diff --git a/CITATION.cff b/CITATION.cff
index c05ac24..188e629 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -39,7 +39,7 @@ repository-code: "https://github.com/bioexcel/biobb"
 title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
 doi: "10.1038/s41597-019-0177-4"
 url: "https://mmb.irbbarcelona.org/biobb/"
-version: 4.2.0
+version: 5.0.0
 preferred-citation:
   type: "article"
   authors:
diff --git a/README.md b/README.md
index 8b28b48..8200cee 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs)
 [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers.
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.1
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_vs>=4.2.0"
+        pip install "biobb_vs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_vs>=4.2.0"
+        conda install -c bioconda "biobb_vs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_vs/__init__.py b/biobb_vs/__init__.py
index 742d883..f8cab32 100644
--- a/biobb_vs/__init__.py
+++ b/biobb_vs/__init__.py
@@ -1,6 +1,5 @@
-from . import fpocket
-from . import vina
-from . import utils
+from . import fpocket, utils, vina
+
 name = "biobb_vs"
 __all__ = ["fpocket", "vina", "utils"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"
diff --git a/biobb_vs/docs/source/change_log.md b/biobb_vs/docs/source/change_log.md
index eb0081f..25bc1aa 100644
--- a/biobb_vs/docs/source/change_log.md
+++ b/biobb_vs/docs/source/change_log.md
@@ -1,5 +1,19 @@
 # Biobb Virtual Screening changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_vs/releases/tag/v5.0.0)?
+
+### Changes
+
+* [FIX](all): Accept lists in different formats on input properties.
+* [CI/CD](env.yaml): Update biobb_common version.
+* [CI/CD](linting_and_testing.yml): Update set-up micromamba.
+* [CI/CD](linting_and_testing): Update GA test workflow to Python >3.9
+* [DOCS](.readthedocs.yaml): Updating to Python 3.9
+* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
+* [FEATURE](__init__): Importing submodules when a module is loaded
+* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
+* [FEATURE] New sandbox_path property
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_vs/releases/tag/v4.2.0)?
 In version 4.2.0 the dependency biobb_common has been updated to 4.2.0 version.
 
@@ -16,7 +30,7 @@ In version 4.1.2 the code has been updated for being compatible with biopython 1
 * Fpocket fixed to 4.1 version.
 
 ## What's new in version [4.1.1](https://github.com/bioexcel/biobb_vs/releases/tag/v4.1.1)?
-In version 4.1.1 some minor bugs have been fixed. 
+In version 4.1.1 some minor bugs have been fixed.
 
 ### New features
 
@@ -30,7 +44,7 @@ In version 4.1.0 the dependency biobb_common has been updated to 4.1.0 version.
 * Update to biobb_common 4.1.0 (general)
 
 ## What's new in version [4.0.0](https://github.com/bioexcel/biobb_vs/releases/tag/v4.0.0)?
-In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version. Also Autodock Vina has been updated from 1.1.2 to 1.2.3. 
+In version 4.0.0 the dependency biobb_common has been updated to 4.0.0 version. Also Autodock Vina has been updated from 1.1.2 to 1.2.3.
 
 ### New features
 
@@ -46,35 +60,35 @@ In version 3.9.0 the dependency biobb_common has been updated to 3.9.0 version.
 * All inputs/outputs are checked for correct file format, extension and type (general)
 
 ## What's new in version [3.8.1](https://github.com/bioexcel/biobb_vs/releases/tag/v3.8.1)?
-In version 3.8.1 the AutoDockVinaRun and FPocketRun tools have added the ability to be executed through docker. 
+In version 3.8.1 the AutoDockVinaRun and FPocketRun tools have added the ability to be executed through docker.
 
 ### New features
 
 * Added docker containers for AutoDockVinaRun and FPocketRun tools
 
 ## What's new in version [3.8.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.8.0)?
-In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version. 
+In version 3.8.0 the dependency biobb_common has been updated to 3.8.1 version.
 
 ### New features
 
 * Update to biobb_common 3.8.0 (general)
 
 ## What's new in version [3.7.1](https://github.com/bioexcel/biobb_vs/releases/tag/v3.7.1)?
-In version 3.7.1 some minor bugs have been fixed. 
+In version 3.7.1 some minor bugs have been fixed.
 
 ### Other changes
 
 * Minor bug fixes in AutoDockVinaRun
 
 ## What's new in version [3.7.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.7.0)?
-In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version. 
+In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.
 
