biobb-io 4.0.0__py3-none-any.whl → 4.1.1__py3-none-any.whl

biobb_io/api/drugbank.py

@@ -3,10 +3,9 @@
 """Module containing the Drugbank class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, download_drugbank, write_sdf
 
 
 class Drugbank(BiobbObject):
@@ -26,10 +25,10 @@ class Drugbank(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.drugbank import drugbank
-            prop = { 
-                'drugbank_id': 'DB00530' 
+            prop = {
+                'drugbank_id': 'DB00530'
             }
-            drugbank(output_sdf_path='/path/to/newComponent.sdf', 
+            drugbank(output_sdf_path='/path/to/newComponent.sdf',
                     properties=prop)
 
     Info:
@@ -42,8 +41,8 @@ class Drugbank(BiobbObject):
 
     """
 
-    def __init__(self, output_sdf_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_sdf_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -51,8 +50,8 @@ class Drugbank(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_sdf_path": output_sdf_path } 
+        self.io_dict = {
+            "out": {"output_sdf_path": output_sdf_path}
         }
 
         # Properties specific for BB
@@ -62,7 +61,7 @@ class Drugbank(BiobbObject):
         # Check the properties
         self.check_properties(properties)
         self.check_arguments()
-        
+
     def check_data_params(self, out_log, err_log):
         """ Checks all the input/output paths and parameters """
         self.output_sdf_path = check_output_path(self.io_dict["out"]["output_sdf_path"], "output_sdf_path", False, out_log, self.__class__.__name__)
@@ -75,15 +74,15 @@ class Drugbank(BiobbObject):
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         check_mandatory_property(self.drugbank_id, 'drugbank_id', self.out_log, self.__class__.__name__)
 
         self.drugbank_id = self.drugbank_id.strip().lower()
         url = "https://www.drugbank.ca/structures/small_molecule_drugs/%s.sdf?type=3d"
 
-        #Downloading SDF file
+        # Downloading SDF file
         sdf_string = download_drugbank(self.drugbank_id, url, self.out_log, self.global_log)
         write_sdf(sdf_string, self.output_sdf_path, self.out_log, self.global_log)
 
@@ -91,6 +90,7 @@ class Drugbank(BiobbObject):
 
         return 0
 
+
 def drugbank(output_sdf_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`Drugbank <api.drugbank.Drugbank>` class and
     execute the :meth:`launch() <api.drugbank.Drugbank.launch>` method."""
@@ -98,12 +98,13 @@ def drugbank(output_sdf_path: str, properties: dict = None, **kwargs) -> int:
     return Drugbank(output_sdf_path=output_sdf_path,
                     properties=properties, **kwargs).launch()
 
+
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
     parser = argparse.ArgumentParser(description="Download a component in SDF format from the Drugbank (https://www.drugbank.ca/).", 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
+    # Specific args of each building block
     required_args = parser.add_argument_group('required arguments')
     required_args.add_argument('-o', '--output_sdf_path', required=True, help="Path to the output SDF component file. Accepted formats: sdf.")
 
@@ -111,9 +112,10 @@ def main():
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    drugbank(output_sdf_path=args.output_sdf_path, 
-            properties=properties)
+    # Specific call of each building block
+    drugbank(output_sdf_path=args.output_sdf_path,
+             properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/ideal_sdf.py

@@ -3,10 +3,9 @@
 """Module containing the IdealSdf class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, download_ideal_sdf, write_sdf
 
 
 class IdealSdf(BiobbObject):
@@ -27,11 +26,11 @@ class IdealSdf(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.ideal_sdf import ideal_sdf
-            prop = { 
-                'ligand_code': 'HYZ', 
-                'api_id': 'pdbe' 
+            prop = {
+                'ligand_code': 'HYZ',
+                'api_id': 'pdbe'
             }
-            ideal_sdf(output_sdf_path='/path/to/newStructure.sdf', 
+            ideal_sdf(output_sdf_path='/path/to/newStructure.sdf',
                         properties=prop)
 
     Info:
@@ -44,8 +43,8 @@ class IdealSdf(BiobbObject):
 
     """
 
-    def __init__(self, output_sdf_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_sdf_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -53,8 +52,8 @@ class IdealSdf(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_sdf_path": output_sdf_path } 
+        self.io_dict = {
+            "out": {"output_sdf_path": output_sdf_path}
         }
 
         # Properties specific for BB
@@ -73,13 +72,13 @@ class IdealSdf(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`IdealSdf <api.ideal_sdf.IdealSdf>` api.ideal_sdf.IdealSdf object."""
-        
+
         # check input/output paths and parameters
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         check_mandatory_property(self.ligand_code, 'ligand_code', self.out_log, self.__class__.__name__)
 
@@ -93,12 +92,14 @@ class IdealSdf(BiobbObject):
 
         return 0
 
+
 def ideal_sdf(output_sdf_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`IdealSdf <api.ideal_sdf.IdealSdf>` class and
     execute the :meth:`launch() <api.ideal_sdf.IdealSdf.launch>` method."""
 
     return IdealSdf(output_sdf_path=output_sdf_path,
-                properties=properties, **kwargs).launch()
+                    properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -114,8 +115,9 @@ def main():
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    ideal_sdf(output_sdf_path=args.output_sdf_path, 
-        properties=properties)
+    ideal_sdf(output_sdf_path=args.output_sdf_path,
+              properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/ligand.py

@@ -3,10 +3,9 @@
 """Module containing the Ligand class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, download_ligand, write_pdb
 
 
 class Ligand(BiobbObject):
@@ -19,7 +18,7 @@ class Ligand(BiobbObject):
         output_pdb_path (str): Path to the output PDB ligand file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_ligand.pdb>`_. Accepted formats: pdb (edam:format_1476).
         properties (dic - Python dictionary object containing the tool parameters, not input/output files):
             * **ligand_code** (*str*) - (None) RSCB PDB ligand code.
-            * **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>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
+            * **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.
 
