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1 #!/usr/bin/env python
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2
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3 from rdkit.Chem import Descriptors
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4 from rdkit import Chem
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5 import sys, os, re
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6 import argparse
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7 import inspect
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8
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9 def get_supplier( infile, format = 'smiles' ):
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10 with open(infile) as handle:
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11 for line in handle:
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12 line = line.strip()
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13 if format == 'smiles':
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14 mol = Chem.MolFromSmiles( line, sanitize=True )
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15 elif format == 'inchi':
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16 mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False )
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17 if mol is None:
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18 yield False
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19 else:
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20 mol.SetProp( '_Name', line.split('\t')[0] )
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21 yield mol
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22
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23
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24 def get_rdkit_descriptor_functions():
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25 ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ]
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26 ret.sort()
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27 return ret
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28
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29
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30 def descriptors( mol, functions ):
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31 """
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32 Calculates the descriptors of a given molecule.
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33 """
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34
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35 for name, function in functions:
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36 yield (name, function( mol ))
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37
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38
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39 if __name__ == "__main__":
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40 parser = argparse.ArgumentParser()
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41 parser.add_argument('-i', '--infile', required=True, help='Path to the input file.')
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42 parser.add_argument("--iformat", help="Specify the input file format.")
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43
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44 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'),
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45 default=sys.stdout, help="path to the result file, default it sdtout")
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46
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47 parser.add_argument("--header", dest="header", action="store_true",
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48 default=False,
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49 help="Write header line.")
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50
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51 args = parser.parse_args()
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52
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53 if args.iformat == 'sdf':
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54 supplier = Chem.SDMolSupplier( args.infile )
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55 elif args.iformat =='smi':
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56 supplier = get_supplier( args.infile, format = 'smiles' )
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57 elif args.iformat == 'inchi':
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58 supplier = get_supplier( args.infile, format = 'inchi' )
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59
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60 functions = get_rdkit_descriptor_functions()
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61
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62 if args.header:
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63 args.outfile.write( '%s\n' % '\t'.join( [name for name, f in functions] ) )
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64
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65 for mol in supplier:
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66 if not mol:
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67 continue
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68 descs = descriptors( mol, functions )
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69 name = mol.GetProp("_Name")
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70 args.outfile.write( "%s\n" % '\t'.join( [name]+ [str(res) for name, res in descs] ) )
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71
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