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

biobb_io/api/mmcif.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
 
 """Module containing the Mmcif 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_mmcif, write_mmcif
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_mmcif,
+    write_mmcif,
+)
 
 
 class Mmcif(BiobbObject):
@@ -21,6 +30,7 @@ class Mmcif(BiobbObject):
             * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the MMCIF structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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 Mmcif(BiobbObject):
 
     """
 
-    def __init__(self, output_mmcif_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_mmcif_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -52,13 +61,11 @@ class Mmcif(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_mmcif_path": output_mmcif_path}
-        }
+        self.io_dict = {"out": {"output_mmcif_path": output_mmcif_path}}
 
         # Properties specific for BB
-        self.api_id = properties.get('api_id', 'pdbe')
-        self.pdb_code = properties.get('pdb_code', None)
+        self.api_id = properties.get("api_id", "pdbe")
+        self.pdb_code = properties.get("pdb_code", None)
         self.properties = properties
 
         # Check the properties
@@ -66,8 +73,14 @@ class Mmcif(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_mmcif_path = check_output_path(self.io_dict["out"]["output_mmcif_path"], "output_mmcif_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_mmcif_path = check_output_path(
+            self.io_dict["out"]["output_mmcif_path"],
+            "output_mmcif_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -80,12 +93,16 @@ class Mmcif(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__
+        )
 
         self.pdb_code = self.pdb_code.strip().lower()
 
         # Downloading PDB file
-        mmcif_string = download_mmcif(self.pdb_code, self.api_id, self.out_log, self.global_log)
+        mmcif_string = download_mmcif(
+            self.pdb_code, self.api_id, self.out_log, self.global_log
+        )
         write_mmcif(mmcif_string, self.output_mmcif_path, self.out_log, self.global_log)
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -93,31 +110,44 @@ class Mmcif(BiobbObject):
         return 0
 
 
-def mmcif(output_mmcif_path: str, properties: dict = None, **kwargs) -> int:
+def mmcif(output_mmcif_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Mmcif <api.mmcif.Mmcif>` class and
     execute the :meth:`launch() <api.mmcif.Mmcif.launch>` method."""
 
-    return Mmcif(output_mmcif_path=output_mmcif_path,
-                 properties=properties, **kwargs).launch()
+    return Mmcif(
+        output_mmcif_path=output_mmcif_path, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.", 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="This class is a wrapper for downloading a MMCIF structure from the Protein Data Bank.",
+        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_mmcif_path', required=True, help="Path to the output MMCIF file. Accepted formats: cif, mmcif.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_mmcif_path",
+        required=True,
+        help="Path to the output MMCIF file. Accepted formats: cif, mmcif.",
+    )
 
     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
-    mmcif(output_mmcif_path=args.output_mmcif_path,
-          properties=properties)
+    mmcif(output_mmcif_path=args.output_mmcif_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/pdb.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
 
 """Module containing the Pdb 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_mandatory_property, check_output_path, download_pdb, write_pdb
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_pdb,
+    write_pdb,
+)
 
 
 class Pdb(BiobbObject):
@@ -22,6 +31,7 @@ class Pdb(BiobbObject):
             * **api_id** (*str*) - ("pdbe") 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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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::
@@ -45,8 +55,7 @@ class Pdb(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
@@ -54,14 +63,12 @@ class Pdb(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', 'pdbe')
-        self.pdb_code = properties.get('pdb_code', None)
-        self.filter = properties.get('filter', ['ATOM', 'MODEL', 'ENDMDL'])
+        self.api_id = properties.get("api_id", "pdbe")
+        self.pdb_code = properties.get("pdb_code", None)
+        self.filter = properties.get("filter", ["ATOM", "MODEL", "ENDMDL"])
         self.properties = properties
 
         # Check the properties
@@ -69,8 +76,14 @@ class Pdb(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:
@@ -83,44 +96,63 @@ class Pdb(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__
+        )
 
         self.pdb_code = self.pdb_code.strip().lower()
 
         # Downloading PDB file
-        pdb_string = download_pdb(self.pdb_code, self.api_id, self.out_log, self.global_log)
-        write_pdb(pdb_string, self.output_pdb_path, self.filter, self.out_log, self.global_log)
+        pdb_string = download_pdb(
+            self.pdb_code, self.api_id, self.out_log, self.global_log
+        )
+        write_pdb(
+            pdb_string, self.output_pdb_path, self.filter, self.out_log, self.global_log
+        )
 
         self.check_arguments(output_files_created=True, raise_exception=False)
 
         return 0
 
 
-def pdb(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
+def pdb(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`Pdb <api.pdb.Pdb>` class and
     execute the :meth:`launch() <api.pdb.Pdb.launch>` method."""
 
