biobb-io 5.0.0__tar.gz → 5.0.1__tar.gz

{biobb_io-5.0.0 → biobb_io-5.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biobb_io
-Version: 5.0.0
+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
@@ -24,7 +24,7 @@ Requires-Dist: biobb_common==5.0.0
 [![](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:5.0.0--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/)
@@ -62,7 +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
-v5.0.0 2024.2
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -71,7 +71,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.0"
+        pip install "biobb_io==5.0.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -79,7 +79,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.0"
+        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)
@@ -88,12 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.0--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).
@@ -105,7 +105,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
 
 
 * Usage:

{biobb_io-5.0.0 → biobb_io-5.0.1}/README.md

@@ -3,7 +3,7 @@
 [![](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:5.0.0--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/)
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v5.0.0 2024.2
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -50,7 +50,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.0"
+        pip install "biobb_io==5.0.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -58,7 +58,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.0"
+        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)
@@ -67,12 +67,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.0--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).
@@ -84,7 +84,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
 
 
 * Usage:

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io/__init__.py

@@ -2,4 +2,4 @@ from . import api
 
 name = "biobb_io"
 __all__ = ["api"]
-__version__ = "5.0.0"
+__version__ = "5.0.1"

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io/api/__init__.py

@@ -2,7 +2,6 @@ from . import (
     alphafold,
     api_binding_site,
     canonical_fasta,
-    drugbank,
     ideal_sdf,
     ligand,
     memprotmd_sim,
@@ -17,7 +16,6 @@ from . import (
 
 name = "api"
 __all__ = [
-    "drugbank",
     "ligand",
     "pdb",
     "alphafold",

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io/api/common.py

@@ -143,25 +143,6 @@ def download_fasta(pdb_code, api_id, out_log=None, global_log=None):
     return requests.get(url, verify=True).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:
-        String: Content of the component file.
-    """
-    url = url % drugbank_id
-
-    fu.log("Downloading %s from: %s" % (drugbank_id, url), out_log, global_log)
-
-    text = requests.get(url, verify=True).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",

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biobb_io
-Version: 5.0.0
+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
@@ -24,7 +24,7 @@ Requires-Dist: biobb_common==5.0.0
 [![](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:5.0.0--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/)
@@ -62,7 +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
-v5.0.0 2024.2
+v5.0.1 2024.2
 
 ### Installation
 Using PIP:
@@ -71,7 +71,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==5.0.0"
+        pip install "biobb_io==5.0.1"
 
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -79,7 +79,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==5.0.0"
+        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)
@@ -88,12 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:5.0.0--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).
@@ -105,7 +105,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.1--pyhdfd78af_0
 
 
 * Usage:

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io.egg-info/SOURCES.txt

@@ -14,7 +14,6 @@ biobb_io/api/alphafold.py
 biobb_io/api/api_binding_site.py
 biobb_io/api/canonical_fasta.py
 biobb_io/api/common.py
-biobb_io/api/drugbank.py
 biobb_io/api/ideal_sdf.py
 biobb_io/api/ligand.py
 biobb_io/api/memprotmd_sim.py

{biobb_io-5.0.0 → biobb_io-5.0.1}/biobb_io.egg-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-5.0.0 → biobb_io-5.0.1}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="biobb_io",
-    version="5.0.0",
+    version="5.0.1",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.",
@@ -26,7 +26,6 @@ setuptools.setup(
             "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_list = biobb_io.api.memprotmd_sim_list:main",

biobb_io-5.0.0/biobb_io/api/drugbank.py

@@ -1,151 +0,0 @@
-#!/usr/bin/env python
-
-"""Module containing the Drugbank class and the command line interface."""
-
-import argparse
-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_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.
-            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
-
-    Examples:
-        This is a use example of how to use the building block from Python::
-
-            from biobb_io.api.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: Optional[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()