From 0a6cbf3534f66852d6a7a3c4c28da7ffefeb15cb Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Thu, 4 Jul 2024 10:48:38 +0200 Subject: [PATCH] [UPDATE] Adding sandbox_path property to the json schemas --- biobb_structure_utils/docs/source/command_line.md | 15 +++++++++++++++ biobb_structure_utils/json_schemas/cat_pdb.json | 6 ++++++ .../json_schemas/closest_residues.json | 6 ++++++ .../json_schemas/extract_atoms.json | 6 ++++++ .../json_schemas/extract_chain.json | 6 ++++++ .../json_schemas/extract_heteroatoms.json | 6 ++++++ .../json_schemas/extract_model.json | 6 ++++++ .../json_schemas/extract_molecule.json | 6 ++++++ .../json_schemas/extract_residues.json | 6 ++++++ .../json_schemas/remove_ligand.json | 6 ++++++ .../json_schemas/remove_molecules.json | 6 ++++++ .../json_schemas/remove_pdb_water.json | 6 ++++++ .../json_schemas/renumber_structure.json | 6 ++++++ .../json_schemas/sort_gro_residues.json | 6 ++++++ .../json_schemas/str_check_add_hydrogens.json | 6 ++++++ .../json_schemas/structure_check.json | 6 ++++++ 16 files changed, 105 insertions(+) diff --git a/biobb_structure_utils/docs/source/command_line.md b/biobb_structure_utils/docs/source/command_line.md index 18f47f3..ea30bc8 100644 --- 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 index e3b9bef..da676a8 100644 --- 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 index 3d2dbc0..395336c 100644 --- 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 index 6cf58d9..22502e7 100644 --- 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 index 3639a4e..18183c7 100644 --- 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 index f278eec..4a0f994 100644 --- 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 index 6578afa..63f830a 100644 --- 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 index 725e438..a013cf3 100644 --- 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 index 1902a35..d2541ea 100644 --- 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 index 62d6732..5504d49 100644 --- 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 index 27be670..db1d6bf 100644 --- 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 index 414cde1..cb8ca4a 100644 --- 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 index 83fa16d..04d8794 100644 --- 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 index c8012dc..a2d2113 100644 --- 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 index 8829fc4..6357ce8 100644 --- 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 index 714a5b5..5fa4580 100644 --- 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." } } }