# HG changeset patch # User bgruening # Date 1571389054 14400 # Node ID 908880455b2d48d7968aba31a1989e87faccc967 # Parent 73c2c9774c2d2eb98a63ed19b403923365b496e4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit deb7ad38cefd13df312431b1138054a68381efdf" diff -r 73c2c9774c2d -r 908880455b2d calc_vina_box_params.py --- a/calc_vina_box_params.py Wed Oct 02 12:49:11 2019 -0400 +++ b/calc_vina_box_params.py Fri Oct 18 04:57:34 2019 -0400 @@ -4,12 +4,21 @@ import argparse from random import randint +def get_mol_from_file(fname, ftype): + if ftype in ['mol', 'sdf']: + mol = Chem.MolFromMolFile(options.ligand_path) + elif ftype == 'pdb': + mol = Chem.MolFromPDBFile(options.ligand_path) + elif ftype == 'mol2': + mol = Chem.MolFromMol2File(options.ligand_path) + else: + raise IOError + if not mol: + raise IOError + return mol 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 + mol = get_mol_from_file(options.ligand_path, options.ftype) # get rdkit conformer and compute x,y,z of top and bottom corner of confounding cuboid conf = mol.GetConformer() @@ -51,14 +60,15 @@ if __name__ == "__main__": parser = argparse.ArgumentParser(description=""" - This tool calculates a confounding box around an input ligand (mol file), and uses it to + This tool calculates a confounding box around an input ligand, 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 Å), 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('--ligand', dest='ligand_path', help='The input ligand filepath.') + parser.add_argument('--ftype', dest='ftype', help='Filetype of the input ligand (mol, sdf, pdb, mol2)') parser.add_argument('--config', dest='output', help='The output file containing calculated params (txt)') parser.add_argument('--exh', dest='exhaustiveness', type=int, help='Exhaustiveness of global search') parser.add_argument('--bufx', dest='bufx', default=0, type=float, help='the buffer in the x direction ' diff -r 73c2c9774c2d -r 908880455b2d prepare_box.xml --- a/prepare_box.xml Wed Oct 02 12:49:11 2019 -0400 +++ b/prepare_box.xml Fri Oct 18 04:57:34 2019 -0400 @@ -1,12 +1,13 @@ - - job from an input mol file (confounding box) + + job from a ligand input file (confounding box) - rdkit + rdkit numpy - + - + - + + + + + + + + + + + + + + + + + @@ -60,10 +77,10 @@ **Description** -This tool calculates a confounding box around an input ligand (mol file), and +This tool calculates a confounding box around an input ligand 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 +The output file can be fed into the AutoDock Vina tool as an alternative to creating the parameter file manually. ----- @@ -74,7 +91,7 @@ This tool requires: -* An input ligand - This should be a mol file representing the ligand you wish to dock. This should be derived from the file you use to prepare the ligand for the docking job (see prepare ligand tool). +* An input ligand - This should be a file (MOL, SDF, PDB or MOL2 format) representing the ligand you wish to dock. * (OPTIONAL) Buffers for each direction (x,y,z), which defaults to 0 Å. This value will be added to the confounding box that the tool generates in each respective direction. We recommend that you visualise the calculated box from an initial run of this tool, and calculate the expansion needed in each direction to cover the area of the binding site you wish to explore. diff -r 73c2c9774c2d -r 908880455b2d test-data/NUDT5A-x0114_2.mol2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NUDT5A-x0114_2.mol2 Fri Oct 18 04:57:34 2019 -0400 @@ -0,0 +1,37 @@ +@MOLECULE +***** + 14 15 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 N -29.7210 5.1080 -63.9440 N.am 1 UNL1 -0.1674 + 2 C -32.1200 1.4200 -65.7380 C.3 1 UNL1 0.0031 + 3 O -32.3550 4.2720 -63.4470 O.3 1 UNL1 -0.3470 + 4 C -32.1450 2.9190 -65.4240 C.3 1 UNL1 0.0388 + 5 C -33.5610 3.5680 -65.3800 C.3 1 UNL1 0.0350 + 6 C -33.4090 4.6780 -64.3250 C.3 1 UNL1 0.1428 + 7 C -31.5300 3.2840 -64.0390 C.3 1 UNL1 0.1928 + 8 C -30.0640 3.7560 -64.2700 C.2 1 UNL1 0.2733 + 9 C -28.4710 5.7300 -64.0910 C.ar 1 UNL1 0.1429 + 10 C -28.1090 7.0310 -63.7420 C.ar 1 UNL1 0.1474 + 11 N -26.7490 7.3080 -64.0480 N.ar 1 UNL1 -0.1374 + 12 N -26.1180 6.3750 -64.5730 N.ar 1 UNL1 -0.1080 + 13 O -29.2560 2.9400 -64.7040 O.2 1 UNL1 -0.2703 + 14 S -27.0620 4.9230 -64.8090 S.2 1 UNL1 0.0542 +@BOND + 1 1 8 am + 2 1 9 1 + 3 3 6 1 + 4 3 7 1 + 5 4 2 1 + 6 4 5 1 + 7 4 7 1 + 8 5 6 1 + 9 7 8 1 + 10 8 13 2 + 11 9 10 ar + 12 9 14 ar + 13 10 11 ar + 14 11 12 ar + 15 12 14 ar diff -r 73c2c9774c2d -r 908880455b2d test-data/NUDT5A-x0114_2.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NUDT5A-x0114_2.pdb Fri Oct 18 04:57:34 2019 -0400 @@ -0,0 +1,32 @@ +COMPND UNNAMED +AUTHOR GENERATED BY OPEN BABEL 2.4.1 +HETATM 1 N UNL 1 -29.721 5.108 -63.944 1.00 0.00 N +HETATM 2 C UNL 1 -32.120 1.420 -65.738 1.00 0.00 C +HETATM 3 O UNL 1 -32.355 4.272 -63.447 1.00 0.00 O +HETATM 4 C UNL 1 -32.145 2.919 -65.424 1.00 0.00 C +HETATM 5 C UNL 1 -33.561 3.568 -65.380 1.00 0.00 C +HETATM 6 C UNL 1 -33.409 4.678 -64.325 1.00 0.00 C +HETATM 7 C UNL 1 -31.530 3.284 -64.039 1.00 0.00 C +HETATM 8 C UNL 1 -30.064 3.756 -64.270 1.00 0.00 C +HETATM 9 C UNL 1 -28.471 5.730 -64.091 1.00 0.00 C +HETATM 10 C UNL 1 -28.109 7.031 -63.742 1.00 0.00 C +HETATM 11 N UNL 1 -26.749 7.308 -64.048 1.00 0.00 N +HETATM 12 N UNL 1 -26.118 6.375 -64.573 1.00 0.00 N +HETATM 13 O UNL 1 -29.256 2.940 -64.704 1.00 0.00 O +HETATM 14 S UNL 1 -27.062 4.923 -64.809 1.00 0.00 S +CONECT 1 8 9 +CONECT 2 4 +CONECT 3 6 7 +CONECT 4 2 5 7 +CONECT 5 4 6 +CONECT 6 3 5 +CONECT 7 3 4 8 +CONECT 8 1 7 13 +CONECT 9 1 10 14 +CONECT 10 9 11 +CONECT 11 10 12 +CONECT 12 11 14 +CONECT 13 8 +CONECT 14 9 12 +MASTER 0 0 0 0 0 0 0 0 14 0 14 0 +END diff -r 73c2c9774c2d -r 908880455b2d test-data/NUDT5A-x0114_2.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NUDT5A-x0114_2.sdf Fri Oct 18 04:57:34 2019 -0400 @@ -0,0 +1,35 @@ + + OpenBabel10171911383D + + 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 0 0 0 + 1 9 1 0 0 0 0 + 3 6 1 0 0 0 0 + 3 7 1 0 0 0 0 + 4 2 1 1 0 0 0 + 4 5 1 0 0 0 0 + 4 7 1 0 0 0 0 + 5 6 1 0 0 0 0 + 7 8 1 6 0 0 0 + 8 13 2 0 0 0 0 + 9 10 2 0 0 0 0 + 9 14 1 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 + 12 14 1 0 0 0 0 +M END +$$$$