 ### New features
 
 * Update to biobb_common 3.7.0 (general)
 
 ## What's new in version [3.6.0](https://github.com/bioexcel/biobb_vs/releases/tag/v3.6.0)?
-In version 3.6.0 the dependency biobb_common has been updated to 3.6.0 version. 
+In version 3.6.0 the dependency biobb_common has been updated to 3.6.0 version.
 
 ### New features
 
diff --git a/biobb_vs/docs/source/conf.py b/biobb_vs/docs/source/conf.py
index ec01d51..c44aeab 100644
--- a/biobb_vs/docs/source/conf.py
+++ b/biobb_vs/docs/source/conf.py
@@ -18,26 +18,26 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, str(Path('../../').resolve()))
+sys.path.insert(0, str(Path("../../").resolve()))
 
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "recommonmark",
 ]
 
 # Using Google docstring style
@@ -45,40 +45,39 @@
 napoleon_google_docstring = True
 
 
-
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 # source_suffix = ['.rst', '.md']
 
 # -- Integrate markdown ---------------------------------------------------
-#source_parsers = {
+# source_parsers = {
 #   '.md': 'recommonmark.parser.CommonMarkParser',
-#}
+# }
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'biobb_vs'
-copyright = u'2024, Bioexcel Project'
-author = u'Bioexcel Project'
+project = "biobb_vs"
+copyright = "2024, Bioexcel Project"
+author = "Bioexcel Project"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'4.2.0'
+version = "5.0.0"
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.0'
+release = "5.0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -89,37 +88,37 @@
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns: list = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -127,162 +126,161 @@
 
 # -- Options for HTML output ----------------------------------------------
 def setup(app):
-    app.add_css_file('theme_overrides.css')
-    app.add_js_file('theme_overrides.js')
+    app.add_css_file("theme_overrides.css")
+    app.add_js_file("theme_overrides.js")
 
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Language to be used for generating the HTML full-text search index.
 # Sphinx supports the following languages:
 #   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
 #   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
-#html_search_language = 'en'
+# html_search_language = 'en'
 
 # A dictionary with options for the search language support, empty by default.
 # Now only 'ja' uses this config value
-#html_search_options = {'type': 'default'}
+# html_search_options = {'type': 'default'}
 
 # The name of a javascript file (relative to the configuration directory) that
 # implements a search results scorer. If empty, the default will be used.
-#html_search_scorer = 'scorer.js'
+# html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biobb_vs_doc'
+htmlhelp_basename = "biobb_vs_doc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
-
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
+latex_elements: dict = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #'preamble': '',
+    # Latex figure (float) alignment
+    #'figure_align': 'htbp',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biobb_vs.tex', u'biobb_vs Documentation',
-     u'Bioexcel Project', 'manual'),
+    (
+        master_doc,
+        "biobb_vs.tex",
+        "biobb_vs Documentation",
+        "Bioexcel Project",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'biobb_vs', u'biobb_vs Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "biobb_vs", "biobb_vs Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -291,19 +289,25 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biobb_vs', u'biobb_vs Documentation',
-     author, 'biobb_vs', 'biobb_vs molecular dynamics ml building blocks',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "biobb_vs",
+        "biobb_vs Documentation",
+        author,
+        "biobb_vs",
+        "biobb_vs molecular dynamics ml building blocks",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
diff --git a/biobb_vs/docs/source/readme.md b/biobb_vs/docs/source/readme.md
index 8b28b48..8200cee 100644
--- a/biobb_vs/docs/source/readme.md
+++ b/biobb_vs/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_vs?label=Conda)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_vs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_vs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_vs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_vs)
 [![](https://img.shields.io/pypi/pyversions/biobb-vs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-vs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 > At the time of publishing the current version, **autodock_vina has not been compiled for the new ARM mac M1/M2 chips**. So the vina.autodock_vina_run only work in these computers through docker containers.
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.1
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_vs>=4.2.0"
+        pip install "biobb_vs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_vs>=4.2.0"
+        conda install -c bioconda "biobb_vs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-vs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-vs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0 <command>
 
 Using SINGULARITY:
 
