Mercurial > repos > bgruening > autodock_vina_prepare_box

comparison calc_vina_box_params.py @ 3:908880455b2d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf"
author bgruening
date Fri, 18 Oct 2019 04:57:34 -0400
parents 73c2c9774c2d
children 668c60aa4799
comparison
equal deleted inserted replaced
2:73c2c9774c2d 3:908880455b2d
2 from rdkit import Chem 2 from rdkit import Chem
3 from rdkit.Chem import rdShapeHelpers 3 from rdkit.Chem import rdShapeHelpers
4 import argparse 4 import argparse
5 from random import randint 5 from random import randint
6 6
7 def get_mol_from_file(fname, ftype):
8 if ftype in ['mol', 'sdf']:
9 mol = Chem.MolFromMolFile(options.ligand_path)
10 elif ftype == 'pdb':
11 mol = Chem.MolFromPDBFile(options.ligand_path)
12 elif ftype == 'mol2':
13 mol = Chem.MolFromMol2File(options.ligand_path)
14 else:
15 raise IOError
16 if not mol:
17 raise IOError
18 return mol
7 19
8 def get_params(options): 20 def get_params(options):
9 # make sure we have a mol file by initiating rdkit mol object from input 21 mol = get_mol_from_file(options.ligand_path, options.ftype)
10 mol = Chem.MolFromMolFile(options.ligand_path)
11 if not mol:
12 raise IOError
13 22
14 # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid 23 # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
15 conf = mol.GetConformer() 24 conf = mol.GetConformer()
16 params = rdShapeHelpers.ComputeConfBox(conf) 25 params = rdShapeHelpers.ComputeConfBox(conf)
17 26
49 ) 58 )
50 59
51 60
52 if __name__ == "__main__": 61 if __name__ == "__main__":
53 parser = argparse.ArgumentParser(description=""" 62 parser = argparse.ArgumentParser(description="""
54 This tool calculates a confounding box around an input ligand (mol file), and uses it to 63 This tool calculates a confounding box around an input ligand, and uses it to
55 generate the input parameters for an autodock vina job. The output file can be fed into 64 generate the input parameters for an autodock vina job. The output file can be fed into
56 the autodock vina tool as an alternative to creating the parameter file manually. 65 the autodock vina tool as an alternative to creating the parameter file manually.
57 66
58 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å), 67 Optionally, you can include a 'buffer' in each of the x,y and z directions (in Å),
59 which will be added to the confounding box in the appropriate direction. 68 which will be added to the confounding box in the appropriate direction.
60 """) 69 """)
61 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)') 70 parser.add_argument('--ligand', dest='ligand_path', help='The input ligand filepath.')
71 parser.add_argument('--ftype', dest='ftype', help='Filetype of the input ligand (mol, sdf, pdb, mol2)')
62 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)') 72 parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
63 parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search') 73 parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search')
64 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction ' 74 parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
65 '(float - in angs.)') 75 '(float - in angs.)')
66 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction ' 76 parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '