Updated autodck_vina JSON & command line

bioexcel · Apr 2, 2024 · edf7f84 · edf7f84
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diff --git a/biobb_vs/docs/source/command_line.md b/biobb_vs/docs/source/command_line.md
@@ -47,6 +47,9 @@ 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)..
+* **num_modes** (*integer*): (9) maximum number of binding modes to generate..
+* **min_rmsd** (*integer*): (1) minimum RMSD between output poses..
+* **energy_range** (*integer*): (3) 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** (*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
@@ -124,6 +124,33 @@
                     "max": 10000,
                     "step": 1
                 },
+                "num_modes": {
+                    "type": "integer",
+                    "default": 9,
+                    "wf_prop": false,
+                    "description": "maximum number of binding modes to generate.",
+                    "min": 1,
+                    "max": 1000,
+                    "step": 1
+                },
+                "min_rmsd": {
+                    "type": "integer",
+                    "default": 1,
+                    "wf_prop": false,
+                    "description": "minimum RMSD between output poses.",
+                    "min": 1,
+                    "max": 1000,
+                    "step": 1
+                },
+                "energy_range": {
+                    "type": "integer",
+                    "default": 3,
+                    "wf_prop": false,
+                    "description": "maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).",
+                    "min": 1,
+                    "max": 1000,
+                    "step": 1
+                },
                 "binary_path": {
                     "type": "string",
                     "default": "vina",