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

biobb_io/__init__.py

@@ -1,3 +1,3 @@
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "4.0.0"
+__version__ = "4.1.1"

biobb_io/api/__init__.py

@@ -1,2 +1,2 @@
 name = "api"
-__all__ = ["drugbank", "ligand", "pdb", "alphafold", "pdb_cluster_zip", "pdb_variants", "memprotmd_sim_list", "memprotmd_sim_search", "memprotmd_sim", "api_binding_site","canonical_fasta", "mmcif", "ideal_sdf", "structure_info"]
+__all__ = ["drugbank", "ligand", "pdb", "alphafold", "pdb_cluster_zip", "pdb_variants", "memprotmd_sim_list", "memprotmd_sim_search", "memprotmd_sim", "api_binding_site", "canonical_fasta", "mmcif", "ideal_sdf", "structure_info"]

biobb_io/api/alphafold.py

@@ -3,10 +3,9 @@
 """Module containing the AlphaFold 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, check_uniprot_code, download_af, write_pdb
 
 
 class AlphaFold(BiobbObject):
@@ -26,10 +25,10 @@ class AlphaFold(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.alphafold import alphafold
-            prop = { 
+            prop = {
                 'uniprot_code': 'P00489'
             }
-            alphafold(output_pdb_path='/path/to/newStructure.pdb', 
+            alphafold(output_pdb_path='/path/to/newStructure.pdb',
                 properties=prop)
 
     Info:
@@ -42,8 +41,8 @@ class AlphaFold(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
@@ -51,8 +50,8 @@ class AlphaFold(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
@@ -70,13 +69,13 @@ class AlphaFold(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` api.alphafold.AlphaFold 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.uniprot_code, 'uniprot_code', self.out_log, self.__class__.__name__)
 
@@ -92,12 +91,14 @@ class AlphaFold(BiobbObject):
 
         return 0
 
+
 def alphafold(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` class and
     execute the :meth:`launch() <api.alphafold.AlphaFold.launch>` method."""
 
     return AlphaFold(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."""
@@ -113,8 +114,9 @@ def main():
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    alphafold(output_pdb_path=args.output_pdb_path, 
-        properties=properties)
+    alphafold(output_pdb_path=args.output_pdb_path,
+              properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/api_binding_site.py

@@ -2,11 +2,12 @@
 
 """Module containing the ApiBindingSite class and the command line interface."""
 import argparse
+import json
 from biobb_common.generic.biobb_object import BiobbObject
-from biobb_common.configuration import  settings
+from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
 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_binding_site, write_json
 
 
 class ApiBindingSite(BiobbObject):
@@ -26,10 +27,10 @@ class ApiBindingSite(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.api_binding_site import api_binding_site
-            prop = { 
-                'pdb_code': '4i23' 
+            prop = {
+                'pdb_code': '4i23'
             }
-            api_binding_site(output_json_path='/path/to/newBindingSites.json', 
+            api_binding_site(output_json_path='/path/to/newBindingSites.json',
                     properties=prop)
 
     Info:
@@ -42,8 +43,8 @@ class ApiBindingSite(BiobbObject):
 
     """
 
-    def __init__(self, output_json_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_json_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -51,8 +52,8 @@ class ApiBindingSite(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_json_path": output_json_path } 
+        self.io_dict = {
+            "out": {"output_json_path": output_json_path}
         }
 
         # Properties specific for BB
@@ -62,7 +63,7 @@ class ApiBindingSite(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_json_path = check_output_path(self.io_dict["out"]["output_json_path"], "output_json_path", False, out_log, self.__class__.__name__)
@@ -75,8 +76,9 @@ class ApiBindingSite(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
+        # self.stage_files()
 
         check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
 
@@ -96,19 +98,21 @@ class ApiBindingSite(BiobbObject):
 
         return 0
 
+
 def api_binding_site(output_json_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` class and
     execute the :meth:`launch() <api.api_binding_site.ApiBindingSite.launch>` method."""
 
     return ApiBindingSite(output_json_path=output_json_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="This class is a wrapper for the PDBe REST API Binding Sites endpoint", 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_json_path', required=True, help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.")
 
