Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate calc_vina_box_params.py @ 4:ad35eaa204ea draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:16:17 -0400
parents 908880455b2d
children 668c60aa4799
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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
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4 import argparse
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5 from random import randint
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6
3
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7 def get_mol_from_file(fname, ftype):
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8 if ftype in ['mol', 'sdf']:
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9 mol = Chem.MolFromMolFile(options.ligand_path)
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10 elif ftype == 'pdb':
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11 mol = Chem.MolFromPDBFile(options.ligand_path)
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12 elif ftype == 'mol2':
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13 mol = Chem.MolFromMol2File(options.ligand_path)
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14 else:
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15 raise IOError
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16 if not mol:
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17 raise IOError
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18 return mol
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20 def get_params(options):
3
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21 mol = get_mol_from_file(options.ligand_path, options.ftype)
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23 # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
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24 conf = mol.GetConformer()
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25 params = rdShapeHelpers.ComputeConfBox(conf)
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27 # change tuples to arrays
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28 coords1 = np.array(params[0])
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29 coords2 = np.array(params[1])
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31 # get the centre of the box
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32 center = np.mean((coords1, coords2), axis=0)
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34 # calculate box dimensions
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35 dims = np.abs(coords1 - coords2)
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37 # optionally add buffers in each direction - expansion
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38 box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz]
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39
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40 optionalvals = ""
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43 if options.seed != None:
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44 optionalvals += "seed = " + str(options.seed) + "\n"
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45 if options.exhaustiveness != None:
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46 optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n"
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47
0
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48 with open(options.output, 'w') as f:
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49 f.write(
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50 """
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51 size_x = {}
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52 size_y = {}
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53 size_z = {}
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54 center_x = {}
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55 center_y = {}
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56 center_z = {}
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57 {}""".format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], optionalvals)
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58 )
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59
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60
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61 if __name__ == "__main__":
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62 parser = argparse.ArgumentParser(description="""
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63 This tool calculates a confounding box around an input ligand, and uses it to
0
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64 generate the input parameters for an autodock vina job. The output file can be fed into
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65 the autodock vina tool as an alternative to creating the parameter file manually.
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66
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67 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
0
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68 which will be added to the confounding box in the appropriate direction.
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69 """)
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70 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand filepath.')
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71 parser.add_argument('--ftype', dest='ftype', help='Filetype of the input ligand (mol, sdf, pdb, mol2)')
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72 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
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73 parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search')
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74 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
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75 '(float - in angs.)')
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76 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
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77 '(float - in angs.)')
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78 parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction '
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79 '(float - in angs.)')
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80 parser.add_argument('--seed', dest='seed', default=None, type=int, help='Random seed for reproducibility')
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81
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82 options = parser.parse_args()
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83 get_params(options)