@@ -87,7 +87,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_vs/docs/source/schema.html b/biobb_vs/docs/source/schema.html
index 98314ea..7a23ad6 100644
--- a/biobb_vs/docs/source/schema.html
+++ b/biobb_vs/docs/source/schema.html
@@ -10,7 +10,7 @@
   "applicationSubCategory": "http://www.edamontology.org/topic_3892",
   "citation": "https://www.nature.com/articles/s41597-019-0177-4",
   "license": "https://www.apache.org/licenses/LICENSE-2.0",
-  "softwareVersion": "4.2.0",
+  "softwareVersion": "5.0.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_vs",
   "isAccessibleForFree": "True",
diff --git a/biobb_vs/json_schemas/biobb_vs.json b/biobb_vs/json_schemas/biobb_vs.json
index db29668..b676a95 100644
--- a/biobb_vs/json_schemas/biobb_vs.json
+++ b/biobb_vs/json_schemas/biobb_vs.json
@@ -4,87 +4,87 @@
     "github": "https://github.com/bioexcel/biobb_vs",
     "readthedocs": "https://biobb-vs.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_vs",
-    "docker": "https://quay.io/biocontainers/biobb_vs:4.2.0--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:4.2.0--pyhdfd78af_0",
-    "version": "4.2.0",
+    "docker": "https://quay.io/biocontainers/biobb_vs:5.0.0--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_vs:5.0.0--pyhdfd78af_0",
+    "version": "5.0.0",
     "rest": true,
-    "tools" : [
+    "tools": [
         {
-            "block" : "AutoDockVinaRun", 
-            "tool" : "AutoDock Vina", 
-            "desc" : "Wrapper of the AutoDock Vina software.",
-            "exec" : "autodock_vina_run",
+            "block": "AutoDockVinaRun",
+            "tool": "AutoDock Vina",
+            "desc": "Wrapper of the AutoDock Vina software.",
+            "exec": "autodock_vina_run",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/vina.html#module-vina.autodock_vina_run",
             "rest": true
         },
         {
-            "block" : "BindingSite", 
-            "tool" : "in house using biopython", 
-            "desc" : "This class finds the binding site of the input_pdb.",
-            "exec" : "bindingsite",
+            "block": "BindingSite",
+            "tool": "in house using biopython",
+            "desc": "This class finds the binding site of the input_pdb.",
+            "exec": "bindingsite",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.bindingsite",
             "rest": true
         },
         {
-            "block" : "Box", 
-            "tool" : "in house", 
-            "desc" : "This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.",
-            "exec" : "box",
+            "block": "Box",
+            "tool": "in house",
+            "desc": "This class sets the center and the size of a rectangular parallelepiped box around a set of residues or a pocket.",
+            "exec": "box",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.box",
             "rest": true
         },
         {
-            "block" : "BoxResidues", 
-            "tool" : "in house using biopython", 
-            "desc" : "This class sets the center and the size of a rectangular parallelepiped box around a set of residues.",
-            "exec" : "box_residues",
+            "block": "BoxResidues",
+            "tool": "in house using biopython",
+            "desc": "This class sets the center and the size of a rectangular parallelepiped box around a set of residues.",
+            "exec": "box_residues",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.box_residues",
             "rest": true
         },
         {
-            "block" : "ExtractModelPDBQT", 
-            "tool" : "in house using biopython", 
-            "desc" : "Extracts a model from a PDBQT file with several models.",
-            "exec" : "extract_model_pdbqt",
+            "block": "ExtractModelPDBQT",
+            "tool": "in house using biopython",
+            "desc": "Extracts a model from a PDBQT file with several models.",
+            "exec": "extract_model_pdbqt",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/utils.html#module-utils.extract_model_pdbqt",
             "rest": true
         },
         {
-            "block" : "FPocketRun", 
-            "tool" : "fpocket", 
-            "desc" : "Wrapper of the fpocket software for finding the binding sites of a structure.",
-            "exec" : "fpocket_run",
+            "block": "FPocketRun",
+            "tool": "fpocket",
+            "desc": "Wrapper of the fpocket software for finding the binding sites of a structure.",
+            "exec": "fpocket_run",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/fpocket.html#module-fpocket.fpocket_run",
             "rest": true
         },
         {
-            "block" : "FPocketFilter", 
-            "tool" : "in house", 
-            "desc" : "Performs a search over the outputs of the fpocket building block.",
-            "exec" : "fpocket_filter",
+            "block": "FPocketFilter",
+            "tool": "in house",
+            "desc": "Performs a search over the outputs of the fpocket building block.",
+            "exec": "fpocket_filter",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/fpocket.html#module-fpocket.fpocket_filter",
             "rest": true
         },
         {
-            "block" : "FPocketSelect", 
-            "tool" : "in house", 
-            "desc" : "Selects a single pocket in the outputs of the fpocket building block..",
-            "exec" : "fpocket_select",
+            "block": "FPocketSelect",
+            "tool": "in house",
+            "desc": "Selects a single pocket in the outputs of the fpocket building block..",
+            "exec": "fpocket_select",
             "docs": "https://biobb-vs.readthedocs.io/en/latest/fpocket.html#module-fpocket.fpocket_select",
             "rest": true
         }
     ],
-    "dep_pypi" : [
-        "install_requires=['biobb_common==4.2.0']", 
-        "python_requires='>=3.8'"
-    ], 
-    "dep_conda" : [
-        "python >=3.8", 
-        "biobb_common ==4.2.0", 
+    "dep_pypi": [
+        "install_requires=['biobb_common==5.0.0']",
+        "python_requires='>=3.9'"
+    ],
+    "dep_conda": [
+        "python >=3.9",
+        "biobb_common ==5.0.0",
         "vina ==1.2.3",
         "fpocket ==4.1"
     ],
-    "keywords" : [
+    "keywords": [
         "virtual screening",
         "autodock",
         "vina",
diff --git a/biobb_vs/utils/__init__.py b/biobb_vs/utils/__init__.py
index c37edcf..7a67531 100644
--- a/biobb_vs/utils/__init__.py
+++ b/biobb_vs/utils/__init__.py
@@ -1,6 +1,4 @@
-from . import bindingsite
-from . import box
-from . import box_residues
-from . import extract_model_pdbqt
+from . import bindingsite, box, box_residues, extract_model_pdbqt
+
 name = "utils"
 __all__ = ["bindingsite", "box", "box_residues", "extract_model_pdbqt"]
diff --git a/biobb_vs/utils/bindingsite.py b/biobb_vs/utils/bindingsite.py
index ce849d3..069ab8e 100755
--- a/biobb_vs/utils/bindingsite.py
+++ b/biobb_vs/utils/bindingsite.py
@@ -1,27 +1,37 @@
 #!/usr/bin/env python3
 
