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

biobb_io/api/pdb_variants.py

@@ -1,14 +1,23 @@
 #!/usr/bin/env python
 
 """PdbVariants Module"""
-import re
+
 import argparse
+import re
+from typing import Optional
+
 import requests
-from biobb_common.generic.biobb_object import BiobbObject
 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_uniprot, get_variants
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    get_uniprot,
+    get_variants,
+)
 
 
 class PdbVariants(BiobbObject):
@@ -23,6 +32,7 @@ class PdbVariants(BiobbObject):
             * **pdb_code** (*str*) - (None) RSCB PDB four letter 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 PdbVariants module from Python
@@ -31,7 +41,7 @@ class PdbVariants(BiobbObject):
             prop = {
                 'pdb_code': '2VGB'
             }
-            pdb_variants(output_mutations_list_txt='/path/to/newMutationsList.txt',
+            pdb_variants(output_mutations_list_txt='/path/to/newMutationslist.txt',
                         properties=prop)
 
     Info:
@@ -44,8 +54,7 @@ class PdbVariants(BiobbObject):
 
     """
 
-    def __init__(self, output_mutations_list_txt,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_mutations_list_txt, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -53,12 +62,10 @@ class PdbVariants(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_mutations_list_txt": output_mutations_list_txt}
-        }
+        self.io_dict = {"out": {"output_mutations_list_txt": output_mutations_list_txt}}
 
         # 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
@@ -66,8 +73,14 @@ class PdbVariants(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_mutations_list_txt = check_output_path(self.io_dict["out"]["output_mutations_list_txt"], "output_mutations_list_txt", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_mutations_list_txt = check_output_path(
+            self.io_dict["out"]["output_mutations_list_txt"],
+            "output_mutations_list_txt",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -80,36 +93,72 @@ class PdbVariants(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()
 
-        url = 'http://mmb.irbbarcelona.org/api'
+        url = "http://mmb.irbbarcelona.org/api"
         uniprot_id = get_uniprot(self.pdb_code, url, self.out_log, self.global_log)
-        url_mapPDBRes = (url+"/uniprot/"+uniprot_id+"/mapPDBRes?pdbId="+self.pdb_code)
-        pattern = re.compile((r"p.(?P<wt>[a-zA-Z]{3})(?P<resnum>\d+)(?P<mt>[a-zA-Z]{3})"))
-
-        fu.log('Fetching variants for uniprot_id: %s and pdb_code: %s' % (uniprot_id, self.pdb_code), self.out_log, self.global_log)
-        unfiltered_dic = requests.get(url_mapPDBRes, verify=False).json()
+        url_mapPDBRes = (
+            url + "/uniprot/" + uniprot_id + "/mapPDBRes?pdbId=" + self.pdb_code
+        )
+        pattern = re.compile(
+            (r"p.(?P<wt>[a-zA-Z]{3})(?P<resnum>\d+)(?P<mt>[a-zA-Z]{3})")
+        )
+
+        fu.log(
+            "Fetching variants for uniprot_id: %s and pdb_code: %s"
+            % (uniprot_id, self.pdb_code),
+            self.out_log,
+            self.global_log,
+        )
+        unfiltered_dic = requests.get(url_mapPDBRes, verify=True).json()
         if not unfiltered_dic:
             fu.log("No mutation found", self.out_log, self.global_log)
-            return None
+            return 1
 
