Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate 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
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761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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1 import numpy as np
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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2 from rdkit import Chem
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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3 from rdkit.Chem import rdShapeHelpers
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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4 import argparse
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5 from random import randint
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8 def get_params(options):
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9 # make sure we have a mol file by initiating rdkit mol object from input
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10 mol = Chem.MolFromMolFile(options.ligand_path)
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11 if not mol:
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12 raise IOError
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761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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14 # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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15 conf = mol.GetConformer()
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16 params = rdShapeHelpers.ComputeConfBox(conf)
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18 # change tuples to arrays
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19 coords1 = np.array(params[0])
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20 coords2 = np.array(params[1])
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22 # get the centre of the box
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23 center = np.mean((coords1, coords2), axis=0)
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25 # calculate box dimensions
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26 dims = np.abs(coords1 - coords2)
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28 # optionally add buffers in each direction - expansion
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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29 box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz]
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31 optionalvals = ""
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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34 if options.seed != None:
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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35 optionalvals += "seed = " + str(options.seed) + "\n"
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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36 if options.exhaustiveness != None:
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37 optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n"
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38
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39 with open(options.output, 'w') as f:
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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40 f.write(
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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41 """
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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42 size_x = {}
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43 size_y = {}
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44 size_z = {}
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45 center_x = {}
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46 center_y = {}
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47 center_z = {}
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48 {}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], optionalvals)
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49 )
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52 if __name__ == "__main__":
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53 parser = argparse.ArgumentParser(description="""
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54 This tool calculates a confounding box around an input ligand (mol file), and uses it to
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55 generate the input parameters for an autodock vina job. The output file can be fed into
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56 the autodock vina tool as an alternative to creating the parameter file manually.
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57
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58 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
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59 which will be added to the confounding box in the appropriate direction.
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60 """)
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61 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)')
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62 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
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73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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63 parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search')
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64 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
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65 '(float - in angs.)')
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66 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
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67 '(float - in angs.)')
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68 parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction '
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69 '(float - in angs.)')
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70 parser.add_argument('--seed', dest='seed', default=None, type=int, help='Random seed for reproducibility')
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72 options = parser.parse_args()
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73 get_params(options)