 """Module containing the BindingSite class and the command line interface."""
+
 import argparse
-from typing import Optional
 import re
+import warnings
 from pathlib import PurePath
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
+from Bio import BiopythonDeprecationWarning
 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_vs.utils.common import check_input_path, check_output_path, get_pdb_sequence, get_ligand_residues, align_sequences, calculate_alignment_identity, get_residue_by_id
 
-from Bio import BiopythonDeprecationWarning
-import warnings
+from biobb_vs.utils.common import (
+    align_sequences,
+    calculate_alignment_identity,
+    check_input_path,
+    check_output_path,
+    get_ligand_residues,
+    get_pdb_sequence,
+    get_residue_by_id,
+)
+
 with warnings.catch_warnings():
     warnings.simplefilter("ignore", BiopythonDeprecationWarning)
-    import Bio.PDB
-    import Bio.pairwise2
     # try:
     #    import Bio.SubsMat.MatrixInfo
     # except ImportError:
-
     import Bio.Align.substitution_matrices
+    import Bio.pairwise2
+    import Bio.PDB
 
 
 class BindingSite(BiobbObject):
@@ -73,8 +83,14 @@ class BindingSite(BiobbObject):
 
     """
 
-    def __init__(self, input_pdb_path, input_clusters_zip, output_pdb_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_pdb_path,
+        input_clusters_zip,
+        output_pdb_path,
+        properties=None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -83,17 +99,20 @@ def __init__(self, input_pdb_path, input_clusters_zip, output_pdb_path,
 
         # Input/Output files
         self.io_dict = {
-            "in": {"input_pdb_path": input_pdb_path, "input_clusters_zip": input_clusters_zip},
-            "out": {"output_pdb_path": output_pdb_path}
+            "in": {
+                "input_pdb_path": input_pdb_path,
+                "input_clusters_zip": input_clusters_zip,
+            },
+            "out": {"output_pdb_path": output_pdb_path},
         }
 
         # Properties specific for BB
-        self.ligand = properties.get('ligand', None)
-        self.radius = float(properties.get('radius', 5.0))
-        self.max_num_ligands = properties.get('max_num_ligands', 15)
-        self.matrix_name = properties.get('matrix_name', 'BLOSUM62')
-        self.gap_open = properties.get('gap_open', -10.0)
-        self.gap_extend = properties.get('gap_extend', -0.5)
+        self.ligand = properties.get("ligand", None)
+        self.radius = float(properties.get("radius", 5.0))
+        self.max_num_ligands = properties.get("max_num_ligands", 15)
+        self.matrix_name = properties.get("matrix_name", "BLOSUM62")
+        self.gap_open = properties.get("gap_open", -10.0)
+        self.gap_extend = properties.get("gap_extend", -0.5)
         self.properties = properties
 