-        mapdic = requests.get(url_mapPDBRes, verify=False).json()
+        mapdic = requests.get(url_mapPDBRes, verify=True).json()
         mutations = []
         uniprot_var_list = get_variants(uniprot_id, url, self.out_log, self.global_log)
         for var in uniprot_var_list:
-            uni_mut = pattern.match(var).groupdict()
+            match = pattern.match(var)
+            if match:
+                uni_mut = match.groupdict()
+            else:
+                continue
             for k in mapdic.keys():
                 for fragment in mapdic[k]:
-                    if int(fragment['unp_start']) <= int(uni_mut['resnum']) <= int(fragment['unp_end']):
-                        resnum = int(uni_mut['resnum']) + int(fragment['pdb_start']) - int(fragment['unp_start'])
-                        mutations.append(k[-1]+'.'+uni_mut['wt']+str(resnum)+uni_mut['mt'])
-
-        fu.log('Found %d mutations mapped to PDB: %s' % (len(mutations), self.pdb_code), self.out_log, self.global_log)
-        fu.log('Writting mutations to: %s' % self.output_mutations_list_txt, self.out_log, self.global_log)
-
-        with open(self.output_mutations_list_txt, 'w') as mut_file:
+                    if (
+                        int(fragment["unp_start"])
+                        <= int(uni_mut["resnum"])
+                        <= int(fragment["unp_end"])
+                    ):
+                        resnum = (
+                            int(uni_mut["resnum"])
+                            + int(fragment["pdb_start"])
+                            - int(fragment["unp_start"])
+                        )
+                        mutations.append(
+                            k[-1] + "." + uni_mut["wt"] + str(resnum) + uni_mut["mt"]
+                        )
+
+        fu.log(
+            "Found %d mutations mapped to PDB: %s" % (len(mutations), self.pdb_code),
+            self.out_log,
+            self.global_log,
+        )
+        fu.log(
+            "Writting mutations to: %s" % self.output_mutations_list_txt,
+            self.out_log,
+            self.global_log,
+        )
+
+        if not self.output_mutations_list_txt:
+            raise ValueError("Output mutations list file path is not specified.")
+
+        with open(self.output_mutations_list_txt, "w") as mut_file:
             mutations.sort()
             mut_file.write(",".join(mutations))
 
@@ -118,31 +167,50 @@ class PdbVariants(BiobbObject):
         return 0
 
 
-def pdb_variants(output_mutations_list_txt: str, properties: dict = None, **kwargs) -> int:
+def pdb_variants(
+    output_mutations_list_txt: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` class and
     execute the :meth:`launch() <api.pdb_variants.PdbVariants.launch>` method."""
 
-    return PdbVariants(output_mutations_list_txt=output_mutations_list_txt,
-                       properties=properties, **kwargs).launch()
+    return PdbVariants(
+        output_mutations_list_txt=output_mutations_list_txt,
+        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 UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.", 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 UNIPROT (http://www.uniprot.org/) mirror of the MMB group REST API (http://mmb.irbbarcelona.org/api/) for creating a list of all the variants mapped to a PDB code from the corresponding UNIPROT entries.",
+        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_mutations_list_txt', required=True, help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_mutations_list_txt",
+        required=True,
+        help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.",
+    )
 
     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_variants(output_mutations_list_txt=args.output_mutations_list_txt,
-                 properties=properties)
+    pdb_variants(
+        output_mutations_list_txt=args.output_mutations_list_txt, properties=properties
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

biobb_io/api/structure_info.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
 
 """Module containing the StructureInfo 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_str_info, write_json
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_str_info,
+    write_json,
+)
 
 
 class StructureInfo(BiobbObject):
@@ -20,6 +29,7 @@ class StructureInfo(BiobbObject):
             * **pdb_code** (*str*) - (None) RSCB PDB structure 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 +51,7 @@ class StructureInfo(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
@@ -50,12 +59,10 @@ class StructureInfo(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
-        self.pdb_code = properties.get('pdb_code', None)
+        self.pdb_code = properties.get("pdb_code", None)
         self.properties = properties
 
         # Check the properties
@@ -63,8 +70,14 @@ class StructureInfo(BiobbObject):
         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__)
+        """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__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -77,13 +90,17 @@ class StructureInfo(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()
         url = "http://mmb.irbbarcelona.org/api/pdb/%s.json"
 
         # Downloading PDB file
-        json_string = download_str_info(self.pdb_code, url, self.out_log, self.global_log)
+        json_string = download_str_info(
+            self.pdb_code, url, self.out_log, self.global_log
+        )
         write_json(json_string, self.output_json_path, self.out_log, self.global_log)
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -91,31 +108,46 @@ class StructureInfo(BiobbObject):
         return 0
 
 
-def structure_info(output_json_path: str, properties: dict = None, **kwargs) -> int:
+def structure_info(
+    output_json_path: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`StructureInfo <api.structure_info.StructureInfo>` class and
     execute the :meth:`launch() <api.structure_info.StructureInfo.launch>` method."""
 
-    return StructureInfo(output_json_path=output_json_path,
-                         properties=properties, **kwargs).launch()
+    return StructureInfo(
+        output_json_path=output_json_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 getting all the available information of a 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 getting all the available information of a 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_json_path', required=True, help="Path to the output JSON file with all the structure information. Accepted formats: json.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_json_path",
+        required=True,
+        help="Path to the output JSON file with all the structure information. 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
-    structure_info(output_json_path=args.output_json_path,
-                   properties=properties)
+    structure_info(output_json_path=args.output_json_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

{biobb_io-4.2.0.dist-info → biobb_io-5.0.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: biobb-io
-Version: 4.2.0
+Name: biobb_io
+Version: 5.0.1
 Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
 Home-page: https://github.com/bioexcel/biobb_io
 Author: Biobb developers
@@ -8,24 +8,23 @@ Author-email: pau.andrio@bsc.es
 Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
 Project-URL: Bioexcel, https://bioexcel.eu/
 Keywords: Bioinformatics Workflows BioExcel Compatibility
-Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
-Requires-Python: >=3.8
+Classifier: Operating System :: Unix
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biobb-common ==4.2.0
+Requires-Dist: biobb-common==5.0.0
 
 [![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/)
 [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/)
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -34,7 +33,7 @@ Requires-Dist: biobb-common ==4.2.0
 
 [![](https://readthedocs.org/projects/biobb-io/badge/?version=latest&label=Docs)](https://biobb-io.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
-[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
 [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
 [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
 
@@ -63,7 +62,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.1
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -72,15 +71,15 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.2.0"
-        
+        pip install "biobb_io==5.0.1"
+
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
 Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.2.0"
+        conda install -c bioconda "biobb_io==5.0.1"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -89,12 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -106,7 +105,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
 
 
 * Usage:

biobb_io-5.0.1.dist-info/RECORD

@@ -0,0 +1,24 @@
+biobb_io/__init__.py,sha256=5fB4i9qgGOZ0ZrZRiZrdxgVxzntL56ErhlDSvnqqnP8,77
+biobb_io/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biobb_io/api/__init__.py,sha256=fR17sA2mh78x2NoyM25XN3vlsjka4aNubzaP4SvpCDc,538
+biobb_io/api/alphafold.py,sha256=e_5N0yntKTjI-Sd9cM1IGv56FwlD1HqeODXooSLmSBg,5402
+biobb_io/api/api_binding_site.py,sha256=cu6McFh1e75J8JMaZHjnfiK2ljQVOsREsXH3ZvOyUyU,5884
+biobb_io/api/canonical_fasta.py,sha256=DTwvoV8yY_xX_X3E9PbhucNaLk21jJ-K_34db1p9SOU,5785
+biobb_io/api/common.py,sha256=TQD3oSWL-WtXxJHnNp9469Iun-REqFeAb8dmKWU3UJc,13384
+biobb_io/api/ideal_sdf.py,sha256=MxNiFLoQU0tF7k3mztDYHkIpmZ5s9Z0p4BI-NlTW7Dc,5599
+biobb_io/api/ligand.py,sha256=_iFZWxuMPz2c0IOQPpeaBsvjsFcOr0wqtf0c6QICX2M,5654
+biobb_io/api/memprotmd_sim.py,sha256=bnZFaAMkMIYzS75VognyNh0H8F5gZCwQM1ErhLrrtWw,5167
+biobb_io/api/memprotmd_sim_list.py,sha256=zFsaM-d2efmiWPbMEMFEUmKKet9P18O4-7XsMxgh3a4,5099
+biobb_io/api/memprotmd_sim_search.py,sha256=_bTzx552Sn2GiogGojWL5uR8mPNsgJwEUxA9P_jgiKE,7452
+biobb_io/api/mmcif.py,sha256=kntBTLcWpxAubyjtSMEokP7ZyzmTWRyx36zqCEfnVgg,5690
+biobb_io/api/pdb.py,sha256=mpaMklW3N5avUO08W3bB75cPRfPHcRccDB8TaG-xLF8,6024
+biobb_io/api/pdb_cluster_zip.py,sha256=eml2QmX0NTUk8YkEwDPqSPu3ZjTtBqYUVl9r4eWtFzs,7749
+biobb_io/api/pdb_variants.py,sha256=GbovaDIQZQDPiSQaHp1ohr_Ds3eucdkdLR7bcW3c7Q4,7969
+biobb_io/api/structure_info.py,sha256=VKy9lxMTpbkGMuxWoEwP9NLwdw8AapLFutHs8J0qgjA,5503
+biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biobb_io-5.0.1.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+biobb_io-5.0.1.dist-info/METADATA,sha256=fbV5Ca_iWW37qv4RVIsre4cCvwBx7BPtwUGWduZBsk4,6713
+biobb_io-5.0.1.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+biobb_io-5.0.1.dist-info/entry_points.txt,sha256=UdQz4F28f13ergWXqKMrx15mH05nX7G85xBaP8W2Wdw,614
+biobb_io-5.0.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
+biobb_io-5.0.1.dist-info/RECORD,,

