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

biobb_io/api/mmcif.py

@@ -3,10 +3,9 @@
 """Module containing the Mmcif 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_mmcif, write_mmcif
 
 
 class Mmcif(BiobbObject):
@@ -27,11 +26,11 @@ class Mmcif(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.mmcif import mmcif
-            prop = { 
-                'pdb_code': '2VGB', 
-                'api_id': 'pdbe' 
+            prop = {
+                'pdb_code': '2VGB',
+                'api_id': 'pdbe'
             }
-            mmcif(output_mmcif_path='/path/to/newStructure.mmcif', 
+            mmcif(output_mmcif_path='/path/to/newStructure.mmcif',
                 properties=prop)
 
     Info:
@@ -44,8 +43,8 @@ class Mmcif(BiobbObject):
 
     """
 
-    def __init__(self, output_mmcif_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_mmcif_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -53,8 +52,8 @@ class Mmcif(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_mmcif_path": output_mmcif_path } 
+        self.io_dict = {
+            "out": {"output_mmcif_path": output_mmcif_path}
         }
 
         # Properties specific for BB
@@ -73,13 +72,13 @@ class Mmcif(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`Mmcif <api.mmcif.Mmcif>` api.mmcif.Mmcif 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__)
 
@@ -93,12 +92,14 @@ class Mmcif(BiobbObject):
 
         return 0
 
+
 def mmcif(output_mmcif_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`Mmcif <api.mmcif.Mmcif>` class and
     execute the :meth:`launch() <api.mmcif.Mmcif.launch>` method."""
 
     return Mmcif(output_mmcif_path=output_mmcif_path,
-                properties=properties, **kwargs).launch()
+                 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
-    mmcif(output_mmcif_path=args.output_mmcif_path, 
-        properties=properties)
+    mmcif(output_mmcif_path=args.output_mmcif_path,
+          properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/pdb.py

@@ -3,10 +3,9 @@
 """Module containing the Pdb 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_mandatory_property, check_output_path, download_pdb, write_pdb
 
 
 class Pdb(BiobbObject):
@@ -28,12 +27,12 @@ class Pdb(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.pdb import pdb
-            prop = { 
-                'pdb_code': '2VGB', 
-                'filter': ['ATOM', 'MODEL', 'ENDMDL'], 
-                'api_id': 'pdbe' 
+            prop = {
+                'pdb_code': '2VGB',
+                'filter': ['ATOM', 'MODEL', 'ENDMDL'],
+                'api_id': 'pdbe'
             }
-            pdb(output_pdb_path='/path/to/newStructure.pdb', 
+            pdb(output_pdb_path='/path/to/newStructure.pdb',
                 properties=prop)
 
     Info:
@@ -46,8 +45,8 @@ class Pdb(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -55,8 +54,8 @@ class Pdb(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_pdb_path": output_pdb_path } 
+        self.io_dict = {
+            "out": {"output_pdb_path": output_pdb_path}
         }
 
         # Properties specific for BB
@@ -76,13 +75,13 @@ class Pdb(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`Pdb <api.pdb.Pdb>` api.pdb.Pdb 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__)
 
@@ -96,12 +95,14 @@ class Pdb(BiobbObject):
 
         return 0
 
+
 def pdb(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`Pdb <api.pdb.Pdb>` class and
     execute the :meth:`launch() <api.pdb.Pdb.launch>` method."""
 
     return Pdb(output_pdb_path=output_pdb_path,
-                properties=properties, **kwargs).launch()
+               properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -117,8 +118,9 @@ def main():
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    pdb(output_pdb_path=args.output_pdb_path, 
+    pdb(output_pdb_path=args.output_pdb_path,
         properties=properties)
 
