[UPDATE] Adding sandbox_path property to the json schemas

bioexcel · Jul 4, 2024 · 0a6cbf3 · 0a6cbf3
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diff --git a/biobb_structure_utils/docs/source/command_line.md b/biobb_structure_utils/docs/source/command_line.md
@@ -42,6 +42,7 @@ Syntax: input_parameter (datatype) - (default_value) Definition
 Config parameters for this building block:
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_cat_pdb.yml)
 ```python
@@ -103,6 +104,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_molecule.yml)
 ```python
@@ -162,6 +164,7 @@ Config parameters for this building block:
 * **regular_expression_pattern** (*string*): (^D) Python style regular expression matching the selected atom names..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_atoms.yml)
 ```python
@@ -226,6 +229,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_str_check_add_hydrogens.yml)
 ```python
@@ -289,6 +293,7 @@ Config parameters for this building block:
 * **residue_name_list** (*array*): ([NA, CL, SOL]) Ordered residue name list..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_sort_gro_residues.yml)
 ```python
@@ -357,6 +362,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_chain.yml)
 ```python
@@ -423,6 +429,7 @@ Config parameters for this building block:
 * **molecules** (*array*): (None) List of comma separated res_id (will remove all molecules that match the res_id) or list of dictionaries with the name | res_id  | chain | model of the molecules to be removed. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}]..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_remove_molecules.yml)
 ```python
@@ -492,6 +499,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_structure_check.yml)
 ```python
@@ -556,6 +564,7 @@ Config parameters for this building block:
 * **residues** (*array*): (None) List of comma separated res_id (will extract all residues that match the res_id) or list of dictionaries with the name | res_id  | chain | model of the residues to be extracted. Format: [{"name": "HIS", "res_id": "72", "chain": "A", "model": "1"}]..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_residues.yml)
 ```python
@@ -624,6 +633,7 @@ Config parameters for this building block:
 * **ligand** (*string*): (AQ4) Residue code of the ligand to be removed..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_remove_ligand.yml)
 ```python
@@ -687,6 +697,7 @@ Config parameters for this building block:
 * **renumber_residues_per_chain** (*boolean*): (True) Restart residue enumeration every time a new chain is detected..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_renumber_structure.yml)
 ```python
@@ -746,6 +757,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_remove_pdb_water.yml)
 ```python
@@ -806,6 +818,7 @@ Config parameters for this building block:
 * **water** (*boolean*): (False) Add or not waters..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_heteroatoms.yml)
 ```python
@@ -878,6 +891,7 @@ Config parameters for this building block:
 * **preserve_target** (*boolean*): (True) Whether or not to preserve the target residues in the output structure..
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_closest_residues.yml)
 ```python
@@ -951,6 +965,7 @@ Config parameters for this building block:
 * **binary_path** (*string*): (check_structure) path to the check_structure application.
 * **remove_tmp** (*boolean*): (True) Remove temporal files..
 * **restart** (*boolean*): (False) Do not execute if output files exist..
+* **sandbox_path** (*string*): (./) Parent path to the sandbox directory..
 ### YAML
 #### [Common config file](https://github.com/bioexcel/biobb_structure_utils/blob/master/biobb_structure_utils/test/data/config/config_extract_model.yml)
 ```python

diff --git a/biobb_structure_utils/json_schemas/cat_pdb.json b/biobb_structure_utils/json_schemas/cat_pdb.json
@@ -101,6 +101,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/closest_residues.json b/biobb_structure_utils/json_schemas/closest_residues.json
@@ -97,6 +97,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_atoms.json b/biobb_structure_utils/json_schemas/extract_atoms.json
@@ -84,6 +84,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_chain.json b/biobb_structure_utils/json_schemas/extract_chain.json
@@ -97,6 +97,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_heteroatoms.json b/biobb_structure_utils/json_schemas/extract_heteroatoms.json
@@ -91,6 +91,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_model.json b/biobb_structure_utils/json_schemas/extract_model.json
@@ -91,6 +91,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_molecule.json b/biobb_structure_utils/json_schemas/extract_molecule.json
@@ -131,6 +131,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/extract_residues.json b/biobb_structure_utils/json_schemas/extract_residues.json
@@ -85,6 +85,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/remove_ligand.json b/biobb_structure_utils/json_schemas/remove_ligand.json
@@ -84,6 +84,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/remove_molecules.json b/biobb_structure_utils/json_schemas/remove_molecules.json
@@ -85,6 +85,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/remove_pdb_water.json b/biobb_structure_utils/json_schemas/remove_pdb_water.json
@@ -73,6 +73,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/renumber_structure.json b/biobb_structure_utils/json_schemas/renumber_structure.json
@@ -107,6 +107,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/sort_gro_residues.json b/biobb_structure_utils/json_schemas/sort_gro_residues.json
@@ -72,6 +72,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/str_check_add_hydrogens.json b/biobb_structure_utils/json_schemas/str_check_add_hydrogens.json
@@ -131,6 +131,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }

diff --git a/biobb_structure_utils/json_schemas/structure_check.json b/biobb_structure_utils/json_schemas/structure_check.json
@@ -144,6 +144,12 @@
                     "default": false,
                     "wf_prop": true,
                     "description": "Do not execute if output files exist."
+                },
+                "sandbox_path": {
+                    "type": "string",
+                    "default": "./",
+                    "wf_prop": true,
+                    "description": "Parent path to the sandbox directory."
                 }
             }
         }