diff --git "a/swisssidechain.py" "b/swisssidechain.py" new file mode 100644--- /dev/null +++ "b/swisssidechain.py" @@ -0,0 +1,4526 @@ +"""Definitions and properties of amino-acids adapted from p2smi (https://github.com/AaronFeller/p2smi)""" + +# Natural Amino-acids: + +all_aminos = { + "Phenylglycine": { + "Code": "PG", + "Formula": "C8H9NO2", + "Letter": "Ḁ", + "MolWeight": 151.063328528, + "SMILES": "N[C@@H](c1ccccc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-methoxy-Phenylalanine": { + "Code": "0A1", + "Formula": "C10H13NO3", + "Letter": "Ạ", + "MolWeight": 195.089543276, + "SMILES": "N[C@@H](Cc1ccc(OC)cc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "7-hydroxy-l-tryptophan": { + "Code": "0AF", + "Formula": "C11H12N2O3", + "Letter": "Ả", + "MolWeight": 220.084792244, + "SMILES": "N[C@@H](Cc1c[nH]c2c1cccc2O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-carbamimidoyl-l-phenylalanine": { + "Code": "0BN", + "Formula": "C10H13N3O2", + "Letter": "Ấ", + "MolWeight": 207.100776656, + "SMILES": "N[C@@H](Cc1ccc(cc1)C(=N)N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](Cc1ccc(cc1)C(=N*)N)C(=O)O", + }, + "4-chloro-Phenylalanine": { + "Code": "4CP", + "Formula": "C9H10ClNO2", + "Letter": "Ầ", + "MolWeight": 199.04000624, + "SMILES": "N[C@@H](Cc1ccc(cc1)Cl)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-Allyl-glycine": { + "Code": "2AG", + "Formula": "C7H11NO5", + "Letter": "Ẫ", + "MolWeight": 189.063722452, + "SMILES": "N[C@@H](CCCC(C(=O)O)=O)C(=O)O", + "cterm": "N[C@@H](CCCC(C*(=O))=O)C(=O)O", + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-methyl-aspartic-acid": { + "Code": "2AS", + "Formula": "C5H9NO4", + "Letter": "Ậ", + "MolWeight": 147.053157768, + "SMILES": "N[C@H]([C@H](C)(C(=O)O))C(=O)O", + "cterm": "N[C@H]([C@H](C)(C*(=O)))C(=O)O", + "disulphide": False, + "ester": False, + "nterm": False, + }, + "s-(difluoromethyl)-homocysteine": { + "Code": "2FM", + "Formula": "C5H9F2NO2S", + "Letter": "Ắ", + "MolWeight": 185.032205968, + "SMILES": "N[C@@H](CCSC(F)F)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-fluoro-l-histidine": { + "Code": "2HF", + "Formula": "C6H12FN3O2", + "Letter": "Ằ", + "MolWeight": 177.091354844, + "SMILES": "N[C@@H](C[C@@H]1CN[C@@H](N1)F)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-fluoro-l-histidine(1)": { + "Code": "2HF1", + "Formula": "C6H8FN3O2", + "Letter": "Ẳ", + "MolWeight": 173.060054716, + "SMILES": "N[C@@H](Cc1cnc(F)N1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-fluoro-l-histidine(2)": { + "Code": "2HF2", + "Formula": "C6H8FN3O2", + "Letter": "Ẵ", + "MolWeight": 173.060054716, + "SMILES": "N[C@@H](Cc1c[nH]c(n1)F)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "l-2-amino-6-methylene-pimelic-acid": { + "Code": "2NP", + "Formula": "C8H13NO4", + "Letter": "Ặ", + "MolWeight": 187.084457896, + "SMILES": "N[C@@H](CCCC(=C)C(=O)O)C(=O)O", + "cterm": "N[C@@H](CCCC(=C)C*(=O))C(=O)O", + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-(4H-thieno[3,2-b]pyrrol-6-yl)-L-alanine": { + "Code": "32T", + "Formula": "C9H10N2O2S", + "Letter": "Ḃ", + "MolWeight": 210.04629856, + "SMILES": "N[C@H](Cc1c[nH]c2c1scc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-cyano-phenylalanine": { + "Code": "3CF", + "Formula": "C10H10N2O2", + "Letter": "Ḅ", + "MolWeight": 190.07422756, + "SMILES": "N[C@@H](Cc1cccc(C#N)c1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "(2s)-amino(3,5-dihydroxyphenyl)-ethanoic-acid": { + "Code": "3FG", + "Formula": "C8H9NO4", + "Letter": "Ḇ", + "MolWeight": 183.053157768, + "SMILES": "N[C@@H](c1cc(O)cc(c1)O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": "N[C@@H](c1cc(O*)cc(c1)O)C(=O)O", + "nterm": False, + }, + "4-hydroxy-glutamic-acid": { + "Code": "3GL", + "Formula": "C5H9NO5", + "Letter": "Ḉ", + "MolWeight": 163.048072388, + "SMILES": "N[C@@H](C[C@@H](C(=O)O)O)C(=O)O", + "cterm": "N[C@@H](C[C@@H](C*(=O))O)C(=O)O", + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-Chloro-tyrosine": { + "Code": "3MY", + "Formula": "C9H10ClNO3", + "Letter": "Ḋ", + "MolWeight": 