Mercurial > repos > bgruening > autodock_vina_prepare_box

annotate calc_vina_box_params.py @ 5:668c60aa4799 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
author bgruening
date Thu, 22 Jul 2021 14:04:57 +0000
parents 908880455b2d
children
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5
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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diff changeset
1 import argparse
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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3 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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4 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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5 from rdkit.Chem import rdShapeHelpers
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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7
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8 def get_mol_from_file(fname, ftype):
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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9 if ftype in ["mol", "sdf"]:
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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10 mol = Chem.MolFromMolFile(options.ligand_path, strictParsing=False, sanitize=False)
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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11 elif ftype == "pdb":
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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12 mol = Chem.MolFromPDBFile(options.ligand_path, sanitize=False)
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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13 elif ftype == "mol2":
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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14 mol = Chem.MolFromMol2File(options.ligand_path, sanitize=False)
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15 else:
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16 raise IOError
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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17 if not mol:
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18 raise IOError
908880455b2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
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19 return mol
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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21
0
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22 def get_params(options):
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23 mol = get_mol_from_file(options.ligand_path, options.ftype)
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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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25 # 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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26 conf = mol.GetConformer()
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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27 params = rdShapeHelpers.ComputeConfBox(conf)
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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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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29 # change tuples to arrays
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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30 coords1 = np.array(params[0])
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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31 coords2 = np.array(params[1])
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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32
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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33 # get the centre of the box
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34 center = np.mean((coords1, coords2), axis=0)
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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35
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36 # calculate box dimensions
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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37 dims = np.abs(coords1 - coords2)
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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38
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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39 # 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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40 box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz]
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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41
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42 optionalvals = ""
73c2c9774c2d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ef86cfa5f7ab5043de420511211579d03df58645"
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43
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44 if options.seed is not None:
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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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45 optionalvals += "seed = " + str(options.seed) + "\n"
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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46 if options.exhaustiveness is not None:
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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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47 optionalvals += "exhaustiveness = " + str(options.exhaustiveness) + "\n"
1
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48
5
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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49 with open(options.output, "w") as f:
0
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50 f.write(
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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51 """
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52 size_x = {}
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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53 size_y = {}
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54 size_z = {}
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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55 center_x = {}
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56 center_y = {}
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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57 center_z = {}
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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58 {}""".format(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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59 box_dims[0],
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60 box_dims[1],
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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61 box_dims[2],
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62 center[0],
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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63 center[1],
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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64 center[2],
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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65 optionalvals,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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66 )
0
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67 )
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
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68
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69
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70 if __name__ == "__main__":
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71 parser = argparse.ArgumentParser(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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72 description="""
3
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73 This tool calculates a confounding box around an input ligand, and uses it to
0
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74 generate the input parameters for an autodock vina job. The output file can be fed into
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668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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75 the autodock vina tool as an alternative to creating the parameter file manually.
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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76
1
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77 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
0
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78 which will be added to the confounding box in the appropriate direction.
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79 """
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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80 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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81 parser.add_argument(
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82 "--ligand", dest="ligand_path", help="The input ligand filepath."
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83 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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84 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
85 "--ftype",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
86 dest="ftype",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
87 help="Filetype of the input ligand (mol, sdf, pdb, mol2)",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
88 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
89 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
90 "--config",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
91 dest="output",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
92 help="The output file containing calculated params (txt)",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
93 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
94 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
95 "--exh", dest="exhaustiveness", type=int, help="Exhaustiveness of global search"
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
96 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
97 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
98 "--bufx",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
99 dest="bufx",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
100 default=0,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
101 type=float,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
102 help="the buffer in the x direction " "(float - in angs.)",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
103 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
104 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
105 "--bufy",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
106 dest="bufy",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
107 default=0,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
108 type=float,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
109 help="the buffer in the y direction " "(float - in angs.)",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
110 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
111 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
112 "--bufz",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
113 dest="bufz",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
114 default=0,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
115 type=float,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
116 help="the buffer in the z direction " "(float - in angs.)",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
117 )
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
118 parser.add_argument(
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
119 "--seed",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
120 dest="seed",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
121 default=None,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
122 type=int,
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
123 help="Random seed for reproducibility",
668c60aa4799 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents: 3
diff changeset
124 )
0
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
bgruening
parents:
diff changeset
125
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
bgruening
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diff changeset
126 options = parser.parse_args()
761762031eee planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
bgruening
parents:
diff changeset
127 get_params(options)