@@ -116,9 +120,10 @@ def main():
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    api_binding_site(output_json_path=args.output_json_path, 
-            properties=properties)
+    # Specific call of each building block
+    api_binding_site(output_json_path=args.output_json_path,
+                     properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/canonical_fasta.py

@@ -3,10 +3,9 @@
 """Module containing the CanonicalFasta 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_fasta, write_fasta
 
 
 class CanonicalFasta(BiobbObject):
@@ -27,11 +26,11 @@ class CanonicalFasta(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.canonical_fasta import canonical_fasta
-            prop = { 
+            prop = {
                 'pdb_code': '4i23',
                 'api_id': 'pdb'
             }
-            canonical_fasta(output_fasta_path='/path/to/newFasta.fasta', 
+            canonical_fasta(output_fasta_path='/path/to/newFasta.fasta',
                     properties=prop)
 
     Info:
@@ -44,8 +43,8 @@ class CanonicalFasta(BiobbObject):
 
     """
 
-    def __init__(self, output_fasta_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_fasta_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -53,8 +52,8 @@ class CanonicalFasta(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_fasta_path": output_fasta_path } 
+        self.io_dict = {
+            "out": {"output_fasta_path": output_fasta_path}
         }
 
         # Properties specific for BB
@@ -65,7 +64,7 @@ class CanonicalFasta(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_fasta_path = check_output_path(self.io_dict["out"]["output_fasta_path"], "output_fasta_path", False, out_log, self.__class__.__name__)
@@ -78,8 +77,8 @@ class CanonicalFasta(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.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
 
@@ -93,19 +92,21 @@ class CanonicalFasta(BiobbObject):
 
         return 0
 
+
 def canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
     execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
 
     return CanonicalFasta(output_fasta_path=output_fasta_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="This class is a wrapper for downloading a FASTA 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
+    # Specific args of each building block
     required_args = parser.add_argument_group('required arguments')
     required_args.add_argument('-o', '--output_fasta_path', required=True, help="Path to the canonical FASTA file. Accepted formats: fasta.")
 
@@ -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
-    canonical_fasta(output_fasta_path=args.output_fasta_path, 
-            properties=properties)
+    # Specific call of each building block
+    canonical_fasta(output_fasta_path=args.output_fasta_path,
+                    properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/common.py

@@ -7,8 +7,9 @@ import urllib.request
 from pathlib import Path, PurePath
 from biobb_common.tools import file_utils as fu
 
+
 def check_output_path(path, argument, optional, out_log, classname):
-    """ Checks output file """ 
+    """ Checks output file """
     if optional and not path:
         return None
     if PurePath(path).parent and not Path(PurePath(path).parent).exists():
@@ -20,6 +21,7 @@ def check_output_path(path, argument, optional, out_log, classname):
         raise SystemExit(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument))
     return path
 
+
 def is_valid_file(ext, argument):
     """ Checks if file format is compatible """
     formats = {
@@ -35,6 +37,7 @@ def is_valid_file(ext, argument):
     }
     return ext in formats[argument]
 
+
 def download_pdb(pdb_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -51,6 +54,7 @@ def download_pdb(pdb_code, api_id, out_log=None, global_log=None):
     fu.log("Downloading %s from: %s" % (pdb_code, url), out_log, global_log)
     return requests.get(url).content.decode('utf-8')
 
+
 def download_af(uniprot_code, out_log=None, global_log=None, classname=None):
     """
     Returns:
@@ -62,12 +66,13 @@ def download_af(uniprot_code, out_log=None, global_log=None, classname=None):
     fu.log("Downloading %s from: %s" % (uniprot_code, url), out_log, global_log)
 
     r = requests.get(url)
-    if(r.status_code == 404):
+    if (r.status_code == 404):
         fu.log(classname + ': Incorrect Uniprot Code: %s' % (uniprot_code), out_log)
         raise SystemExit(classname + ': Incorrect Uniprot Code: %s' % (uniprot_code))
 
     return r.content.decode('utf-8')
 
+
 def download_mmcif(pdb_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -84,6 +89,7 @@ def download_mmcif(pdb_code, api_id, out_log=None, global_log=None):
     fu.log("Downloading %s from: %s" % (pdb_code, url), out_log, global_log)
     return requests.get(url, verify=False).content.decode('utf-8')
 
+
 def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -94,16 +100,17 @@ def download_ligand(ligand_code, api_id, out_log=None, global_log=None):
         url = "http://mmb.irbbarcelona.org/api/pdbMonomer/" + ligand_code.lower()
         text = requests.get(url, verify=False).content.decode('utf-8')
     elif api_id == 'pdbe':
-        url="ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.pdb".format(ligand_code.upper()[0], ligand_code.upper(), ligand_code.upper())
+        url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.pdb"
         text = urllib.request.urlopen(url).read().decode('utf-8')
 
     fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)
 
