Mercurial > repos > bgruening > openbabel_remove_protonation_state

annotate distance_finder.py @ 14:e376ba0fcde0 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:34:01 +0000
parents b578d0c101cd
children 22a866858b81
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1 # Reports distances of ligands to reference points. An example input for the points is:
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2 #
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3 # 5.655 1.497 18.223
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4 # 1.494 -8.367 18.574
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5 # 13.034 6.306 25.232
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6 #
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7 # Data can be space or tab separated but must contain 3 and only 3 numbers for the x, y and z coordinates
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8 #
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9 # That would encode 3 points.
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10 # Each record in the SDF input is read and the closest heavy atom to each of the reference points is recorded as
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11 # a property named distance1 where the numeric part is the index (starting from 1) of the points (in that example
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12 # there would be properties for distance1, distance2 and distance3.
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13
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14 import argparse
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15 import math
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16 import sys
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18 from openbabel import pybel
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21 def log(*args, **kwargs):
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22 """Log output to STDERR
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23 """
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24 print(*args, file=sys.stderr, ** kwargs)
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27 def execute(ligands_sdf, points_file, outfile):
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28 """
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29 :param ligands_sdf: A SDF with the 3D molecules to test
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30 :param points_file: A file with the points to consider.
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31 :param outfile: The name of the file for the SDF output
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32 :return:
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33 """
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35 points = []
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37 # read the points
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38 with open(points_file, 'r') as f:
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39 for line in f.readlines():
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40 line.strip()
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41 if line:
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42 p = line.split()
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43 if len(p) == 3:
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44 points.append((float(p[0]), float(p[1]), float(p[2])))
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45 log("Read points", p)
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46 continue
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47 log("Failed to read line:", line)
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48 log('Found', len(points), 'atom points')
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49
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50 sdf_writer = pybel.Outputfile("sdf", outfile, overwrite=True)
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51
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52 count = 0
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53 for mol in pybel.readfile("sdf", ligands_sdf):
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54 count += 1
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55 if count % 50000 == 0:
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56 log('Processed', count)
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57
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58 try:
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59 # print("Processing mol", mol.title)
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60 clone = pybel.Molecule(mol)
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61 clone.removeh()
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62
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63 coords = []
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64 for atom in clone.atoms:
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65 coords.append(atom.coords)
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66
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67 p = 0
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68 for point in points:
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69 p += 1
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70 distances = []
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71 for i in coords:
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72 # calculates distance based on cartesian coordinates
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73 distance = math.sqrt((point[0] - i[0])**2 + (point[1] - i[1])**2 + (point[2] - i[2])**2)
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74 distances.append(distance)
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75 # log("distance:", distance)
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76 min_distance = min(distances)
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77 # log('Min:', min_distance)
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78 # log(count, p, min_distance)
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79
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80 mol.data['distance' + str(p)] = min_distance
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81
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82 sdf_writer.write(mol)
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83
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84 except Exception as e:
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85 log('Failed to handle molecule: ' + str(e))
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86 continue
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87
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88 sdf_writer.close()
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89 log('Wrote', count, 'molecules')
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90
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91
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92 def main():
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93 global work_dir
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94
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95 parser = argparse.ArgumentParser(description='XChem distances - measure distances to particular points')
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96 parser.add_argument('-i', '--input', help="SDF containing the 3D molecules to score)")
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97 parser.add_argument('-p', '--points', help="PDB format file with atoms")
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98 parser.add_argument('-o', '--outfile', default='output.sdf', help="File name for results")
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99
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100 args = parser.parse_args()
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101 log("XChem distances args: ", args)
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102
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103 execute(args.input, args.points, args.outfile)
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104
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105
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106 if __name__ == "__main__":
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107 main()