215.03492086, + "SMILES": "N[C@H](Cc1ccc(c(c1)Cl)O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-Bromo-phenylalanine": { + "Code": "4BF", + "Formula": "C9H10BrNO2", + "Letter": "Ḍ", + "MolWeight": 242.98949066, + "SMILES": "N[C@@H](Cc1ccc(cc1)Br)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-cyano-phenylalanine": { + "Code": "4CF", + "Formula": "C10H10N2O2", + "Letter": "Ḏ", + "MolWeight": 190.07422756, + "SMILES": "N[C@@H](Cc1ccc(cc1)C#N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "nitrilo-l-methionine": { + "Code": "4CY", + "Formula": "C5H8N2O2S", + "Letter": "Ḑ", + "MolWeight": 160.030648496, + "SMILES": "N[C@@H](CCSC#N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-fluoro-tryptophan": { + "Code": "4FW", + "Formula": "C11H11FN2O2", + "Letter": "Ḓ", + "MolWeight": 222.080455812, + "SMILES": "N[C@@H](Cc1c[nH]c2c1c(F)ccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-hydroxymethyl-phenylalanine": { + "Code": "4HMP", + "Formula": "C10H13NO3", + "Letter": "Ḕ", + "MolWeight": 195.089543276, + "SMILES": "N[C@@H](Cc1ccc(CO)cc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-hydroxy-tryptophan": { + "Code": "4HT", + "Formula": "C11H12N2O3", + "Letter": "Ḗ", + "MolWeight": 220.084792244, + "SMILES": "N[C@@H](Cc1c[nH]c2c1c(O)ccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": "N[C@@H](Cc1c[nH]c2c1c(O*)ccc2)C(=O)O", + "nterm": False, + }, + "4-amino-l-tryptophan": { + "Code": "4IN", + "Formula": "C11H13N3O2", + "Letter": "Ḙ", + "MolWeight": 219.100776656, + "SMILES": "N[C@@H](Cc1c[nH]c2c1c(N)ccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4-methyl-phenylalanine": { + "Code": "4PH", + "Formula": "C10H13NO2", + "Letter": "Ḛ", + "MolWeight": 179.094628656, + "SMILES": "N[C@@H](Cc1ccc(cc1)C)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "6-carboxylysine": { + "Code": "6CL", + "Formula": "C7H14N2O4", + "Letter": "Ḝ", + "MolWeight": 190.095356928, + "SMILES": "N[C@@H](CCC[C@H](C(=O)O)N)C(=O)O", + "cterm": "N[C@@H](CCC[C@H](C*(=O))N)C(=O)O", + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](CCC[C@H](C(=O)O)N*)C(=O)O", + }, + "6-chloro-l-tryptophan": { + "Code": "6CW", + "Formula": "C11H11ClN2O2", + "Letter": "Ẹ", + "MolWeight": 238.050905272, + "SMILES": "N[C@@H](Cc1c[nH]c2c1ccc(c2)Cl)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-amino-5-hydroxypentanoic-acid": { + "Code": "AA4", + "Formula": "C5H11NO3", + "Letter": "Ẻ", + "MolWeight": 133.073893212, + "SMILES": "N[C@@H](CCCO)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": "N[C@@H](CCCO*)C(=O)O", + "nterm": False, + }, + "2-Aminobutyric-acid": { + "Code": "ABA", + "Formula": "C4H9NO2", + "Letter": "Ẽ", + "MolWeight": 103.063328528, + "SMILES": "N[C@@H](CC)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "cis-amiclenomycin": { + "Code": "ACZ", + "Formula": "C10H16N2O2", + "Letter": "Ế", + "MolWeight": 196.121177752, + "SMILES": "N[C@@H](CC[C@@H]1C=C[C@@H](C=C1)N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](CC[C@@H]1C=C[C@@H](C=C1)N*)C(=O)O", + }, + "Adamanthane": { + "Code": "ADAM", + "Formula": "C13H21NO2", + "Letter": "Ề", + "MolWeight": 223.157228912, + "SMILES": "N[C@@H](C[C@]12C[C@H]3C[C@@H](C2)C[C@@H](C1)C3)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "5-methyl-arginine": { + "Code": "AGM", + "Formula": "C7H16N4O2", + "Letter": "Ể", + "MolWeight": 188.127325752, + "SMILES": "N[C@@H](CC[C@H](C)NC(=N)N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](CC[C@H](C)NC(=N*)N)C(=O)O", + }, + "beta-hydroxyasparagine": { + "Code": "AHB", + "Formula": "C4H8N2O4", + "Letter": "Ễ", + "MolWeight": 148.048406736, + "SMILES": "N[C@@H]([C@@H](C(=O)N)O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "2-Aminoheptanoic-acid": { + "Code": "AHP", + "Formula": "C7H15NO2", + "Letter": "Ệ", + "MolWeight": 145.11027872, + "SMILES": "N[C@@H](CCCCC)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-cyclohexyl-alanine": { + "Code": "ALC", + "Formula": "C9H17NO2", + "Letter": "Ḟ", + "MolWeight": 