biobb-io 4.2.0__py3-none-any.whl → 5.0.1__py3-none-any.whl

biobb_io/api/ligand.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
 
 """Module containing the Ligand class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, download_ligand, write_pdb
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_ligand,
+    write_pdb,
+)
 
 
 class Ligand(BiobbObject):
@@ -21,6 +30,7 @@ class Ligand(BiobbObject):
             * **api_id** (*str*) - ("mmb") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -43,8 +53,7 @@ class Ligand(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -52,13 +61,11 @@ class Ligand(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_pdb_path": output_pdb_path}
-        }
+        self.io_dict = {"out": {"output_pdb_path": output_pdb_path}}
 
         # Properties specific for BB
-        self.api_id = properties.get('api_id', 'mmb')
-        self.ligand_code = properties.get('ligand_code', None)
+        self.api_id = properties.get("api_id", "mmb")
+        self.ligand_code = properties.get("ligand_code", None)
         self.properties = properties
 
         # Check the properties
@@ -66,8 +73,14 @@ class Ligand(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_pdb_path = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_pdb_path = check_output_path(
+            self.io_dict["out"]["output_pdb_path"],
+            "output_pdb_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -80,12 +93,16 @@ class Ligand(BiobbObject):
         if self.check_restart():
             return 0
 
-        check_mandatory_property(self.ligand_code, 'ligand_code', self.out_log, self.__class__.__name__)
+        check_mandatory_property(
+            self.ligand_code, "ligand_code", self.out_log, self.__class__.__name__
+        )
 
         self.ligand_code = self.ligand_code.strip().lower()
 
         # Downloading PDB file
-        pdb_string = download_ligand(self.ligand_code, self.api_id, self.out_log, self.global_log)
+        pdb_string = download_ligand(
+            self.ligand_code, self.api_id, self.out_log, self.global_log
+        )
         write_pdb(pdb_string, self.output_pdb_path, None, self.out_log, self.global_log)
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -93,31 +110,44 @@ class Ligand(BiobbObject):
         return 0
 
 
-def ligand(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
+def ligand(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Ligand <api.ligand.Ligand>` class and
     execute the :meth:`launch() <api.ligand.Ligand.launch>` method."""
 
-    return Ligand(output_pdb_path=output_pdb_path,
-                  properties=properties, **kwargs).launch()
+    return Ligand(
+        output_pdb_path=output_pdb_path, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a single PDB ligand.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_pdb_path', required=True, help="Path to the output PDB ligand file. Accepted formats: pdb.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_pdb_path",
+        required=True,
+        help="Path to the output PDB ligand file. Accepted formats: pdb.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    ligand(output_pdb_path=args.output_pdb_path,
-           properties=properties)
+    ligand(output_pdb_path=args.output_pdb_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim.py

@@ -1,11 +1,19 @@
 #!/usr/bin/env python
 
 """Module containing the MemProtMDSim class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, get_memprotmd_sim
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    get_memprotmd_sim,
+)
 
 
 class MemProtMDSim(BiobbObject):
@@ -20,6 +28,7 @@ class MemProtMDSim(BiobbObject):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -41,8 +50,7 @@ class MemProtMDSim(BiobbObject):
 
     """
 
-    def __init__(self, output_simulation,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_simulation, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -50,12 +58,10 @@ class MemProtMDSim(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_simulation": output_simulation}
-        }
+        self.io_dict = {"out": {"output_simulation": output_simulation}}
 
         # Properties specific for BB
-        self.pdb_code = properties.get('pdb_code', None)
+        self.pdb_code = properties.get("pdb_code", None)
         self.properties = properties
 
         # Check the properties
@@ -63,8 +69,14 @@ class MemProtMDSim(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_simulation = check_output_path(self.io_dict["out"]["output_simulation"], "output_simulation", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_simulation = check_output_path(
+            self.io_dict["out"]["output_simulation"],
+            "output_simulation",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -77,41 +89,60 @@ class MemProtMDSim(BiobbObject):
         if self.check_restart():
             return 0
 
-        check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
+        check_mandatory_property(
+            self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__
+        )
 
         # get simulation files and save to output
-        get_memprotmd_sim(self.pdb_code, self.output_simulation, self.out_log, self.global_log)
+        get_memprotmd_sim(
+            self.pdb_code, self.output_simulation, self.out_log, self.global_log
+        )
 
         self.check_arguments(output_files_created=True, raise_exception=False)
 
         return 0
 
 
-def memprotmd_sim(output_simulation: str, properties: dict = None, **kwargs) -> int:
+def memprotmd_sim(
+    output_simulation: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`MemProtMDSim <api.memprotmd_sim.MemProtMDSim>` class and
     execute the :meth:`launch() <api.memprotmd_sim.MemProtMDSim.launch>` method."""
 
