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annotate structure_pipeline.py @ 7:1d6fb7967ae9 draft

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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e-dirty"
author bgruening
date Sat, 10 Oct 2020 09:43:14 +0000
parents a57de37f12c2
children
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1 import argparse
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3 from chembl_structure_pipeline import checker, standardizer
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6 def load_mols(input_file):
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7 """
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8 Returns a list of strings, each a molblock
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9 """
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10 with open(input_file) as f:
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11 mols = [''.join(('\n', mol.strip())) for mol in f.read().strip().split('$$$$\n')]
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12 return mols
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15 def write_mols(mols, output_file):
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16 """
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17 Writes a list of molblocks to an SDF
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18 """
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19 with open(output_file, 'w') as f:
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20 f.write('\n$$$$'.join(mols))
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23 def standardize_molblock(mol):
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24 return standardizer.standardize_molblock(mol)
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27 def get_parent_molblock(mol):
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28 return standardizer.get_parent_molblock(mol)[0]
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31 def check_molblock(mol):
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32 issues = checker.check_molblock(mol)
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33 max_penalty_score = str(max([issue[0] for issue in issues])) if issues else '0'
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34 message = '; '.join([issue[1] for issue in issues])
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35 mol_with_issues = '\n'.join((mol, '> <MaxPenaltyScore>', max_penalty_score, '> <IssueMessages>', message))
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36 return mol_with_issues
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39 def main():
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40 parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
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41 parser.add_argument('-i', '--input', help='SDF/MOL input')
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42 parser.add_argument('-o', '--output', help="Standardized output")
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43 parser.add_argument('--standardize', action='store_true', help="Standardize molblock")
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44 parser.add_argument('--get_parent', action='store_true', help="Get parent molblock.")
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45 parser.add_argument('--check', action='store_true', help="Check molblock")
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46 args = parser.parse_args()
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48 mols = load_mols(args.input)
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49 if args.standardize:
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50 mols = [standardize_molblock(mol) for mol in mols]
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51 if args.get_parent:
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52 mols = [get_parent_molblock(mol) for mol in mols]
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53 if args.check:
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54 mols = [check_molblock(mol) for mol in mols]
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55 write_mols(mols, args.output)
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58 if __name__ == "__main__":
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59 main()