171.125928784, + "SMILES": "N[C@@H](CC1CCCCC1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "1-Naphthyl-alanine": { + "Code": "ALN", + "Formula": "C13H13NO2", + "Letter": "Ḡ", + "MolWeight": 215.094628656, + "SMILES": "N[C@@H](Cc1cccc2c1cccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "Allo-threonine": { + "Code": "ALO", + "Formula": "C4H9NO3", + "Letter": "Ḣ", + "MolWeight": 119.058243148, + "SMILES": "N[C@@H]([C@H](C)O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-(9-anthryl)-alanine": { + "Code": "ANTH", + "Formula": "C17H15NO2", + "Letter": "Ḥ", + "MolWeight": 265.11027872, + "SMILES": "N[C@@H](Cc1c2ccccc2cc2c1cccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-Methyl-phenylalanine": { + "Code": "APD", + "Formula": "C10H13NO2", + "Letter": "Ḧ", + "MolWeight": 179.094628656, + "SMILES": "N[C@@H](Cc1cccc(c1)C)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "m-amidinophenyl-3-alanine": { + "Code": "APM", + "Formula": "C10H13N3O2", + "Letter": "Ḩ", + "MolWeight": 207.100776656, + "SMILES": "N[C@@H](Cc1cccc(c1)C(=N)N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](Cc1cccc(c1)C(=N*)N)C(=O)O", + }, + "c-gamma-hydroxy-arginine": { + "Code": "ARO", + "Formula": "C6H14N4O3", + "Letter": "Ḫ", + "MolWeight": 190.106590308, + "SMILES": "N[C@@H](C[C@@H](O)CN=C(N)N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](C[C@@H](O)CN=C(N)N*)C(=O)O", + }, + "(2r)-2-amino-4-oxobutanoic-acid": { + "Code": "AS2", + "Formula": "C4H7NO3", + "Letter": "Ỉ", + "MolWeight": 117.042593084, + "SMILES": "N[C@@H](CC=O)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "azido-alanine": { + "Code": "AZDA", + "Formula": "C3H7N4O2+", + "Letter": "Ị", + "MolWeight": 131.05635188409, + "SMILES": "N[C@@H](CN=[N+]=N)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "Phenylserine": { + "Code": "BB8", + "Formula": "C9H11NO3", + "Letter": "Ḭ", + "MolWeight": 181.073893212, + "SMILES": "N[C@@H]([C@@H](O)c1ccccc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "benzylcysteine": { + "Code": "BCS", + "Formula": "C10H13NO2S", + "Letter": "Ḯ", + "MolWeight": 211.066699656, + "SMILES": "N[C@@H](CSCc1ccccc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "beta-hydroxyaspartic-acid": { + "Code": "BHD", + "Formula": "C4H7NO5", + "Letter": "Ḱ", + "MolWeight": 149.032422324, + "SMILES": "N[C@@H]([C@H](O)C(=O)O)C(=O)O", + "cterm": "N[C@@H]([C@H](O)C*(=O))C(=O)O", + "disulphide": False, + "ester": False, + "nterm": False, + }, + "4,4-biphenylalanine": { + "Code": "BIF", + "Formula": "C15H15NO2", + "Letter": "Ḳ", + "MolWeight": 241.11027872, + "SMILES": "N[C@@H](Cc1ccc(cc1)c1ccccc1)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "5-bromo-l-isoleucine": { + "Code": "BIU", + "Formula": "C6H12BrNO2", + "Letter": "Ḵ", + "MolWeight": 209.005140724, + "SMILES": "N[C@@H]([C@@H](C)CCBr)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-(3-benzothienyl)-alanine": { + "Code": "BTH3", + "Formula": "C11H11NO2S", + "Letter": "Ḷ", + "MolWeight": 221.051049592, + "SMILES": "N[C@@H](Cc1csc2c1cccc2)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "6-bromo-tryptophan": { + "Code": "BTR", + "Formula": "C11H11BrN2O2", + "Letter": "Ḹ", + "MolWeight": 282.000389692, + "SMILES": "N[C@@H](Cc1c[nH]c2c1ccc(c2)Br)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "Tertleucine": { + "Code": "BUG", + "Formula": "C6H13NO2", + "Letter": "Ḻ", + "MolWeight": 131.094628656, + "SMILES": "N[C@@H](C(C)(C)C)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "3-chloro-l-alanine": { + "Code": "C2N", + "Formula": "C3H6ClNO2", + "Letter": "Ḽ", + "MolWeight": 123.008706112, + "SMILES": "N[C@@H](CCl)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": False, + }, + "canaline": { + "Code": "CAN", + "Formula": "C4H10N2O3", + "Letter": "Ḿ", + "MolWeight": 134.06914218, + "SMILES": "N[C@@H](CCON)C(=O)O", + "cterm": False, + "disulphide": False, + "ester": False, + "nterm": "N[C@@H](CCON*)C(=O)O", + }, + "carboxymethylated-cysteine": { + "Code": "CCS", + "Formula": 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