Mercurial > repos > bgruening > sucos_clustering

annotate utils.py @ 1:334ad24525db draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 6fa2a0294d615c9f267b766337dca0b2d3637219"
author bgruening
date Fri, 11 Oct 2019 18:26:08 -0400
parents f80cfac80c53
children b8725fec8c7b
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f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 #!/usr/bin/env python
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2 """
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3 Utility functions for SuCOS and other RDKit modules
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4 """
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f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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6 from __future__ import print_function
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7 import sys, gzip
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8 from rdkit import Chem
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9
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10 def log(*args, **kwargs):
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11 """Log output to STDERR
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12 """
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13 print(*args, file=sys.stderr, **kwargs)
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14
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15 def open_file_for_reading(filename):
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16 """Open the file gunzipping it if it ends with .gz."""
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17 if filename.lower().endswith('.gz'):
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18 return gzip.open(filename, 'rb')
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19 else:
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20 return open(filename, 'rb')
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21
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22 def open_file_for_writing(filename):
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23 if filename.lower().endswith('.gz'):
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24 return gzip.open(filename, 'at')
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25 else:
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26 return open(filename, 'w+')
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27
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28 def read_single_molecule(filename, index=1, format=None):
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29 """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format.
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30 If SDF then you can also specify an index of the molecule that is read (default is the first)
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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31 """
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32 mol = None
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33 if format == 'mol' or filename.lower().endswith('.mol') or filename.lower().endswith('.mol.gz'):
f80cfac80c53 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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34 file = open_file_for_reading(filename)
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35 mol = Chem.MolFromMolBlock(file.read())
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36 file.close()
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37 elif format == 'sdf' or filename.lower().endswith('.sdf') or filename.lower().endswith('.sdf.gz'):
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38 file = open_file_for_reading(filename)
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39 supplier = Chem.ForwardSDMolSupplier(file)
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40 for i in range(0,index):
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41 if supplier.atEnd():
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42 break
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43 mol = next(supplier)
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44 file.close()
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45
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46 if not mol:
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47 raise ValueError("Unable to read molecule")
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48
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49 return mol