Mercurial > repos > bgruening > sdf_to_tab

annotate rdkit_descriptors.py @ 4:67b9a5b22bf0 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 12:05:30 +0000
parents d58dbfb01a29
children 48c536413a2f
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d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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1 #!/usr/bin/env python
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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2
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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3 from rdkit.Chem import Descriptors
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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4 from rdkit import Chem
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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5 import sys, os, re
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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6 import argparse
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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7 import inspect
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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8
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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9 def get_supplier( infile, format = 'smiles' ):
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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10 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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11 Returns a generator over a SMILES or InChI file. Every element is of RDKit
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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12 molecule and has its original string as _Name property.
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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13 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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14 with open(infile) as handle:
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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15 for line in handle:
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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16 line = line.strip()
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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17 if format == 'smiles':
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18 mol = Chem.MolFromSmiles( line, sanitize=True )
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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19 elif format == 'inchi':
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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20 mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False )
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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21 if mol is None:
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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22 yield False
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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23 else:
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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24 mol.SetProp( '_Name', line.split('\t')[0] )
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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25 yield mol
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26
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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27 def get_rdkit_descriptor_functions():
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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28 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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29 Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function)
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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30 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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31 ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ]
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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32 ret.sort()
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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33 return ret
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34
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35
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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36 def descriptors( mol, functions ):
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37 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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38 Calculates the descriptors of a given molecule.
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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39 """
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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40 for name, function in functions:
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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41 yield (name, function( mol ))
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42
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43
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44 if __name__ == "__main__":
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45 parser = argparse.ArgumentParser()
d58dbfb01a29 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
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46 parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
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47 parser.add_argument("--iformat", help="Specify the input file format.")
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48
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49 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
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50 default=sys.stdout, help="path to the result file, default it sdtout")
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51
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52 parser.add_argument("--header", dest="header", action="store_true",
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53 default=False,
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54 help="Write header line.")
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56 args = parser.parse_args()
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58 if args.iformat == 'sdf':
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59 supplier = Chem.SDMolSupplier( args.infile )
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60 elif args.iformat =='smi':
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61 supplier = get_supplier( args.infile, format = 'smiles' )
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62 elif args.iformat == 'inchi':
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63 supplier = get_supplier( args.infile, format = 'inchi' )
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64
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65 functions = get_rdkit_descriptor_functions()
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67 if args.header:
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68 args.outfile.write( '%s\n' % '\t'.join( ['MoleculeID'] + [name for name, f in functions] ) )
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70 for mol in supplier:
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71 if not mol:
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72 continue
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73 descs = descriptors( mol, functions )
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74 molecule_id = mol.GetProp("_Name")
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75 args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(round(res, 6)) for name, res in descs] ) )
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76