Mercurial > repos > bgruening > enumerate_charges

annotate rdconf.py @ 5:67ee76f0e497 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
author bgruening
date Sat, 04 Dec 2021 16:40:23 +0000
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67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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1 #!/usr/bin/python3
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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3 import gzip
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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4 import os
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5 import sys
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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6 from optparse import OptionParser
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7
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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8 from rdkit.Chem import AllChem as Chem
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9
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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10 """
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11 This script was originally written by David Koes, University of Pittsburgh:
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12 https://github.com/dkoes/rdkit-scripts/blob/master/rdconf.py
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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13 It is licensed under the MIT licence.
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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14
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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15 Given a smiles file, generate 3D conformers in output sdf.
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16 Energy minimizes and filters conformers to meet energy window and rms constraints.
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17
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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18 Some time ago I compared this to alternative conformer generators and
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19 it was quite competitive (especially after RDKit's UFF implementation
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20 added OOP terms).
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21 """
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22
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23
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24 # convert smiles to sdf
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25 def getRMS(mol, c1, c2):
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26 rms = Chem.GetBestRMS(mol, mol, c1, c2)
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27 return rms
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28
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29
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30 parser = OptionParser(usage="Usage: %prog [options] <input>.smi <output>.sdf")
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31 parser.add_option(
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32 "--maxconfs",
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33 dest="maxconfs",
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34 action="store",
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35 help="maximum number of conformers to generate per a molecule (default 20)",
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36 default="20",
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37 type="int",
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38 metavar="CNT",
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39 )
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40 parser.add_option(
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41 "--sample_multiplier",
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42 dest="sample",
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43 action="store",
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44 help="sample N*maxconfs conformers and choose the maxconformers with lowest energy (default 1)",
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45 default="1",
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46 type="float",
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47 metavar="N",
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48 )
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49 parser.add_option(
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50 "--seed",
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51 dest="seed",
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52 action="store",
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53 help="random seed (default 9162006)",
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54 default="9162006",
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55 type="int",
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56 metavar="s",
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57 )
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58 parser.add_option(
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59 "--rms_threshold",
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60 dest="rms",
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61 action="store",
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62 help="filter based on rms (default 0.7)",
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63 default="0.7",
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64 type="float",
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65 metavar="R",
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66 )
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67 parser.add_option(
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68 "--energy_window",
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69 dest="energy",
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70 action="store",
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71 help="filter based on energy difference with lowest energy conformer",
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72 default="10",
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73 type="float",
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74 metavar="E",
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75 )
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76 parser.add_option(
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77 "-v",
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78 "--verbose",
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79 dest="verbose",
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80 action="store_true",
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81 default=False,
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82 help="verbose output",
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83 )
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84 parser.add_option(
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85 "--mmff",
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86 dest="mmff",
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87 action="store_true",
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88 default=False,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
89 help="use MMFF forcefield instead of UFF",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
90 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
91 parser.add_option(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
92 "--nomin",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
93 dest="nomin",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
94 action="store_true",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
95 default=False,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
96 help="don't perform energy minimization (bad idea)",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
97 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
98 parser.add_option(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
99 "--etkdg",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
100 dest="etkdg",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
101 action="store_true",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
102 default=False,
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
103 help="use new ETKDG knowledge-based method instead of distance geometry",
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
104 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
105
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
106
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
107 (options, args) = parser.parse_args()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
108
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
109 if len(args) < 2:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
110 parser.error("Need input and output")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
111 sys.exit(-1)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
112
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
