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annotate cheminfolib.py @ 15:9adf3fae2771 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:04:41 +0000
parents bd678d7db2ae
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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1 #!/usr/bin/env python
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
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2 """
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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3 Small library with cheminformatic functions based on openbabel and pgchem.
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Copyright 2012, Bjoern Gruening and Xavier Lucas
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 """
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6
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bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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7 import glob
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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8 import re
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
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9 import subprocess
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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10 import sys
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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11 import tempfile
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
bgruening
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12 from multiprocessing import Pool
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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13
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 try:
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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15 from galaxy import eggs
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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16
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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17 eggs.require("psycopg2")
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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18 except ImportError:
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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19 psycopg2 = None
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
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20 print(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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21 "psycopg2 is not available. It is currently used in the pgchem wrappers, that are not shipped with default CTB"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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22 )
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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23
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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24 try:
12
171c94786a56 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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25 from openbabel import openbabel, pybel
15
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26
12
171c94786a56 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
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27 openbabel.obErrorLog.StopLogging()
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bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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28 except ImportError:
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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29 openbabel, pybel = None, None
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9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
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30 print(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
bgruening
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31 "OpenBabel could not be found. A few functions are not available without OpenBabel."
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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32 )
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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34
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bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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35 def CountLines(path):
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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36 out = subprocess.Popen(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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37 ["wc", "-l", path], stdout=subprocess.PIPE, stderr=subprocess.STDOUT
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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38 ).communicate()[0]
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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39 return int(out.partition(b" ")[0])
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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40
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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41
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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42 def grep(pattern, file_obj):
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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43 grepper = re.compile(pattern)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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44 for line in file_obj:
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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45 if grepper.search(line):
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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46 return True
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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47 return False
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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48
13
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49
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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50 def check_filetype(filepath):
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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51 mol = False
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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52 possible_inchi = True
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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53 for line_counter, line in enumerate(open(filepath)):
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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54 if line_counter > 10000:
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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55 break
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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56 if line.find("$$$$") != -1:
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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57 return "sdf"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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58 elif line.find("@<TRIPOS>MOLECULE") != -1:
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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59 return "mol2"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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60 elif line.find("ligand id") != -1:
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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61 return "drf"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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62 elif possible_inchi and re.findall("^InChI=", line):
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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63 return "inchi"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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64 elif re.findall(r"^M\s+END", line):
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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65 mol = True
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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66 # first line is not an InChI, so it can't be an InChI file
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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67 possible_inchi = False
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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68
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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69 if mol:
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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70 # END can occures before $$$$, so and SDF file will
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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71 # be recognised as mol, if you not using this hack'
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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72 return "mol"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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73 return "smi"
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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74
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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75
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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76 def db_connect(args):
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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77 try:
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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78 db_conn = psycopg2.connect(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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79 "dbname=%s user=%s host=%s password=%s"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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80 % (args.dbname, args.dbuser, args.dbhost, args.dbpasswd)
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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81 )
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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82 return db_conn
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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83 except psycopg2.Error:
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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84 sys.exit("Unable to connect to the db")
0
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85
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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86
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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87 ColumnNames = {
15
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88 "can_smiles": "Canonical SMILES",
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89 "can": "Canonical SMILES",
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90 "inchi": "InChI",
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91 "inchi_key": "InChI key",
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92 "inchi_key_first": "InChI key first",
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93 "inchi_key_last": "InChI key last",
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94 "molwt": "Molecular weight",
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95 "hbd": "Hydrogen-bond donors",
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96 "donors": "Hydrogen-bond donors",
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97 "hba": "Hydrogen-bond acceptors",
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98 "acceptors": "Hydrogen-bond acceptors",
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99 "rotbonds": "Rotatable bonds",