-    return Pdb(output_pdb_path=output_pdb_path,
-               properties=properties, **kwargs).launch()
+    return Pdb(
+        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="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.", 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="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.",
+        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 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 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
-    pdb(output_pdb_path=args.output_pdb_path,
-        properties=properties)
+    pdb(output_pdb_path=args.output_pdb_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/pdb_cluster_zip.py

@@ -1,13 +1,23 @@
 #!/usr/bin/env python
 
 """PdbClusterZip Module"""
-import os
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+import os
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_mandatory_property, check_output_path, get_cluster_pdb_codes, download_pdb, write_pdb
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_pdb,
+    get_cluster_pdb_codes,
+    write_pdb,
+)
 
 
 class PdbClusterZip(BiobbObject):
@@ -25,6 +35,7 @@ class PdbClusterZip(BiobbObject):
             * **api_id** (*str*) - ("pdbe") 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>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), 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::
@@ -49,8 +60,7 @@ class PdbClusterZip(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_zip_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_zip_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -58,15 +68,13 @@ class PdbClusterZip(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_pdb_zip_path": output_pdb_zip_path}
-        }
+        self.io_dict = {"out": {"output_pdb_zip_path": output_pdb_zip_path}}
 
         # Properties specific for BB
-        self.api_id = properties.get('api_id', 'pdbe')
-        self.pdb_code = properties.get('pdb_code', None)
-        self.filter = properties.get('filter', ['ATOM', 'MODEL', 'ENDMDL'])
-        self.cluster = properties.get('cluster', 90)
+        self.api_id = properties.get("api_id", "pdbe")
+        self.pdb_code = properties.get("pdb_code", None)
+        self.filter = properties.get("filter", ["ATOM", "MODEL", "ENDMDL"])
+        self.cluster = properties.get("cluster", 90)
         self.properties = properties
 
         # Check the properties
@@ -74,8 +82,14 @@ class PdbClusterZip(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_pdb_zip_path = check_output_path(self.io_dict["out"]["output_pdb_zip_path"], "output_pdb_zip_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_pdb_zip_path = check_output_path(
+            self.io_dict["out"]["output_pdb_zip_path"],
+            "output_pdb_zip_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -88,17 +102,29 @@ class PdbClusterZip(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__
+        )
 
         self.pdb_code = self.pdb_code.strip().lower()
 
         file_list = []
         # Downloading PDB_files
-        pdb_code_list = get_cluster_pdb_codes(pdb_code=self.pdb_code, cluster=self.cluster, out_log=self.out_log, global_log=self.global_log)
+        pdb_code_list = get_cluster_pdb_codes(
+            pdb_code=self.pdb_code,
+            cluster=self.cluster,
+            out_log=self.out_log,
+            global_log=self.global_log,
+        )
         unique_dir = fu.create_unique_dir()
         for pdb_code in pdb_code_list:
-            pdb_file = os.path.join(unique_dir, pdb_code+".pdb")
-            pdb_string = download_pdb(pdb_code=pdb_code, api_id=self.api_id, out_log=self.out_log, global_log=self.global_log)
+            pdb_file = os.path.join(unique_dir, pdb_code + ".pdb")
+            pdb_string = download_pdb(
+                pdb_code=pdb_code,
+                api_id=self.api_id,
+                out_log=self.out_log,
+                global_log=self.global_log,
+            )
             write_pdb(pdb_string, pdb_file, self.filter, self.out_log, self.global_log)
             file_list.append(os.path.abspath(pdb_file))
 
@@ -106,10 +132,7 @@ class PdbClusterZip(BiobbObject):
         fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
         fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
 
-        self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
-            unique_dir
-        ])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", ""), unique_dir])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -117,31 +140,46 @@ class PdbClusterZip(BiobbObject):
         return 0
 
 
-def pdb_cluster_zip(output_pdb_zip_path: str, properties: dict = None, **kwargs) -> int:
+def pdb_cluster_zip(
+    output_pdb_zip_path: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` class and
     execute the :meth:`launch() <api.pdb_cluster_zip.PdbClusterZip.launch>` method."""
 
-    return PdbClusterZip(output_pdb_zip_path=output_pdb_zip_path,
-                         properties=properties, **kwargs).launch()
+    return PdbClusterZip(
+        output_pdb_zip_path=output_pdb_zip_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/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.", 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/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.",
+        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_zip_path', required=True, help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_pdb_zip_path",
+        required=True,
+        help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, 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
-    pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path,
-                    properties=properties)
+    pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()