@@ -27,11 +26,11 @@ class Ligand(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.ligand import ligand
-            prop = { 
-                'ligand_code': 'CPB', 
-                'api_id': 'pdbe' 
+            prop = {
+                'ligand_code': 'CPB',
+                'api_id': 'mmb'
             }
-            ligand(output_pdb_path='/path/to/newLigand.pdb', 
+            ligand(output_pdb_path='/path/to/newLigand.pdb',
                     properties=prop)
 
     Info:
@@ -44,8 +43,8 @@ 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
@@ -53,19 +52,19 @@ 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', 'pdbe')
+        self.api_id = properties.get('api_id', 'mmb')
         self.ligand_code = properties.get('ligand_code', None)
         self.properties = properties
 
         # Check the properties
         self.check_properties(properties)
         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__)
@@ -78,14 +77,14 @@ class Ligand(BiobbObject):
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         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
+        # Downloading PDB file
         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)
 
@@ -93,19 +92,21 @@ class Ligand(BiobbObject):
 
         return 0
 
+
 def ligand(output_pdb_path: str, properties: 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()
+                  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")
 
-    #Specific args of each building block
+    # 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.")
 
@@ -113,9 +114,10 @@ def main():
     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)
+    # Specific call of each building block
+    ligand(output_pdb_path=args.output_pdb_path,
+           properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/memprotmd_sim.py

@@ -3,10 +3,9 @@
 """Module containing the MemProtMDSim class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, check_mandatory_property, get_memprotmd_sim
 
 
 class MemProtMDSim(BiobbObject):
@@ -26,10 +25,10 @@ class MemProtMDSim(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.memprotmd_sim import memprotmd_sim
-            prop = { 
-                'pdb_code': '2VGB' 
+            prop = {
+                'pdb_code': '2VGB'
             }
-            memprotmd_sim(output_simulation='/path/to/newSimulation.zip', 
+            memprotmd_sim(output_simulation='/path/to/newSimulation.zip',
                         properties=prop)
 
     Info:
@@ -42,8 +41,8 @@ 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
@@ -51,8 +50,8 @@ 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
@@ -70,29 +69,31 @@ class MemProtMDSim(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`MemProtMDSim <api.memprotmd_sim.MemProtMDSim>` api.memprotmd_sim.MemProtMDSim object."""
-        
+
         # check input/output paths and parameters
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
 
         # get simulation files and save to output
-        json_string = 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:
     """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()
+                        properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -108,8 +109,9 @@ def main():
     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__':
     main()

biobb_io/api/memprotmd_sim_list.py

@@ -3,10 +3,9 @@
 """Module containing the MemProtMDSimList class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, get_memprotmd_sim_list, write_json
 
 
 class MemProtMDSimList(BiobbObject):
@@ -26,7 +25,7 @@ class MemProtMDSimList(BiobbObject):
 
             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:
@@ -39,8 +38,8 @@ 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
@@ -48,8 +47,8 @@ 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
@@ -66,13 +65,13 @@ class MemProtMDSimList(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`MemProtMDSimList <api.memprotmd_sim_list.MemProtMDSimList>` api.memprotmd_sim_list.MemProtMDSimList object."""
-        
+
         # check input/output paths and parameters
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         # get JSON object
         json_string = get_memprotmd_sim_list(self.out_log, self.global_log)
@@ -84,12 +83,14 @@ class MemProtMDSimList(BiobbObject):
 
         return 0
 
+
 def memprotmd_sim_list(output_simulations: str, properties: 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()
+                            properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -107,5 +108,6 @@ def main():
     # Specific call of each building block
     memprotmd_sim_list(output_simulations=args.output_simulations, properties=properties)
 
+
 if __name__ == '__main__':
     main()

biobb_io/api/memprotmd_sim_search.py

@@ -3,10 +3,9 @@
 """Module containing the MemProtMDSimSearch class and the command line interface."""
 import argparse
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
-from biobb_common.tools import file_utils as fu
+from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import *
+from biobb_io.api.common import check_output_path, get_memprotmd_sim_search, write_json
 
 
 class MemProtMDSimSearch(BiobbObject):
@@ -27,11 +26,11 @@ class MemProtMDSimSearch(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.memprotmd_sim_search import memprotmd_sim_search
-            prop = { 
-                'collection_name': 'refs', 
-                'keyword': 'porin' 
+            prop = {
+                'collection_name': 'refs',
+                'keyword': 'porin'
             }
-            memprotmd_sim_search(output_simulations='/path/to/newSimulationSearch.json', 
+            memprotmd_sim_search(output_simulations='/path/to/newSimulationSearch.json',
                                 properties=prop).launch()
 
     Info:
@@ -44,8 +43,8 @@ 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
@@ -53,8 +52,8 @@ 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
@@ -73,13 +72,13 @@ class MemProtMDSimSearch(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`MemProtMDSimSearch <api.memprotmd_sim_search.MemProtMDSimSearch>` api.memprotmd_sim_search.MemProtMDSimSearch object."""
-        
+
         # check input/output paths and parameters
         self.check_data_params(self.out_log, self.err_log)
 
         # Setup Biobb
-        if self.check_restart(): return 0
-        #self.stage_files()
+        if self.check_restart():
+            return 0
 
         self.keyword = self.keyword.strip().lower()
 
@@ -93,12 +92,14 @@ class MemProtMDSimSearch(BiobbObject):
 
         return 0
 
+
 def memprotmd_sim_search(output_simulations: str, properties: 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()
+                              properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -114,8 +115,9 @@ def main():
     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__':
     main()