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100 "logp": "logP",
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101 "psa": "Polar surface area",
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102 "mr": "Molecular refractivity",
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103 "atoms": "Number of heavy atoms",
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104 "rings": "Number of rings",
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105 "set_bits": "FP2 bits",
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106 "id": "Internal identifier",
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107 "tani": "Tanimoto coefficient",
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108 "spectrophore": "Spectrophores(TM)",
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109 "dist_spectrophore": "Spectrophores(TM) distance to target",
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110 "synonym": "Entry id",
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111 }
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112
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113 OBDescriptor = {
15
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114 "atoms": ["atoms", "Number of atoms"],
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115 "hatoms": [
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116 "hatoms",
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117 "Number of heavy atoms",
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118 ], # self defined tag hatoms in plugindefines.txt
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119 "can_smiles": ["cansmi", "Canonical SMILES"],
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120 "can_smilesNS": ["cansmiNS", "Canonical SMILES without isotopes or stereo"],
13
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121 # ["abonds", "Number of aromatic bonds"],
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122 # ["bonds", "Number of bonds"],
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123 # ["dbonds", "Number of double bonds"],
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124 # ["formula", "Chemical formula"],
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125 "hba": ["HBA1", "Number of Hydrogen Bond Acceptors 1 (JoelLib)"],
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126 "hba2": ["HBA2", "Number of Hydrogen Bond Acceptors 2 (JoelLib)"],
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127 "hbd": ["HBD", "Number of Hydrogen Bond Donors (JoelLib)"],
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128 "inchi": ["InChI", "IUPAC InChI identifier"],
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129 "inchi_key": ["InChIKey", "InChIKey"],
13
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130 # ["L5", "Lipinski Rule of Five"],
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131 "logp": ["logP", "octanol/water partition coefficient"],
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132 "mr": ["MR", "molar refractivity"],
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133 "molwt": ["MW", "Molecular Weight filter"],
13
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134 # ["nF", "Number of Fluorine Atoms"],
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135 # ["s", "SMARTS filter"],
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136 # ["sbonds", "Number of single bonds"],
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137 # ["smarts", "SMARTS filter"],
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138 # ["tbonds", "Number of triple bonds"],
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139 # ["title", "For comparing a molecule's title"],
15
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140 "psa": ["TPSA", "topological polar surface area"],
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141 "rotbonds": ["ROTATABLE_BOND", "rotatable bonds"],
0
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142 }
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143
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144
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145 def print_output(args, rows):
15
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146 if args.oformat == "table":
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147 outfile = open(args.output, "w")
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148 requested_fields = (
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149 filter(lambda x: x not in ["[", "]", "'"], args.fetch)
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150 ).split(", ")
0
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151 if args.header:
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152 outfile.write(
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153 "Identifier\t"
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154 + "\t".join([ColumnNames[key] for key in requested_fields])
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155 + "\n"
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156 )
0
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157 for row in rows:
15
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158 outfile.write(
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159 row["synonym"]
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160 + "\t"
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161 + "\t".join([str(row[key]) for key in requested_fields])
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162 + "\n"
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163 )
0
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164
15
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165 elif args.oformat in ["sdf", "mol2"]:
0
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166 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
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167 for row in rows:
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168 try:
15
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169 mol = pybel.readstring("sdf", row["mol"])
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170 if args.oformat == "sdf":
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171 keys = filter(lambda x: x not in ["[", "]", "'"], args.fetch).split(
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172 ", "
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173 )
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174 mol.data.update({ColumnNames["synonym"]: row["synonym"]})
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175 if "inchi_key" in keys:
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176 keys = (
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177 ", ".join(keys).replace(
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178 "inchi_key", "inchi_key_first, inchi_key_last"
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179 )
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180 ).split(", ")
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181 [
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182 mol.data.update({ColumnNames[key]: row[key]})
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183 for key in keys
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184 if key
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185 ]
0
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186 outfile.write(mol)
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187 except OSError:
0
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188 pass
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189 else:
15
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190 outfile = open(args.output, "w")
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191 outfile.write(
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192 "\n".join(["%s\t%s" % (row[args.oformat], row["synonym"]) for row in rows])
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193 )
0
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194 outfile.close()
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195
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196
0
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197 def pybel_stop_logging():
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198 openbabel.obErrorLog.StopLogging()
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199
13
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200
0
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201 def get_properties_ext(mol):
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202 HBD = pybel.Smarts("[!#6;!H0]")
15
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203 HBA = pybel.Smarts(
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204 (
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205 "[$([$([#8,#16]);!$(*=N~O);"
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206 "!$(*~N=O);X1,X2]),$([#7;v3;"
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207 "!$([nH]);!$(*(-a)-a)])]"
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208 )
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209 )
0
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210 calc_desc_dict = mol.calcdesc()
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211
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212 try:
15
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213 logp = calc_desc_dict["logP"]
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214 except KeyError:
15
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215 logp = calc_desc_dict["LogP"]
0
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216
15
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217 return {
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218 "molwt": mol.molwt,
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219 "logp": logp,
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220 "donors": len(HBD.findall(mol)),
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221 "acceptors": len(HBA.findall(mol)),
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222 "psa": calc_desc_dict["TPSA"],
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223 "mr": calc_desc_dict["MR"],
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224 "rotbonds": mol.OBMol.NumRotors(),
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225 "can": mol.write("can")
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226 .split()[0]
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227 .strip(), # tthis one works fine for both zinc and chembl (no ZINC code added after can descriptor string)
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228 "inchi": mol.write("inchi").strip(),
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229 "inchi_key": get_inchikey(mol).strip(),
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230 "rings": len(mol.sssr),
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231 "atoms": mol.OBMol.NumHvyAtoms(),
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232 "spectrophore": OBspectrophore(mol),
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233 }
13
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234
0
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235
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236 def get_inchikey(mol):
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237 conv = openbabel.OBConversion()
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238 conv.SetInAndOutFormats("mol", "inchi")
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239 conv.SetOptions("K", conv.OUTOPTIONS)
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240 inchikey = conv.WriteString(mol.OBMol)
0
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241 return inchikey
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242
13
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243
0
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244 def OBspectrophore(mol):
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245 spectrophore = pybel.ob.OBSpectrophore()
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246 # Parameters: rotation angle = 20, normalization for mean and sd, accuracy = 3.0 A and non-stereospecific cages.
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247 spectrophore.SetNormalization(spectrophore.NormalizationTowardsZeroMeanAndUnitStd)
15
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248 return ", ".join(
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249 ["%.3f" % value for value in spectrophore.GetSpectrophore(mol.OBMol)]
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250 )
13
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251
0
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252
15
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253 def split_library(lib_path, lib_format="sdf", package_size=None):
0
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254 """
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255 Split a library of compounds. Usage: split_library(lib_path, lib_format, package_size)
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256 IT currently ONLY WORKS FOR SD-Files
0
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257 """
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258 pack = 1
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259 mol_counter = 0
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260
15
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261 outfile = open(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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262 "/%s/%s_pack_%i.%s"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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263 % (
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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264 "/".join(lib_path.split("/")[:-1]),
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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265 lib_path.split("/")[-1].split(".")[0],
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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266 pack,
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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267 "sdf",
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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268 ),
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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269 "w",
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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270 )
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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271
15
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272 for line in open(lib_path, "r"):
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273 outfile.write(line)
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274 if line.strip() == "$$$$":
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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275 mol_counter += 1
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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276 if mol_counter % package_size == 0:
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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277 outfile.close()
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278 pack += 1
15
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279 outfile = open(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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280 "/%s/%s_pack_%i.%s"
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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281 % (
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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282 "/".join(lib_path.split("/")[:-1]),
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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283 lib_path.split("/")[-1].split(".")[0],
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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284 pack,
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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285 "sdf",
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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286 ),
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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287 "w",
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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288 )
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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289 if mol_counter * 10 % package_size == 0:
15
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290 print(
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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291 "%i molecules parsed, starting pack nr. %i"
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292 % (mol_counter, pack - 1)
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293 )
0
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294 outfile.close()
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295
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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296 return True
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297
13
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298
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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299 def split_smi_library(smiles_file, structures_in_one_file):
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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300 """
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301 Split a file with SMILES to several files for multiprocessing usage.
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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302 Usage: split_smi_library(smiles_file, 10)
0
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303 """
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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304 output_files = []
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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305 tfile = tempfile.NamedTemporaryFile(delete=False)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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306
15
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307 smiles_handle = open(smiles_file, "r")
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308 for count, line in enumerate(smiles_handle):
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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309 if count % structures_in_one_file == 0 and count != 0:
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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310 tfile.close()
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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311 output_files.append(tfile.name)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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312 tfile = tempfile.NamedTemporaryFile(delete=False)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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313 tfile.write(line)
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314 tfile.close()
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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315 output_files.append(tfile.name)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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316 smiles_handle.close()
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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317 return output_files
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318
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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319
13
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320 def mp_run(input_path, regex, PROCESSES, function_to_call):
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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321 paths = []
15
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322 [
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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323 paths.append(compound_file)
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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324 for compound_file in glob.glob(str(input_path) + str(regex))
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325 ]
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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326 paths.sort()
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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327
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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328 pool = Pool(processes=PROCESSES)
15
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329 print("Process initialized with", PROCESSES, "processors")
0
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330 result = pool.map_async(function_to_call, paths)
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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331 result.get()
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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332
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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333 return paths
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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334
13
bd678d7db2ae "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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diff changeset
335
15
9adf3fae2771 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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diff changeset
336 if __name__ == "__main__":
0
98e12cc1f3a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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337 print(check_filetype(sys.argv[1]))