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annotate ob_spectrophore_search.py @ 15:2956017a9244 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 10:53:50 +0000
parents ad98596cf471
children
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1 #!/usr/bin/env python
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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2 """
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3 Input: tabular format file with one column storing the unique id for the compounds and any other with the Spectrophores(TM) descriptors.
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 Output: parse the target file using the same protocol used to generate the databases in our servers. Physico-chemical properties are computed and stored as metadata in the sdf output file.
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 """
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7 import argparse
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8
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9 import numpy as np
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10 from openbabel import openbabel, pybel
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12 openbabel.obErrorLog.StopLogging()
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13 # TODO get rid of eval()
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15 global spectrophore
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16 spectrophore = pybel.ob.OBSpectrophore()
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19 def parse_command_line():
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20 parser = argparse.ArgumentParser()
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21 parser.add_argument(
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22 "--target",
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23 required=True,
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24 help="target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data",
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25 )
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26 parser.add_argument(
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27 "--library",
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28 required=True,
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29 help="library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format",
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30 )
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31 parser.add_argument(
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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32 "-c",
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33 "--column",
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34 required=True,
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35 type=int,
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36 help="#column containing the Spectrophores(TM) descriptors in the library file",
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37 )
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38 parser.add_argument("-o", "--output", required=True, help="output file name")
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39 parser.add_argument(
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40 "-n",
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41 "--normalization",
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42 default="ZeroMeanAndUnitStd",
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43 choices=["No", "ZeroMean", "UnitStd", "ZeroMeanAndUnitStd"],
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44 help="Normalization method",
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45 )
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46 parser.add_argument(
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47 "-a",
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48 "--accuracy",
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49 default="20",
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50 choices=["1", "2", "5", "10", "15", "20", "30", "36", "45", "60"],
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51 help="Accuracy expressed as angular stepsize",
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52 )
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53 parser.add_argument(
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54 "-s",
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55 "--stereo",
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56 default="No",
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57 choices=["No", "Unique", "Mirror", "All"],
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58 help="Stereospecificity of the cage",
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59 )
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60 parser.add_argument(
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61 "-r", "--resolution", type=float, default="3.0", help="Resolution"
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62 )
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63 return parser.parse_args()
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64
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65
0
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66 def set_parameters(args):
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67 if args.normalization == "No":
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68 spectrophore.SetNormalization(spectrophore.NoNormalization)
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69 else:
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70 spectrophore.SetNormalization(
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71 eval("spectrophore.NormalizationTowards" + args.normalization)
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72 )
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73 spectrophore.SetAccuracy(eval("spectrophore.AngStepSize" + args.accuracy))
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74 spectrophore.SetStereo(eval("spectrophore." + args.stereo + "StereoSpecificProbes"))
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75 spectrophore.SetResolution(args.resolution)
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76 return True
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77
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78
0
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79 def Compute_Spectrophores_distance(target_spectrophore, args):
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80 outfile = open(args.output, "w")
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81 for mol in open(args.library, "r"):
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82 try:
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83 distance = (
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84 (
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85 np.asarray(target_spectrophore, dtype=float)
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86 - np.asarray(
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87 mol.split("\t")[args.column - 1].strip().split(", "),
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88 dtype=float,
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89 )
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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90 )
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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91 ** 2
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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92 ).sum()
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93 except ValueError:
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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94 distance = 0
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95 outfile.write("%s\t%f\n" % (mol.strip(), distance))
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96 outfile.close()
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97
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98
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99 def __main__():
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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100 """
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101 Computation of Spectrophores(TM) distances to a target molecule.
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102 """
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103 args = parse_command_line()
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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104 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool
6f511affb852 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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105 set_parameters(args)
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106
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107 mol = next(pybel.readfile("sdf", args.target))
2956017a9244 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
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108 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(", ")
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109 # Compute the paired-distance between every molecule in the library and the target
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110 Compute_Spectrophores_distance(target_spectrophore, args)
ad98596cf471 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
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111
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112
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113 if __name__ == "__main__":
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114 __main__()