+
 if __name__ == '__main__':
     main()

biobb_io/api/pdb_cluster_zip.py

@@ -4,10 +4,10 @@
 import os
 import argparse
 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_mandatory_property, check_output_path, get_cluster_pdb_codes, download_pdb, write_pdb
 
 
 class PdbClusterZip(BiobbObject):
@@ -30,13 +30,13 @@ class PdbClusterZip(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.pdb_cluster_zip import pdb_cluster_zip
-            prop = { 
-                'pdb_code': '2VGB', 
-                'filter': ['ATOM', 'MODEL', 'ENDMDL'], 
-                'cluster': 90, 
-                'api_id': 'pdbe' 
+            prop = {
+                'pdb_code': '2VGB',
+                'filter': ['ATOM', 'MODEL', 'ENDMDL'],
+                'cluster': 90,
+                'api_id': 'pdbe'
             }
-            pdb_cluster_zip(output_pdb_zip_path='/path/to/newStructures.zip', 
+            pdb_cluster_zip(output_pdb_zip_path='/path/to/newStructures.zip',
                             properties=prop)
 
     Info:
@@ -49,8 +49,8 @@ class PdbClusterZip(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_zip_path, 
-                properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_zip_path,
+                 properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -58,8 +58,8 @@ class PdbClusterZip(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = { 
-            "out": { "output_pdb_zip_path": output_pdb_zip_path } 
+        self.io_dict = {
+            "out": {"output_pdb_zip_path": output_pdb_zip_path}
         }
 
         # Properties specific for BB
@@ -80,20 +80,20 @@ class PdbClusterZip(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` api.pdb_cluster_zip.PdbClusterZip 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__)
 
         self.pdb_code = self.pdb_code.strip().lower()
 
         file_list = []
-        #Downloading PDB_files
+        # Downloading PDB_files
         pdb_code_list = get_cluster_pdb_codes(pdb_code=self.pdb_code, cluster=self.cluster, out_log=self.out_log, global_log=self.global_log)
         unique_dir = fu.create_unique_dir()
         for pdb_code in pdb_code_list:
@@ -102,7 +102,7 @@ class PdbClusterZip(BiobbObject):
             write_pdb(pdb_string, pdb_file, self.filter, self.out_log, self.global_log)
             file_list.append(os.path.abspath(pdb_file))
 
-        #Zipping files
+        # Zipping files
         fu.log("Zipping the pdb files to: %s" % self.output_pdb_zip_path)
         fu.zip_list(self.output_pdb_zip_path, file_list, out_log=self.out_log)
 
@@ -116,29 +116,32 @@ class PdbClusterZip(BiobbObject):
 
         return 0
 
+
 def pdb_cluster_zip(output_pdb_zip_path: str, properties: dict = None, **kwargs) -> int:
     """Execute the :class:`PdbClusterZip <api.pdb_cluster_zip.PdbClusterZip>` class and
     execute the :meth:`launch() <api.pdb_cluster_zip.PdbClusterZip.launch>` method."""
 
     return PdbClusterZip(output_pdb_zip_path=output_pdb_zip_path,
-                        properties=properties, **kwargs).launch()
+                         properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
     parser = argparse.ArgumentParser(description="Wrapper for the Protein Data Bank in Europe (https://www.ebi.ac.uk/pdbe/), the Protein Data Bank (https://www.rcsb.org/) and the MMB PDB mirror (http://mmb.irbbarcelona.org/api/) for downloading a PDB cluster.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
     parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
 
-    #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_zip_path', required=True, help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.")
+    required_args.add_argument('-o', '--output_pdb_zip_path', required=True, help="Path to the ZIP or PDB file containing the output PDB files. Accepted formats: pdb, zip.")
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path, 
-                properties=properties)
+    # Specific call of each building block
+    pdb_cluster_zip(output_pdb_zip_path=args.output_pdb_zip_path,
+                    properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/pdb_variants.py

@@ -5,10 +5,10 @@ import re
 import argparse
 import requests
 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_mandatory_property, check_output_path, get_uniprot, get_variants
 
 
 class PdbVariants(BiobbObject):
@@ -28,10 +28,10 @@ class PdbVariants(BiobbObject):
             This is a use example of how to use the PdbVariants module from Python
 
             from biobb_io.api.pdb_variants import pdb_variants
-            prop = { 
-                'pdb_code': '2VGB' 
+            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 +44,8 @@ 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
@@ -53,8 +53,8 @@ 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
@@ -72,13 +72,13 @@ class PdbVariants(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`PdbVariants <api.pdb_variants.PdbVariants>` api.pdb_variants.PdbVariants 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__)
 
@@ -117,19 +117,21 @@ class PdbVariants(BiobbObject):
 
         return 0
 
+
 def pdb_variants(output_mutations_list_txt: str, properties: 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()
+                       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")
 
-    #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_mutations_list_txt', required=True, help="Path to the TXT file containing an ASCII comma separated values of the mutations. Accepted formats: txt.")
 