-    return MemProtMDSim(output_simulation=output_simulation,
-                        properties=properties, **kwargs).launch()
+    return MemProtMDSim(
+        output_simulation=output_simulation, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_simulation', required=True, help="Path to the output simulation in a ZIP file. Accepted formats: zip.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_simulation",
+        required=True,
+        help="Path to the output simulation in a ZIP file. Accepted formats: zip.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    memprotmd_sim(output_simulation=args.output_simulation,
-                  properties=properties)
+    memprotmd_sim(output_simulation=args.output_simulation, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim_list.py

@@ -1,10 +1,14 @@
 #!/usr/bin/env python
 
 """Module containing the MemProtMDSimList class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
+
 from biobb_io.api.common import check_output_path, get_memprotmd_sim_list, write_json
 
 
@@ -19,13 +23,14 @@ class MemProtMDSimList(BiobbObject):
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.memprotmd_sim_list import memprotmd_sim_list
             prop = { }
-            memprotmd_sim_list(output_simulations='/path/to/newSimulationList.json',
+            memprotmd_sim_list(output_simulations='/path/to/newSimulationlist.json',
                                 properties=prop)
 
     Info:
@@ -38,8 +43,7 @@ class MemProtMDSimList(BiobbObject):
 
     """
 
-    def __init__(self, output_simulations,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_simulations, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -47,9 +51,7 @@ class MemProtMDSimList(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_simulations": output_simulations}
-        }
+        self.io_dict = {"out": {"output_simulations": output_simulations}}
 
         # Properties specific for BB
         self.properties = properties
@@ -59,8 +61,14 @@ class MemProtMDSimList(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_simulations = check_output_path(self.io_dict["out"]["output_simulations"], "output_simulations", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_simulations = check_output_path(
+            self.io_dict["out"]["output_simulations"],
+            "output_simulations",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -84,30 +92,48 @@ class MemProtMDSimList(BiobbObject):
         return 0
 
 
-def memprotmd_sim_list(output_simulations: str, properties: dict = None, **kwargs) -> int:
+def memprotmd_sim_list(
+    output_simulations: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`MemProtMDSimList <api.memprotmd_sim_list.MemProtMDSimList>` class and
     execute the :meth:`launch() <api.memprotmd_sim_list.MemProtMDSimList.launch>` method."""
 
-    return MemProtMDSimList(output_simulations=output_simulations,
-                            properties=properties, **kwargs).launch()
+    return MemProtMDSimList(
+        output_simulations=output_simulations, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_simulations', required=True, help="Path to the output JSON file. Accepted formats: json.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_simulations",
+        required=True,
+        help="Path to the output JSON file. Accepted formats: json.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    memprotmd_sim_list(output_simulations=args.output_simulations, properties=properties)
+    memprotmd_sim_list(
+        output_simulations=args.output_simulations, properties=properties
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/memprotmd_sim_search.py

@@ -1,10 +1,14 @@
 #!/usr/bin/env python
 
 """Module containing the MemProtMDSimSearch class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
+
 from biobb_io.api.common import check_output_path, get_memprotmd_sim_search, write_json
 
