Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison calc_vina_box_params.py @ 2:73c2c9774c2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
author bgruening
date Wed, 02 Oct 2019 12:49:11 -0400
parents 4f7c5cad3377
children 908880455b2d
comparison
equal deleted inserted replaced
1:4f7c5cad3377 2:73c2c9774c2d
26 dims = np.abs(coords1 - coords2) 26 dims = np.abs(coords1 - coords2)
27 27
28 # optionally add buffers in each direction - expansion 28 # optionally add buffers in each direction - expansion
29 box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz] 29 box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz]
30 30
31 # if no seed set, then randomly generate one between 0 and 2**31 31 optionalvals = ""
32 if options.seed == None: 32
33 options.seed = randint(0, 2147483647) 33
34 if options.seed != None:
35 optionalvals += "seed = " + str(options.seed) + "\n"
36 if options.exhaustiveness != None:
37 optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n"
34 38
35 with open(options.output, 'w') as f: 39 with open(options.output, 'w') as f:
36 f.write( 40 f.write(
37 """ 41 """
38 size_x = {} 42 size_x = {}
39 size_y = {} 43 size_y = {}
40 size_z = {} 44 size_z = {}
41 center_x = {} 45 center_x = {}
42 center_y = {} 46 center_y = {}
43 center_z = {} 47 center_z = {}
44 num_modes = 9999 48 {}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], optionalvals)
45 energy_range = 9999
46 exhaustiveness = {}
47 cpu = 4
48 seed = {}
49 """.format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], options.exhaustiveness, options.seed)
50 ) 49 )
51 50
52 51
53 if __name__ == "__main__": 52 if __name__ == "__main__":
54 parser = argparse.ArgumentParser(description=""" 53 parser = argparse.ArgumentParser(description="""
59 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å), 58 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
60 which will be added to the confounding box in the appropriate direction. 59 which will be added to the confounding box in the appropriate direction.
61 """) 60 """)
62 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)') 61 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)')
63 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)') 62 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
64 parser.add_argument('--exh', dest='exhaustiveness', default=10, type=int, help='The number of poses ' 63 parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search')
65 'to return from docking job')
66 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction ' 64 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
67 '(float - in angs.)') 65 '(float - in angs.)')
68 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction ' 66 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
69 '(float - in angs.)') 67 '(float - in angs.)')
70 parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction ' 68 parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction '