Mercurial > repos > bgruening > autodock_vina_prepare_box
changeset 0:255b6b88be7c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit a657ca32e9a470d710e483e9c3c2706726bec9a3
| author | bgruening |
|---|---|
| date | Wed, 17 Apr 2019 09:10:38 -0400 |
| parents | |
| children | d965076a0cd2 |
| files | calc_vina_box_params.py prepare_box.xml test-data/NUDT5A-x0114_2.mol test-data/box_params.txt |
| diffstat | 4 files changed, 218 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/calc_vina_box_params.py Wed Apr 17 09:10:38 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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/prepare_box.xml Wed Apr 17 09:10:38 2019 -0400 @@ -0,0 +1,102 @@ +<tool id="prepare_box" name="Calculate the box parameters for an AutoDock Vina" version="0.1.0"> + <description>job from an input mol file (confounding box)</description> + <requirements> + <requirement type="package" version="2019.03.1.0">rdkit</requirement> + <requirement type="package" version="1.16.2">numpy</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/calc_vina_box_params.py' + --ligand '$input1' + --config '$output1' + --bufx '$bufx' + --bufy '$bufy' + --bufz '$bufz' + --exh '$exh' + ]]></command> + <inputs> + <param type="data" name="input1" format="mol" label="input ligand mol file" + help="The input ligand (mol file)"/> + <param name="bufx" type="float" value="0" label="x-axis buffer" + help="the buffer in the x direction (in angs.)"/> + <param name="bufy" type="float" value="0" label="y-axis buffer" + help="the buffer in the y direction (in angs.)"/> + <param name="bufz" type="float" value="0" label="z-axis buffer" + help="the buffer in the z direction (in angs.)"/> + <param name="exh" type="integer" value="0" label="exhaustiveness" + help="The number of poses to return from docking job"/> + </inputs> + <outputs> + <data name="output1" format="txt" /> + </outputs> + <tests> + <test> + <param name="input1" value="NUDT5A-x0114_2.mol" /> + <param name="bufx" value="1" /> + <param name="bufy" value="2" /> + <param name="bufz" value="3" /> + <param name="exh" value="10" /> + <output name="output1" file="box_params.txt" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**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. + +----- +.. class:: infomark + +**Inputs:** + +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). + +* OPTIONAL Buffers for each direction (x,y,z), which defaults to 0 angstroms. 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. + +----- +.. class:: infomark + +**Output:** + +The output for this tool is a txt file containing the parameters needed to run an autodock +vina docking calculation with the docking tool. For example: + +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 + +The values for num_modes, energy range, cpu and seed are set to default values here. + +This file can be used as the box parameter for the docking tool. + + ]]></help> + <citations> + <citation type="bibtex"> + @article{rdkit, + author = {Greg Landrum}, + title = {RDKit: Open-source cheminformatics}, + url ={http://www.rdkit.org} + }</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NUDT5A-x0114_2.mol Wed Apr 17 09:10:38 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/box_params.txt Wed Apr 17 09:10:38 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