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annotate utils.py @ 6:b24259b0b48b draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
author bgruening
date Wed, 14 Apr 2021 09:29:36 +0000
parents 1f19b95adc5c
children
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1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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1 #!/usr/bin/env python
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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2 """
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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3 Utility functions for SuCOS and other RDKit modules
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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4 """
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1f19b95adc5c "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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b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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8 import gzip
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9 import sys
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11 from rdkit import Chem
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1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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14 def log(*args, **kwargs):
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15 """Log output to STDERR"""
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16 print(*args, file=sys.stderr, **kwargs)
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19 def open_file_for_reading(filename):
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20 """Open the file gunzipping it if it ends with .gz."""
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21 if filename.lower().endswith(".gz"):
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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22 return gzip.open(filename, "rb")
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23 else:
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24 return open(filename, "rb")
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27 def open_file_for_writing(filename):
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28 if filename.lower().endswith(".gz"):
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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29 return gzip.open(filename, "at")
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30 else:
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31 return open(filename, "w+")
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1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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34 def read_single_molecule(filename, index=1, format=None):
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 """Read a single molecule as a RDKit Mol object. This can come from a file in molfile or SDF format.
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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36 If SDF then you can also specify an index of the molecule that is read (default is the first)
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37 """
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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38 mol = None
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39 if (
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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40 format == "mol"
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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41 or filename.lower().endswith(".mol")
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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42 or filename.lower().endswith(".mol.gz")
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43 ):
0
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44 file = open_file_for_reading(filename)
1f19b95adc5c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit ef86cfa5f7ab5043de420511211579d03df58645"
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45 mol = Chem.MolFromMolBlock(file.read())
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46 file.close()
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47 elif (
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48 format == "sdf"
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49 or filename.lower().endswith(".sdf")
b24259b0b48b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/sucos commit 05dc325ce687441e5d3bdbdedcc0e3529cd5e070"
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50 or filename.lower().endswith(".sdf.gz")
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51 ):
0
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52 file = open_file_for_reading(filename)
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53 supplier = Chem.ForwardSDMolSupplier(file)
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54 for i in range(0, index):
0
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55 if supplier.atEnd():
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56 break
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57 mol = next(supplier)
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58 file.close()
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59
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60 if not mol:
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61 raise ValueError("Unable to read molecule")
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62
6
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63 return mol