     # removing useless empty lines at the end of the file
     text = os.linesep.join([s for s in text.splitlines() if s])
-    
+
     return text
 
+
 def download_fasta(pdb_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -120,6 +127,7 @@ def download_fasta(pdb_code, api_id, out_log=None, global_log=None):
     fu.log("Downloading %s from: %s" % (pdb_code, url), out_log, global_log)
     return requests.get(url, verify=False).content.decode('utf-8')
 
+
 def download_drugbank(drugbank_id, url="https://www.drugbank.ca/structures/small_molecule_drugs/%s.sdf?type=3d", out_log=None, global_log=None):
     """
     Returns:
@@ -130,9 +138,10 @@ def download_drugbank(drugbank_id, url="https://www.drugbank.ca/structures/small
     fu.log("Downloading %s from: %s" % (drugbank_id, url), out_log, global_log)
 
     text = requests.get(url, verify=False).content.decode('utf-8')
-    
+
     return text
 
+
 def download_binding_site(pdb_code, url="https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s", out_log=None, global_log=None):
     """
     Returns:
@@ -145,10 +154,11 @@ def download_binding_site(pdb_code, url="https://www.ebi.ac.uk/pdbe/api/pdb/entr
     text = urllib.request.urlopen(url).read()
     json_obj = json.loads(text)
     json_string = json.dumps(json_obj, indent=4, sort_keys=True)
-    #json_string = json.dumps(text, indent=4)
-    
+    # json_string = json.dumps(text, indent=4)
+
     return json_string
 
+
 def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
     """
     Returns:
@@ -156,16 +166,17 @@ def download_ideal_sdf(ligand_code, api_id, out_log=None, global_log=None):
     """
 
     if api_id == 'pdb':
-        url = "https://files.rcsb.org/ligands/view/" + ligand_code.upper() + "_ideal.sdf"
+        url = "https://files.rcsb.org/ligands/download/" + ligand_code.upper() + "_ideal.sdf"
         text = requests.get(url, verify=False).content.decode('utf-8')
     elif api_id == 'pdbe':
-        url="ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/{0}/{1}/{1}_ideal.sdf".format(ligand_code.upper()[0], ligand_code.upper(), ligand_code.upper())
+        url = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/" + ligand_code.upper() + "_ideal.sdf"
         text = urllib.request.urlopen(url).read().decode('utf-8')
 
     fu.log("Downloading %s from: %s" % (ligand_code, url), out_log, global_log)
-    
+
     return text
 
+
 def download_str_info(pdb_code, url="http://mmb.irbbarcelona.org/api/pdb/%s.json", out_log=None, global_log=None):
     """
     Returns:
@@ -178,10 +189,11 @@ def download_str_info(pdb_code, url="http://mmb.irbbarcelona.org/api/pdb/%s.json
     text = urllib.request.urlopen(url).read()
     json_obj = json.loads(text)
     json_string = json.dumps(json_obj, indent=4, sort_keys=True)
-    #json_string = json.dumps(text, indent=4)
-    
+    # json_string = json.dumps(text, indent=4)
+
     return json_string
 
+
 def write_pdb(pdb_string, output_pdb_path, filt=None, out_log=None, global_log=None):
     """ Writes and filters a PDB """
     fu.log("Writting pdb to: %s" % (output_pdb_path), out_log, global_log)
@@ -194,30 +206,34 @@ def write_pdb(pdb_string, output_pdb_path, filt=None, out_log=None, global_log=N
         else:
             output_pdb_file.write(pdb_string)
 
+
 def write_mmcif(mmcif_string, output_mmcif_path, out_log=None, global_log=None):
     """ Writes a mmcif """
     fu.log("Writting mmcif to: %s" % (output_mmcif_path), out_log, global_log)
     with open(output_mmcif_path, 'w') as output_mmcif_file:
         output_mmcif_file.write(mmcif_string)
 
+
 def write_fasta(fasta_string, output_fasta_path, out_log=None, global_log=None):
     """ Writes a FASTA """
     fu.log("Writting FASTA to: %s" % (output_fasta_path), out_log, global_log)
     with open(output_fasta_path, 'w') as output_fasta_file:
         output_fasta_file.write(fasta_string)
 
+
 def write_sdf(sdf_string, output_sdf_path, out_log=None, global_log=None):
     """ Writes a SDF """
     fu.log("Writting sdf to: %s" % (output_sdf_path), out_log, global_log)
     with open(output_sdf_path, 'w') as output_sdf_file:
         output_sdf_file.write(sdf_string)
 
