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annotate chembl.py @ 9:a446ea7e2bc1 draft default tip

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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 7ca965e469cce3951d22c854dc7b6cb2a3a4f9f6"
author bgruening
date Tue, 23 Mar 2021 13:48:35 +0000
parents a43a00845834
children
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1 import argparse
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3 from chembl_webresource_client.settings import Settings
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4 Settings.Instance().CACHING = False
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5 from chembl_webresource_client.new_client import new_client # noqa
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8 def open_file(filename):
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9 with open(filename) as f:
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10 return f.readline().split()[0]
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13 def get_smiles(res):
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14 """
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15 Get a list of SMILES from function results
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16 """
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17 smiles = set()
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18 for smi in res:
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19 try:
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20 smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id']))
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21 except TypeError:
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22 continue
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23 return smiles
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26 def sim_search(smiles, tanimoto):
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27 """
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28 Return compounds which are within a Tanimoto range of the SMILES input
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29 """
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30 similarity = new_client.similarity
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31 return similarity.filter(smiles=smiles, similarity=tanimoto).only(['molecule_structures', 'molecule_chembl_id'])
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34 def substr_search(smiles):
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35 """
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36 Return compounds which contain the SMILES substructure input
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37 """
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38 substructure = new_client.substructure
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39 return substructure.filter(smiles=smiles).only(['molecule_structures', 'molecule_chembl_id'])
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42 def filter_drugs(mols):
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43 """
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44 Return only compounds which are approved drugs
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45 """
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46 return mols.filter(max_phase=4)
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49 def filter_biotherapeutic(mols):
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50 """
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51 Return only biotherapeutic molecules
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52 """
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53 return mols.filter(biotherapeutic__isnull=False)
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56 def filter_nat_prod(mols):
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57 """
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58 Return only natural products
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59 """
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60 return mols.filter(natural_product=1)
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63 def filter_ro5(mols):
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64 """
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65 Return only compounds with no RO5 violations
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66 """
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67 return mols.filter(molecule_properties__num_ro5_violations=0)
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70 def main():
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71 parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
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72 parser.add_argument('-i', '--input', help='SMILES input')
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73 parser.add_argument('-f', '--file', help='SMILES input as file')
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74 parser.add_argument('-o', '--output', help="SMILES output")
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75 parser.add_argument('-t', '--tanimoto', type=int, help='Tanimoto similarity score')
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76 parser.add_argument('-s', '--substructure', action='store_true', help='Substructure search using the SMILES input.')
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77 parser.add_argument('-d', '--drugs', action='store_true', help='Filter approved drugs')
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78 parser.add_argument('-b', '--biotherapeutic', action='store_true', help='Filter biotherapeutic molecules')
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79 parser.add_argument('-n', '--nat-prod', action='store_true', help='Filter natural products')
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80 parser.add_argument('-r', '--ro5', action='store_true', help='Filter compounds that pass Lipinski RO5')
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81
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82 args = parser.parse_args()
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83
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84 if args.file: # get SMILES from file rather than -i option
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85 args.input = open_file(args.file)
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86
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87 if len(args.input) < 5:
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88 raise IOError('SMILES must be at least 5 characters long.')
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89
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90 if args.substructure: # specify search type: substructure or similarity
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91 mols = substr_search(args.input)
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92 else:
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93 mols = sim_search(args.input, args.tanimoto)
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95 # filter options:
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96 if args.drugs:
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97 mols = filter_drugs(mols)
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98
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99 if args.biotherapeutic:
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100 mols = filter_biotherapeutic(mols)
915e9be38994 planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 2e3c3c2bd7ecdc9c2968a32f91e81136e0cb3835
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101
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102 if args.nat_prod:
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103 mols = filter_nat_prod(mols)
915e9be38994 planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 2e3c3c2bd7ecdc9c2968a32f91e81136e0cb3835
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104
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105 if args.ro5:
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106 mols = filter_ro5(mols)
915e9be38994 planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 2e3c3c2bd7ecdc9c2968a32f91e81136e0cb3835
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107
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108 # get SMILES from search output
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109 mols = get_smiles(mols)
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110
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111 # write to file
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112 with open(args.output, 'w') as f:
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113 f.write('\n'.join(mols))
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a57de37f12c2 "planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e"
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114
0
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115
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116 if __name__ == "__main__":
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117 main()