Added exhaustiveness flag to autodock_vina_run

bioexcel · Mar 5, 2024 · 8d90ddf · 8d90ddf
1 parent 0df7432
commit 8d90ddf
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diff --git a/biobb_vs/docs/source/command_line.md b/biobb_vs/docs/source/command_line.md
@@ -46,6 +46,7 @@ Syntax: input_parameter (datatype) - (default_value) Definition
 
 Config parameters for this building block:
 * **cpu** (*integer*): (1) the number of CPUs to use..
+* **exhaustiveness** (*integer*): (8) exhaustiveness of the global search (roughly proportional to time)..
 * **binary_path** (*string*): (vina) path to vina in your local computer..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..

diff --git a/biobb_vs/json_schemas/autodock_vina_run.json b/biobb_vs/json_schemas/autodock_vina_run.json
@@ -115,6 +115,15 @@
                     "max": 1000,
                     "step": 1
                 },
+                "exhaustiveness": {
+                    "type": "integer",
+                    "default": 8,
+                    "wf_prop": false,
+                    "description": "exhaustiveness of the global search (roughly proportional to time).",
+                    "min": 1,
+                    "max": 10000,
+                    "step": 1
+                },
                 "binary_path": {
                     "type": "string",
                     "default": "vina",

diff --git a/biobb_vs/vina/autodock_vina_run.py b/biobb_vs/vina/autodock_vina_run.py
@@ -23,6 +23,7 @@ class AutoDockVinaRun(BiobbObject):
         output_log_path (str) (Optional): Path to the log file. File type: output. `Sample file <https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log>`_. Accepted formats: log (edam:format_2330).
         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).
             * **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.
@@ -74,6 +75,7 @@ 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.binary_path = properties.get('binary_path', 'vina')
         self.properties = properties
 
@@ -126,6 +128,7 @@ def launch(self) -> int:
                     '--center_x=' + x0, '--center_y=' + y0, '--center_z=' + z0,
                     '--size_x=' + sidex, '--size_y=' + sidey, '--size_z=' + sidez,
                     '--cpu', str(self.cpu),
+                    '--exhaustiveness', str(self.exhaustiveness),
                     '--out', self.stage_io_dict["out"]["output_pdbqt_path"],
                     '--verbosity', '1',
                     '>', self.stage_io_dict["out"]["output_log_path"]]