From bddf020a336c66e9bf2d5fbc366f5489290d6798 Mon Sep 17 00:00:00 2001 From: Nazanin Donyapour Date: Mon, 25 Mar 2024 16:38:07 -0400 Subject: [PATCH] add new args --- biobb_vs/vina/autodock_vina_run.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/biobb_vs/vina/autodock_vina_run.py b/biobb_vs/vina/autodock_vina_run.py index 1825225..4dfa20a 100755 --- a/biobb_vs/vina/autodock_vina_run.py +++ b/biobb_vs/vina/autodock_vina_run.py @@ -24,6 +24,9 @@ class AutoDockVinaRun(BiobbObject): properties (dic - Python dictionary object containing the tool parameters, not input/output files): * **cpu** (*int*) - (1) [1~1000|1] the number of CPUs to use. * **exhaustiveness** (*int*) - (8) [1~10000|1] exhaustiveness of the global search (roughly proportional to time). + * **num_modes** (*int*) - (9) [1~1000|1] maximum number of binding modes to generate. + * **min_rmsd** (*int*) - (1) [1~1000|1] minimum RMSD between output poses. + * **energy_range** (*int*) - (3) [1~1000|1] maximum energy difference between the best binding mode and the worst one displayed (kcal/mol). * **binary_path** (*string*) - ('vina') path to vina in your local computer. * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. @@ -76,6 +79,9 @@ def __init__(self, input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box # Properties specific for BB self.cpu = properties.get('cpu', 1) self.exhaustiveness = properties.get('exhaustiveness', 8) + self.num_modes = properties.get('num_modes', 9) + self.min_rmsd = properties.get('min_rmsd', 1) + self.energy_range = properties.get('energy_range', 3) self.binary_path = properties.get('binary_path', 'vina') self.properties = properties @@ -129,6 +135,9 @@ def launch(self) -> int: '--size_x=' + sidex, '--size_y=' + sidey, '--size_z=' + sidez, '--cpu', str(self.cpu), '--exhaustiveness', str(self.exhaustiveness), + '--num_modes', str(self.num_modes), + '--min_rmsd', str(self.min_rmsd), + '--energy_range', str(self.energy_range), '--out', self.stage_io_dict["out"]["output_pdbqt_path"], '--verbosity', '1', '>', self.stage_io_dict["out"]["output_log_path"]]