 
@@ -21,6 +25,7 @@ class MemProtMDSimSearch(BiobbObject):
             * **keyword** (*str*) - (None) String to search for in the database metadata. Examples are families like gpcr or porin. Values: porin, outer membrane protein, membrane protein, gpcr (7-transmembrane domain receptors transducing extracellular signals into cells), ion channels, rhodopsin (The most famous GPCRs), abc, mip (Major Intrinsic Protein (MIP)/FNT superfamily: specific for the transport of water and small neutral solutes), ligand-gated (Ligand-dependent signal conversion from chemical signals to electric signals), ammonia (Regulating transepithelial ammonia secretion), mapeg (Eicosanoid and Glutathione metabolism proteins), transmembrane (Heme biosynthesis), protein, kinase (Tyrosine-protein kinases: regulate central nervous system; gene transcription and cell differentiation), glycoprotein (Expression of TCR complex), immunoglobulin (Recognition; binding and adhesion process of cells), integrin (Bridges for cell-cell and cell-extracellular matrix interaction), bnip3 (BNip3 protein family: protect cell from apoptosis), bcl-2 (Regulating cell-death; either induce apoptotic or inhibit apoptosis), atpase (ATPase regulators; P-P-bond hydrolysis-driven transporter), cytochrome (Terminal oxidase enzyme in electron transfer chain), nadp (Transmembrane proteins with NAD(P)-binding Rossmann-fold domains: monoamine oxidase; deaminates norepinephrine; epinephrine; serotonin and dopamine), a4 (Amyloid beta A4 protein; involved in alzheimer's diseases), lysosome (Lysosome-associated membrane glycoprotein: specific to lysosomes; CD107), necrosis (Tumor necrosis factor recepto: binding with TNF and NGF; interacting with a variety of signal molecules; highly associated with apoptosis), oxidoreductase (DHODH; biosynthesis of orotate), ceramidase (Neutral/alkaline ceramidase: converting sphingolipid to sphingosine), dehydrogenase (Aldehyde dehydrogenase:ALDH; Oxidation of aldehydes), mitochondrial, plastid.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -43,8 +48,7 @@ class MemProtMDSimSearch(BiobbObject):
 
     """
 
-    def __init__(self, output_simulations,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_simulations, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -52,13 +56,11 @@ class MemProtMDSimSearch(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_simulations": output_simulations}
-        }
+        self.io_dict = {"out": {"output_simulations": output_simulations}}
 
         # Properties specific for BB
-        self.collection_name = properties.get('collection_name', 'refs')
-        self.keyword = properties.get('keyword', None)
+        self.collection_name = properties.get("collection_name", "refs")
+        self.keyword = properties.get("keyword", None)
         self.properties = properties
 
         # Check the properties
@@ -66,8 +68,14 @@ class MemProtMDSimSearch(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_simulations = check_output_path(self.io_dict["out"]["output_simulations"], "output_simulations", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_simulations = check_output_path(
+            self.io_dict["out"]["output_simulations"],
+            "output_simulations",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -83,7 +91,9 @@ class MemProtMDSimSearch(BiobbObject):
         self.keyword = self.keyword.strip().lower()
 
         # get JSON object
-        json_string = get_memprotmd_sim_search(self.collection_name, self.keyword, self.out_log, self.global_log)
+        json_string = get_memprotmd_sim_search(
+            self.collection_name, self.keyword, self.out_log, self.global_log
+        )
 
         # write JSON file
         write_json(json_string, self.output_simulations, self.out_log, self.global_log)
@@ -93,31 +103,48 @@ class MemProtMDSimSearch(BiobbObject):
         return 0
 
 
-def memprotmd_sim_search(output_simulations: str, properties: dict = None, **kwargs) -> int:
+def memprotmd_sim_search(
+    output_simulations: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`MemProtMDSimSearch <api.memprotmd_sim_search.MemProtMDSimSearch>` class and
     execute the :meth:`launch() <api.memprotmd_sim_search.MemProtMDSimSearch.launch>` method."""
 
-    return MemProtMDSimSearch(output_simulations=output_simulations,
-                              properties=properties, **kwargs).launch()
+    return MemProtMDSimSearch(
+        output_simulations=output_simulations, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to perform advanced searches.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to perform advanced searches.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_simulations', required=True, help="Path to the output JSON file. Accepted formats: json.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_simulations",
+        required=True,
+        help="Path to the output JSON file. Accepted formats: json.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    memprotmd_sim_search(output_simulations=args.output_simulations,
-                         properties=properties)
+    memprotmd_sim_search(
+        output_simulations=args.output_simulations, properties=properties
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()