+
 def get_cluster_pdb_codes(pdb_code, cluster, out_log=None, global_log=None):
     """
     Returns:
         String list: The list of pdb_codes of the selected cluster.
     """
-    url="http://mmb.irbbarcelona.org/api/pdb/"
+    url = "http://mmb.irbbarcelona.org/api/pdb/"
     pdb_codes = set()
 
     url = url+pdb_code.lower()+'/clusters/cl-'+str(cluster)+".json"
@@ -232,6 +248,7 @@ def get_cluster_pdb_codes(pdb_code, cluster, out_log=None, global_log=None):
 
     return pdb_codes
 
+
 def get_uniprot(pdb_code, url, out_log=None, global_log=None):
     """Returns the UNIPROT code corresponding to the `pdb_code`.
 
@@ -248,6 +265,7 @@ def get_uniprot(pdb_code, url, out_log=None, global_log=None):
 
     return uniprot_id
 
+
 def get_variants(uniprot_id, url="http://mmb.irbbarcelona.org/api", out_log=None, global_log=None):
     """Returns the variants of the `uniprot_id` code.
 
@@ -261,12 +279,14 @@ def get_variants(uniprot_id, url="http://mmb.irbbarcelona.org/api", out_log=None
     fu.log('Found: %d variants for uniprot id: %s' % (len(variants), uniprot_id), out_log, global_log)
     return variants if variants else []
 
+
 def write_json(json_string, output_json_path, out_log=None, global_log=None):
     """ Writes a JSON """
     fu.log("Writting json to: %s" % (output_json_path), out_log, global_log)
     with open(output_json_path, 'w') as output_json_file:
         output_json_file.write(json_string)
 
+
 def get_memprotmd_sim_list(out_log=None, global_log=None):
     """ Returns all available membrane-protein systems (simulations) from the MemProtMD DB using its REST API """
 
@@ -280,6 +300,7 @@ def get_memprotmd_sim_list(out_log=None, global_log=None):
 
     return json_string
 
+
 def get_memprotmd_sim_search(collection_name, keyword, out_log=None, global_log=None):
     """ Performs advanced searches in the MemProtMD DB using its REST API and a given keyword """
 
@@ -287,14 +308,14 @@ def get_memprotmd_sim_search(collection_name, keyword, out_log=None, global_log=
 
     url = "http://memprotmd.bioch.ox.ac.uk/api/search/advanced"
     json_query = {
-        "collectionName" : collection_name,
-        "query" : {
-            "keywords" : keyword
+        "collectionName": collection_name,
+        "query": {
+            "keywords": keyword
         },
-        "projection" : {
-            "simulations" : 1
+        "projection": {
+            "simulations": 1
         },
-        "options" : {}
+        "options": {}
     }
 
     json_obj = requests.post(url, json=json_query).json()
@@ -310,18 +331,20 @@ def get_memprotmd_sim_search(collection_name, keyword, out_log=None, global_log=
 
     return json_string
 
+
 def get_memprotmd_sim(pdb_code, output_file, out_log=None, global_log=None):
     """ Gets a single simulation from MemProtMD DB """
 
     fu.log('Getting simulation file from pdb code %s' % (pdb_code), out_log, global_log)
 
-    url = "http://memprotmd.bioch.ox.ac.uk/data/memprotmd/simulations/"+ pdb_code + "_default_dppc/files/run/at.zip"
+    url = "http://memprotmd.bioch.ox.ac.uk/data/memprotmd/simulations/" + pdb_code + "_default_dppc/files/run/at.zip"
     response = requests.get(url)
 
     open(output_file, 'wb').write(response.content)
-    
+
     fu.log("Saving output %s file" % (output_file), out_log, global_log)
 
+
 def check_mandatory_property(property, name, out_log, classname):
     """ Checks mandatory properties """
 
@@ -330,6 +353,7 @@ def check_mandatory_property(property, name, out_log, classname):
         raise SystemExit(classname + ': Unexisting %s property' % name)
     return property
 
+
 def check_uniprot_code(code, out_log, classname):
     """ Checks uniprot code """
 
@@ -339,4 +363,4 @@ def check_uniprot_code(code, out_log, classname):
         fu.log(classname + ': Incorrect uniprot code for %s' % code, out_log)
         raise SystemExit(classname + ': Incorrect uniprot code for %s' % code)
 
-    return True
+    return True