@@ -137,9 +139,10 @@ def main():
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
-    #Specific call of each building block
-    pdb_variants(output_mutations_list_txt=args.output_mutations_list_txt, 
-                properties=properties)
+    # Specific call of each building block
+    pdb_variants(output_mutations_list_txt=args.output_mutations_list_txt,
+                 properties=properties)
+
 
 if __name__ == '__main__':
     main()

biobb_io/api/structure_info.py

@@ -3,10 +3,9 @@
 """Module containing the StructureInfo 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_mandatory_property, check_output_path, download_str_info, write_json
 
 
 class StructureInfo(BiobbObject):
@@ -26,10 +25,10 @@ class StructureInfo(BiobbObject):
         This is a use example of how to use the building block from Python::
 
             from biobb_io.api.structure_info import structure_info
-            prop = { 
+            prop = {
                 'pdb_code': '2vgb'
             }
-            structure_info(output_json_path='/path/to/newStructure.sdf', 
+            structure_info(output_json_path='/path/to/newStructure.sdf',
                         properties=prop)
 
     Info:
@@ -42,17 +41,17 @@ 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
+        # Call parent class constructor
         super().__init__(properties)
         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
@@ -70,13 +69,13 @@ class StructureInfo(BiobbObject):
     @launchlogger
     def launch(self) -> int:
         """Execute the :class:`StructureInfo <api.structure_info.StructureInfo>` api.structure_info.StructureInfo 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__)
 
@@ -91,12 +90,14 @@ class StructureInfo(BiobbObject):
 
         return 0
 
+
 def structure_info(output_json_path: str, properties: 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()
+                         properties=properties, **kwargs).launch()
+
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
@@ -112,8 +113,9 @@ def main():
     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__':
     main()

{biobb_io-4.0.0.dist-info → biobb_io-4.1.1.dist-info}/METADATA

@@ -1,29 +1,31 @@
 Metadata-Version: 2.1
 Name: biobb-io
-Version: 4.0.0
+Version: 4.1.1
 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
 Author-email: pau.andrio@bsc.es
-Project-URL: Documentation, http://biobb_io.readthedocs.io/en/latest/
+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 :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+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: >=3.7,<3.10
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biobb-common (==4.0.0)
+Requires-Dist: biobb-common ==4.1.0
 
 [![](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:4.0.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--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/)
@@ -42,6 +44,13 @@ Requires-Dist: biobb-common (==4.0.0)
 [![](https://img.shields.io/github/last-commit/bioexcel/biobb_io?label=Last%20Commit)](https://github.com/bioexcel/biobb_io/commits/master)
 [![](https://img.shields.io/github/issues/bioexcel/biobb_io.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_io/issues/)
 
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![](https://www.bestpractices.dev/projects/8847/badge)](https://www.bestpractices.dev/projects/8847)
+
+[](https://bestpractices.coreinfrastructure.org/projects/8847/badge)
+
+[//]: # (The previous line invisible link is for compatibility with the howfairis script https://github.com/fair-software/howfairis-github-action/tree/main wich uses the old bestpractices URL)
+
 # biobb_io
 
 ### Introduction
@@ -51,10 +60,10 @@ Biobb (BioExcel building blocks) packages are Python building blocks that
 create new layer of compatibility and interoperability over popular
 bioinformatics tools.
 The latest documentation of this package can be found in our readthedocs site:
-[latest API documentation](http://biobb_io.readthedocs.io/en/latest/).
+[latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.0.0 2023.1
+v4.1.1 2024.1
 
 ### Installation
 Using PIP:
@@ -63,7 +72,7 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.0.0"
+        pip install "biobb_io==4.1.1"
         
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
@@ -71,7 +80,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.0.0"
+        conda install -c bioconda "biobb_io==4.1.1"
 
