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annotate chembl.py @ 5:e907c14ea4be draft

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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 11:54:13 +0000
parents 6aa23d7ae03b
children 9dbc85cd5780
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0291a4af0db6 "planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 594b8bcfa2730fb21de1efa83f89e0380fdcaa0f"
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1 from chembl_webresource_client.settings import Settings
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2 Settings.Instance().CACHING = False
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3 from chembl_webresource_client.new_client import new_client
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4 import argparse
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5
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6 def open_file(filename):
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7 with open(filename) as f:
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8 return f.readline().split()[0]
0
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9
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10 def get_smiles(res):
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11 """
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12 Get a list of SMILES from function results
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13 """
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14 smiles = set()
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15 for smi in res:
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16 try:
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17 smiles.add('{}\t{}'.format(smi['molecule_structures']['canonical_smiles'], smi['molecule_chembl_id']))
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18 except TypeError:
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19 continue
0
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20 return smiles
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21
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22 def sim_search(smiles, tanimoto):
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23 """
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24 Return compounds which are within a Tanimoto range of the SMILES input
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25 """
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26 similarity = new_client.similarity
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27 return similarity.filter(smiles=smiles, similarity=tanimoto).only(['molecule_structures', 'molecule_chembl_id'])
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28
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29 def substr_search(smiles):
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30 """
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31 Return compounds which contain the SMILES substructure input
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32 """
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33 substructure = new_client.substructure
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34 return substructure.filter(smiles=smiles).only(['molecule_structures', 'molecule_chembl_id'])
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35
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36 def filter_drugs(mols):
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37 """
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38 Return only compounds which are approved drugs
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39 """
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40 return mols.filter(max_phase=4)
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41
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42 def filter_biotherapeutic(mols):
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43 """
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44 Return only biotherapeutic molecules
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45 """
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46 return mols.filter(biotherapeutic__isnull=False)
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47
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48 def filter_nat_prod(mols):
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49 """
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50 Return only natural products
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51 """
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52 return mols.filter(natural_product=1)
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53
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54 def filter_ro5(mols):
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55 """
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56 Return only compounds with no RO5 violations
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57 """
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58 return mols.filter(molecule_properties__num_ro5_violations=0)
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59
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60 def main():
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61 parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
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62 parser.add_argument('-i', '--input', help='SMILES input')
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63 parser.add_argument('-f', '--file', help='SMILES input as file')
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64 parser.add_argument('-o', '--output', help="SMILES output")
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65 parser.add_argument('-t', '--tanimoto', type=int, help='Tanimoto similarity score')
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66 parser.add_argument('-s', '--substructure', action='store_true', help='Substructure search using the SMILES input.')
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67 parser.add_argument('-d', '--drugs', action='store_true', help='Filter approved drugs')
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68 parser.add_argument('-b', '--biotherapeutic', action='store_true', help='Filter biotherapeutic molecules')
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69 parser.add_argument('-n', '--nat-prod', action='store_true', help='Filter natural products')
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70 parser.add_argument('-r', '--ro5', action='store_true', help='Filter compounds that pass Lipinski RO5')
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71
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72 args = parser.parse_args()
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73
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74 if args.file: # get SMILES from file rather than -i option
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75 args.input = open_file(args.file)
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76
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77 if len(args.input) < 5:
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78 raise IOError('SMILES must be at least 5 characters long.')
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79
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80 if args.substructure: # specify search type: substructure or similarity
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81 mols = substr_search(args.input)
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82 else:
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83 mols = sim_search(args.input, args.tanimoto)
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84
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85 # filter options:
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86 if args.drugs:
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87 mols = filter_drugs(mols)
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88
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89 if args.biotherapeutic:
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90 mols = filter_biotherapeutic(mols)
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91
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92 if args.nat_prod:
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93 mols = filter_nat_prod(mols)
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94
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95 if args.ro5:
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96 mols = filter_ro5(mols)
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97
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98 # get SMILES from search output
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99 mols = get_smiles(mols)
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100
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101 # write to file
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102 with open(args.output, 'w') as f:
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103 f.write('\n'.join(mols))
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104
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105
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106 if __name__ == "__main__":
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107 main()