view calc_vina_box_params.py @ 0:255b6b88be7c draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3

import numpy as np
from rdkit import Chem
from rdkit.Chem import rdShapeHelpers
import argparse


def get_params(options):
    # make sure we have a mol file by initiating rdkit mol object from input
    mol = Chem.MolFromMolFile(options.ligand_path)
    if not mol:
        raise IOError

    # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid
    conf = mol.GetConformer()
    params = rdShapeHelpers.ComputeConfBox(conf)

    # change tuples to arrays
    coords1 = np.array(params[0])
    coords2 = np.array(params[1])

    # get the centre of the box
    center = np.mean((coords1, coords2), axis=0)

    # calculate box dimensions
    dims = np.abs(coords1 - coords2)

    # optionally add buffers in each direction - expansion
    box_dims = [dims[0] + options.bufx, dims[1] + options.bufy, dims[2] + options.bufz]

    with open(options.output, 'w') as f:
        f.write(
            """
size_x =  {}
size_y =  {}
size_z =  {}
center_x =  {}
center_y =  {}
center_z =  {}
num_modes = 9999
energy_range = 9999
exhaustiveness = {}
cpu = 4
seed = 1
            """.format(box_dims[0], box_dims[1], box_dims[2], center[0], center[1], center[2], options.exhaustiveness)
        )


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="""
    This tool calculates a confounding box around an input ligand (mol file), and uses it to
    generate the input parameters for an autodock vina job. The output file can be fed into
    the autodock vina tool as an alternative to creating the parameter file manually. 
    
    Optionally, you can include a 'buffer' in each of the x,y and z directions (in angstroms),
    which will be added to the confounding box in the appropriate direction.
    """)
    parser.add_argument('--ligand', dest='ligand_path', help='The input ligand (mol file)')
    parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)')
    parser.add_argument('--exh', dest='exhaustiveness', default=10, type=int, help='The number of poses '
                                                                                     'to return from docking job')
    parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction '
                                                                           '(float - in angs.)')
    parser.add_argument('--bufy', dest='bufy', default=0, type=float, help='the buffer in the y direction '
                                                                           '(float - in angs.)')
    parser.add_argument('--bufz', dest='bufz', default=0, type=float, help='the buffer in the z direction '
                                                                           '(float - in angs.)')

    options = parser.parse_args()
    get_params(options)