 
 * 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)
@@ -80,12 +89,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:4.1.1--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.0.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:4.1.1--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).
@@ -97,7 +106,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.0.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.1--pyhdfd78af_0
 
 
 * Usage:
@@ -112,8 +121,8 @@ The command list and specification can be found at the [Command Line documentati
 ### Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

biobb_io-4.1.1.dist-info/RECORD

@@ -0,0 +1,24 @@
+biobb_io/__init__.py,sha256=YnMm0jECNA47bXcB-AlNLM-l2fiyr6W7UGjVK7c2440,58
+biobb_io/api/__init__.py,sha256=5jF02xLDXfTBDU2Pie2NTOwoB71lEv-Dikt1WK9s72Y,243
+biobb_io/api/alphafold.py,sha256=qSnJHUjbgd6p0tTszbl4fNPLKjOOGrrV4-KxCWoS8CE,5082
+biobb_io/api/api_binding_site.py,sha256=wOT2S6FspS7hVh8e8t4tfwI6vcEDxU-lhbWyUKOwQxY,5527
+biobb_io/api/canonical_fasta.py,sha256=rMaomcSY91b3BlwyphQp6kFNpDhKcc4EF81mLny59WM,5474
+biobb_io/api/common.py,sha256=7tcV25MpeUaeC-4Ll07YXTVI3_RukmQ4qFUJN2Qt3Xc,13075
+biobb_io/api/drugbank.py,sha256=adxIVX7BH734zoEv_Y9OYKKzrPWatniXP7Xhk8vMGk0,4942
+biobb_io/api/ideal_sdf.py,sha256=KmoNT9_J4Ilubn0iejOgcs-ST6d0DsCeNeg8z8ca94s,5282
+biobb_io/api/ligand.py,sha256=HTO9bCxPQ3bhwBKzRR1eDxh1SrjRqIUIrLIYl8pLgVI,5332
+biobb_io/api/memprotmd_sim.py,sha256=3fsUCsmetD2gj0NQQ6tMXe5UOQFDlgf_BmjksfnPRLc,4856
+biobb_io/api/memprotmd_sim_list.py,sha256=vecN645pMVLjM7WhHjcJqadzbXWHrA37tKsORclkLfo,4821
+biobb_io/api/memprotmd_sim_search.py,sha256=zWv5ubqcJ765CCUVUFro48XPepzfS5iKR9qIJdSaJfw,7179
+biobb_io/api/mmcif.py,sha256=XnCrYB94r6TtR4K5kPQiNhpdliWyU_rQunCPXbfxFJI,5366
+biobb_io/api/pdb.py,sha256=9qAhep1m-xy50n04EiQxgJn01WHJBlKazLyp06keroY,5674
+biobb_io/api/pdb_cluster_zip.py,sha256=gV3QubG9Vqz9TxunLPTB5TwFGHgaKzMNa8kkPqs6G4c,7345
+biobb_io/api/pdb_variants.py,sha256=kmV_BvXFNTY-REFgZJj2vXmbOjv9RvbrzPXvJb7WJSc,6948
+biobb_io/api/structure_info.py,sha256=_hPSOfBhQZ1cCA1LovitsI4wVMw_lskXHhcsyZTW3V8,5190
+biobb_io/test/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biobb_io-4.1.1.dist-info/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+biobb_io-4.1.1.dist-info/METADATA,sha256=bAUWN7WcPlq8sJFOYTcXHSdzwri0bBKbNFtJ7qoI77g,6761
+biobb_io-4.1.1.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+biobb_io-4.1.1.dist-info/entry_points.txt,sha256=oksijOyG3dbONd1oOcNd5VDcGaHufkIk11ubPka8fJg,652
+biobb_io-4.1.1.dist-info/top_level.txt,sha256=1VPldlX2AnFaqODGFJK10WN8AOQuulpX88bLSaQdoS8,9
+biobb_io-4.1.1.dist-info/RECORD,,

{biobb_io-4.0.0.dist-info → biobb_io-4.1.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.37.1)
+Generator: bdist_wheel (0.41.2)
 Root-Is-Purelib: true
 Tag: py3-none-any