113 input = args[0]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
114 output = args[1]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
115 smifile = open(input)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
116 if options.verbose:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
117 print("Generating a maximum of", options.maxconfs, "per a mol")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
118
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
119 if options.etkdg and not Chem.ETKDG:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
120 print("ETKDB does not appear to be implemented. Please upgrade RDKit.")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
121 sys.exit(1)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
122
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
123 split = os.path.splitext(output)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
124 if split[1] == ".gz":
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
125 outf = gzip.open(output, "wt+")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
126 output = split[0] # strip .gz
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
127 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
128 outf = open(output, "w+")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
129
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
130
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
131 if os.path.splitext(output)[1] == ".pdb":
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
132 sdwriter = Chem.PDBWriter(outf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
133 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
134 sdwriter = Chem.SDWriter(outf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
135
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
136 if sdwriter is None:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
137 print("Could not open ".output)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
138 sys.exit(-1)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
139
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
140 for line in smifile:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
141 toks = line.split()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
142 smi = toks[0]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
143 name = " ".join(toks[1:])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
144
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
145 pieces = smi.split(".")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
146 if len(pieces) > 1:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
147 smi = max(pieces, key=len) # take largest component by length
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
148 print("Taking largest component: %s\t%s" % (smi, name))
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
149
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
150 mol = Chem.MolFromSmiles(smi)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
151 if mol is not None:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
152 if options.verbose:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
153 print(smi)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
154 try:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
155 Chem.SanitizeMol(mol)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
156 mol = Chem.AddHs(mol)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
157 mol.SetProp("_Name", name)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
158
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
159 if options.etkdg:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
160 cids = Chem.EmbedMultipleConfs(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
161 mol, int(options.sample * options.maxconfs), Chem.ETKDG()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
162 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
163 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
164 cids = Chem.EmbedMultipleConfs(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
165 mol, int(options.sample * options.maxconfs), randomSeed=options.seed
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
166 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
167 if options.verbose:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
168 print(len(cids), "conformers found")
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
169 cenergy = []
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
170 for conf in cids:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
171 # not passing confID only minimizes the first conformer
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
172 if options.nomin:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
173 cenergy.append(conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
174 elif options.mmff:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
175 converged = Chem.MMFFOptimizeMolecule(mol, confId=conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
176 mp = Chem.MMFFGetMoleculeProperties(mol)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
177 cenergy.append(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
178 Chem.MMFFGetMoleculeForceField(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
179 mol, mp, confId=conf
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
180 ).CalcEnergy()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
181 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
182 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
183 converged = not Chem.UFFOptimizeMolecule(mol, confId=conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
184 cenergy.append(
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
185 Chem.UFFGetMoleculeForceField(mol, confId=conf).CalcEnergy()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
186 )
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
187 if options.verbose:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
188 print("Convergence of conformer", conf, converged)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
189
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
190 mol = Chem.RemoveHs(mol)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
191 sortedcids = sorted(cids, key=lambda cid: cenergy[cid])
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
192 if len(sortedcids) > 0:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
193 mine = cenergy[sortedcids[0]]
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
194 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
195 mine = 0
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
196 if options.rms == 0:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
197 cnt = 0
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
198 for conf in sortedcids:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
199 if cnt >= options.maxconfs:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
200 break
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
201 if (options.energy < 0) or cenergy[conf] - mine <= options.energy:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
202 sdwriter.write(mol, conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
203 cnt += 1
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
204 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
205 written = {}
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
206 for conf in sortedcids:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
207 if len(written) >= options.maxconfs:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
208 break
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
209 # check rmsd
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
210 passed = True
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
211 for seenconf in written.keys():
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
212 rms = getRMS(mol, seenconf, conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
213 if (rms < options.rms) or (
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
214 options.energy > 0 and cenergy[conf] - mine > options.energy
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
215 ):
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
216 passed = False
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
217 break
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
218 if passed:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
219 written[conf] = True
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
220 sdwriter.write(mol, conf)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
221 except (KeyboardInterrupt, SystemExit):
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
222 raise
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
223 except Exception as e:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
224 print("Exception", e)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
225 else:
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
226 print("ERROR:", smi)
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
227
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
228 sdwriter.close()
67ee76f0e497 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
bgruening
parents:
diff changeset
229 outf.close()