# HG changeset patch # User bgruening # Date 1555506661 14400 # Node ID 761762031eee16c2568d19b2ce73b0862dbd4a16 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3 diff -r 000000000000 -r 761762031eee calc_vina_box_params.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/calc_vina_box_params.py Wed Apr 17 09:11:01 2019 -0400 @@ -0,0 +1,69 @@ +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) diff -r 000000000000 -r 761762031eee prepare_box.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_box.xml Wed Apr 17 09:11:01 2019 -0400 @@ -0,0 +1,102 @@ + + job from an input mol file (confounding box) + + rdkit + numpy + + + + + + + + + + + + + + + + + + + + + + + + + + @article{rdkit, + author = {Greg Landrum}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + } + + diff -r 000000000000 -r 761762031eee test-data/NUDT5A-x0114_2.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NUDT5A-x0114_2.mol Wed Apr 17 09:11:01 2019 -0400 @@ -0,0 +1,34 @@ + + RDKit 3D + + 14 15 0 0 0 0 0 0 0 0999 V2000 + -29.7210 5.1080 -63.9440 N 0 0 0 0 0 0 0 0 0 0 0 0 + -32.1200 1.4200 -65.7380 C 0 0 0 0 0 0 0 0 0 0 0 0 + -32.3550 4.2720 -63.4470 O 0 0 0 0 0 0 0 0 0 0 0 0 + -32.1450 2.9190 -65.4240 C 0 0 1 0 0 0 0 0 0 0 0 0 + -33.5610 3.5680 -65.3800 C 0 0 0 0 0 0 0 0 0 0 0 0 + -33.4090 4.6780 -64.3250 C 0 0 0 0 0 0 0 0 0 0 0 0 + -31.5300 3.2840 -64.0390 C 0 0 1 0 0 0 0 0 0 0 0 0 + -30.0640 3.7560 -64.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 + -28.4710 5.7300 -64.0910 C 0 0 0 0 0 0 0 0 0 0 0 0 + -28.1090 7.0310 -63.7420 C 0 0 0 0 0 0 0 0 0 0 0 0 + -26.7490 7.3080 -64.0480 N 0 0 0 0 0 0 0 0 0 0 0 0 + -26.1180 6.3750 -64.5730 N 0 0 0 0 0 0 0 0 0 0 0 0 + -29.2560 2.9400 -64.7040 O 0 0 0 0 0 0 0 0 0 0 0 0 + -27.0620 4.9230 -64.8090 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1 8 1 0 + 1 9 1 0 + 3 6 1 0 + 3 7 1 0 + 4 2 1 1 + 4 5 1 0 + 4 7 1 0 + 5 6 1 0 + 7 8 1 6 + 8 13 2 0 + 9 10 2 0 + 9 14 1 0 + 10 11 1 0 + 11 12 2 0 + 12 14 1 0 +M END diff -r 000000000000 -r 761762031eee test-data/box_params.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/box_params.txt Wed Apr 17 09:11:01 2019 -0400 @@ -0,0 +1,13 @@ + +size_x = 12.443000000000001 +size_y = 11.888 +size_z = 9.290999999999997 +center_x = -29.8395 +center_y = 4.364 +center_z = -64.5925 +num_modes = 9999 +energy_range = 9999 +exhaustiveness = 10 +cpu = 4 +seed = 1 + \ No newline at end of file