{biobb_io-4.2.0.dist-info → biobb_io-5.0.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{biobb_io-4.2.0.dist-info → biobb_io-5.0.1.dist-info}/entry_points.txt

@@ -2,7 +2,6 @@
 alphafold = biobb_io.api.alphafold:main
 api_binding_site = biobb_io.api.api_binding_site:main
 canonical_fasta = biobb_io.api.canonical_fasta:main
-drugbank = biobb_io.api.drugbank:main
 ideal_sdf = biobb_io.api.ideal_sdf:main
 ligand = biobb_io.api.ligand:main
 memprotmd_sim = biobb_io.api.memprotmd_sim:main

biobb_io/api/drugbank.py

@@ -1,121 +0,0 @@
-#!/usr/bin/env python
-
-"""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.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, download_drugbank, write_sdf
-
-
-class Drugbank(BiobbObject):
-    """
-    | biobb_io Drugbank
-    | This class is a wrapper for the `Drugbank <https://www.drugbank.ca/>`_ REST API.
-    | Download a single component in SDF format from the `Drugbank <https://www.drugbank.ca/>`_ REST API.
-
-    Args:
-        output_sdf_path (str): Path to the output SDF component file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_drugbank.sdf>`_. Accepted formats: sdf (edam:format_3814).
-        properties (dic - Python dictionary object containing the tool parameters, not input/output files):
-            * **drugbank_id** (*str*) - (None) Drugbank component id.
-            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
-            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
-
-    Examples:
-        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'
-            }
-            drugbank(output_sdf_path='/path/to/newComponent.sdf',
-                    properties=prop)
-
-    Info:
-        * wrapped_software:
-            * name: Drugbank
-            * license: Creative Commons
-        * ontology:
-            * name: EDAM
-            * schema: http://edamontology.org/EDAM.owl
-
-    """
-
-    def __init__(self, output_sdf_path,
-                 properties=None, **kwargs) -> None:
-        properties = properties or {}
-
-        # Call parent class constructor
-        super().__init__(properties)
-        self.locals_var_dict = locals().copy()
-
-        # Input/Output files
-        self.io_dict = {
-            "out": {"output_sdf_path": output_sdf_path}
-        }
-
-        # Properties specific for BB
-        self.drugbank_id = properties.get('drugbank_id', 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_sdf_path = check_output_path(self.io_dict["out"]["output_sdf_path"], "output_sdf_path", False, out_log, self.__class__.__name__)
-
-    @launchlogger
-    def launch(self) -> int:
-        """Execute the :class:`Drugbank <api.drugbank.Drugbank>` api.drugbank.Drugbank 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
-
-        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
-        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)
-
-        self.check_arguments(output_files_created=True, raise_exception=False)
-
-        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."""
-
-    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
-    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.")
-
-    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
-    drugbank(output_sdf_path=args.output_sdf_path,
-             properties=properties)
-
-
-if __name__ == '__main__':
-    main()