npclassifier-tf-server:8501/v1/models/PATHWAY/metadata").text) class_metadata = json.loads(requests.get("http://npclassifier-tf-server:8501/v1/models/CLASS/metadata").text) - superclass_metadata = json.loads(requests.get("http://npclassifier-tf-server:8501/v1/models/SUPERCLASS/metadata").text) + superclass_metadata = json.loads( + requests.get("http://npclassifier-tf-server:8501/v1/models/SUPERCLASS/metadata").text) all_metadata["pathway"] = pathway_metadata all_metadata["class"] = class_metadata @@ -303,5 +213,6 @@ def metadata(): return json.dumps(all_metadata) + if __name__ == "__main__": app.run_server(debug=True, port=5000, host="0.0.0.0") diff --git a/classification.py b/classification.py new file mode 100644 index 0000000..59bd8b4 --- /dev/null +++ b/classification.py @@ -0,0 +1,82 @@ +# -*- coding: utf-8 -*- + +import json + +import requests +import numpy as np +from Classifier import fingerprint_handler +from Classifier import prediction_voting + + +def classify_structure(smiles, ontology_dictionary): + isglycoside = fingerprint_handler._isglycoside(smiles) + + fp = fingerprint_handler.calculate_fingerprint(smiles, 2) + + fp1 = fp[0].tolist()[0] + fp2 = fp[1].tolist()[0] + + query_dict = {"input_3": fp1, "input_4": fp2} + + # Handling SUPERCLASS + fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/SUPERCLASS:predict" + payload = json.dumps({"instances": [query_dict]}) + + headers = {"content-type": "application/json"} + json_response = requests.post(fp_pred_url, data=payload, headers=headers) + + pred_super = np.asarray(json.loads(json_response.text)['predictions'])[0] + n_super = set(np.where(pred_super >= 0.3)[0]) + + path_from_superclass = {j for i in n_super for j in ontology_dictionary['Super_hierarchy'][str(i)]['Pathway']} + + query_dict = {"input_3": fp1, "input_4": fp2} + + # Handling CLASS + fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/CLASS:predict" + payload = json.dumps({"instances": [query_dict]}) + + headers = {"content-type": "application/json"} + json_response = requests.post(fp_pred_url, data=payload, headers=headers) + + pred_class = np.asarray(json.loads(json_response.text)['predictions'])[0] + n_class = set(np.where(pred_class >= 0.1)[0]) + + path_from_class = {j for i in n_class for j in ontology_dictionary['Class_hierarchy'][str(i)]['Pathway']} + + query_dict = {"input_1": fp1, "input_2": fp2} + + # Handling PATHWAY + fp_pred_url = "http://npclassifier-tf-server:8501/v1/models/PATHWAY:predict" + payload = json.dumps({"instances": [query_dict]}) + + headers = {"content-type": "application/json"} + json_response = requests.post(fp_pred_url, data=payload, headers=headers) + + pred_path = np.asarray(json.loads(json_response.text)['predictions'])[0] + n_path = set(np.where(pred_path >= 0.5)[0]) + + # Voting on Answer + # + # pred_path, pred_super, pred_class are the nparrays of the totality of the predicted + # n_path, n_class, n_super are sets of the predicted pathways, classes and superclasses that are above noise + # path_from_class, path_from_superclass are sets of the pathways extracted from the superclasses/classes + n_pathway_result, n_superclass_result, n_class_result = prediction_voting.vote_classification(n_path, + n_class, + n_super, + pred_class, + pred_super, + path_from_class, + path_from_superclass, + ontology_dictionary) + + # Get all the existing things of the ontology + index_class = list(ontology_dictionary['Class'].keys()) + index_superclass = list(ontology_dictionary['Superclass'].keys()) + index_pathway = list(ontology_dictionary['Pathway'].keys()) + + class_result = {i: index_class[i] for i in n_class_result} + superclass_result = {i: index_superclass[i] for i in n_superclass_result} + pathway_result = {i: index_pathway[i] for i in n_pathway_result} + + return class_result, superclass_result, pathway_result, fp1, fp2, isglycoside