Mercurial > repos > bgruening > ctb_rdkit_describtors
annotate rdkit_descriptors.py @ 0:d7ea4e8cb1f3 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
author | bgruening |
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date | Sat, 20 May 2017 12:41:19 -0400 |
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children | 2f212f34b80c |
rev | line source |
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0
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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changeset
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1 #!/usr/bin/env python |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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2 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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3 from rdkit.Chem import Descriptors |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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4 from rdkit import Chem |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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5 import sys, os, re |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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6 import argparse |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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7 import inspect |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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8 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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9 def get_supplier( infile, format = 'smiles' ): |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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10 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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11 Returns a generator over a SMILES or InChI file. Every element is of RDKit |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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12 molecule and has its original string as _Name property. |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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13 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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14 with open(infile) as handle: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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15 for line in handle: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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16 line = line.strip() |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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changeset
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17 if format == 'smiles': |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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18 mol = Chem.MolFromSmiles( line, sanitize=True ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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19 elif format == 'inchi': |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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20 mol = Chem.inchi.MolFromInchi( line, sanitize=True, removeHs=True, logLevel=None, treatWarningAsError=False ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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21 if mol is None: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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22 yield False |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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23 else: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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24 mol.SetProp( '_Name', line.split('\t')[0] ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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25 yield mol |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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diff
changeset
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26 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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27 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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28 def get_rdkit_descriptor_functions(): |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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29 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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30 Returns all descriptor functions under the Chem.Descriptors Module as tuple of (name, function) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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31 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
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32 ret = [ (name, f) for name, f in inspect.getmembers( Descriptors ) if inspect.isfunction( f ) and not name.startswith( '_' ) ] |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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33 ret.sort() |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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34 return ret |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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35 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
diff
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36 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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37 def descriptors( mol, functions ): |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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38 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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39 Calculates the descriptors of a given molecule. |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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40 """ |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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41 for name, function in functions: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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42 yield (name, function( mol )) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
diff
changeset
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43 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
diff
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44 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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45 if __name__ == "__main__": |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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46 parser = argparse.ArgumentParser() |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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47 parser.add_argument('-i', '--infile', required=True, help='Path to the input file.') |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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48 parser.add_argument("--iformat", help="Specify the input file format.") |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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49 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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50 parser.add_argument('-o', '--outfile', type=argparse.FileType('w+'), |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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51 default=sys.stdout, help="path to the result file, default it sdtout") |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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52 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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53 parser.add_argument("--header", dest="header", action="store_true", |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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54 default=False, |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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55 help="Write header line.") |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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56 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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57 args = parser.parse_args() |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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58 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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59 if args.iformat == 'sdf': |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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60 supplier = Chem.SDMolSupplier( args.infile ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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61 elif args.iformat =='smi': |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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62 supplier = get_supplier( args.infile, format = 'smiles' ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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63 elif args.iformat == 'inchi': |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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64 supplier = get_supplier( args.infile, format = 'inchi' ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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65 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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66 functions = get_rdkit_descriptor_functions() |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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67 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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68 if args.header: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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69 args.outfile.write( '%s\n' % '\t'.join( [name for name, f in functions] ) ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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70 |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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71 for mol in supplier: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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72 if not mol: |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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73 continue |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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74 descs = descriptors( mol, functions ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents:
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75 molecule_id = mol.GetProp("_Name") |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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76 args.outfile.write( "%s\n" % '\t'.join( [molecule_id]+ [str(res) for name, res in descs] ) ) |
d7ea4e8cb1f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
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77 |