         # Check the properties
@@ -101,10 +120,26 @@ def __init__(self, input_pdb_path, input_clusters_zip, output_pdb_path,
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", self.out_log, self.__class__.__name__)
-        self.io_dict["in"]["input_clusters_zip"] = check_input_path(self.io_dict["in"]["input_clusters_zip"], "input_clusters_zip", self.out_log, self.__class__.__name__)
-        self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, self.out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.io_dict["in"]["input_pdb_path"] = check_input_path(
+            self.io_dict["in"]["input_pdb_path"],
+            "input_pdb_path",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["in"]["input_clusters_zip"] = check_input_path(
+            self.io_dict["in"]["input_clusters_zip"],
+            "input_clusters_zip",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["out"]["output_pdb_path"] = check_output_path(
+            self.io_dict["out"]["output_pdb_path"],
+            "output_pdb_path",
+            False,
+            self.out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -119,10 +154,16 @@ def launch(self) -> int:
         self.stage_files()
 
         # Parse structure
-        fu.log('Loading input PDB structure %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
+        fu.log(
+            "Loading input PDB structure %s" % (self.io_dict["in"]["input_pdb_path"]),
+            self.out_log,
+            self.global_log,
+        )
         structure_name = PurePath(self.io_dict["in"]["input_pdb_path"]).name
         parser = Bio.PDB.PDBParser(QUIET=True)
-        structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdb_path"])
+        structPDB = parser.get_structure(
+            structure_name, self.io_dict["in"]["input_pdb_path"]
+        )
 
         if len(structPDB):
             structPDB = structPDB[0]
@@ -130,7 +171,11 @@ def launch(self) -> int:
         # Use only one chain
         n_chains = structPDB.get_list()
         if len(n_chains) != 1:
-            fu.log('More than one chain found in the input PDB structure. Using only the first chain to find the binding site', self.out_log, self.global_log)
+            fu.log(
+                "More than one chain found in the input PDB structure. Using only the first chain to find the binding site",
+                self.out_log,
+                self.global_log,
+            )
             # get first chain in case there is more than one chain
             for struct_chain in structPDB.get_chains():
                 structPDB = struct_chain
@@ -138,42 +183,66 @@ def launch(self) -> int:
         # Get AA sequence
         structPDB_seq = get_pdb_sequence(structPDB)
         if len(structPDB_seq) == 0:
-            fu.log(self.__class__.__name__ + ': Cannot extract AA sequence from the input PDB structure %s. Wrong format?' % self.io_dict["in"]["input_pdb_path"], self.out_log)
-            raise SystemExit(self.__class__.__name__ + ': Cannot extract AA sequence from the input PDB structure %s. Wrong format?' % self.io_dict["in"]["input_pdb_path"])
+            fu.log(
+                self.__class__.__name__
+                + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
+                % self.io_dict["in"]["input_pdb_path"],
+                self.out_log,
+            )
+            raise SystemExit(
+                self.__class__.__name__
+                + ": Cannot extract AA sequence from the input PDB structure %s. Wrong format?"
+                % self.io_dict["in"]["input_pdb_path"]
+            )
         else:
-            fu.log('Found %s residues in %s' % (len(structPDB_seq), self.io_dict["in"]["input_pdb_path"]), self.out_log)
+            fu.log(
+                "Found %s residues in %s"
+                % (len(structPDB_seq), self.io_dict["in"]["input_pdb_path"]),
+                self.out_log,
+            )
 
         # create temporary folder for decompressing the input_clusters_zip file
         unique_dir = PurePath(fu.create_unique_dir())
-        fu.log('Creating %s temporary folder' % unique_dir, self.out_log, self.global_log)
+        fu.log(
+            "Creating %s temporary folder" % unique_dir, self.out_log, self.global_log
+        )
 
         # decompress the input_clusters_zip file
-        cluster_list = fu.unzip_list(zip_file=self.io_dict["in"]["input_clusters_zip"], dest_dir=unique_dir, out_log=self.out_log)
+        cluster_list = fu.unzip_list(
+            zip_file=self.io_dict["in"]["input_clusters_zip"],
+            dest_dir=str(unique_dir),
+            out_log=self.out_log,
+        )
 
         clusterPDB_ligands_aligned = []
         clusterPDB_ligands_num = 0
 
-        fu.log('Iterating on all clusters:', self.out_log)
+        fu.log("Iterating on all clusters:", self.out_log)
 
         for idx, cluster_path in enumerate(cluster_list):
-
             cluster_name = PurePath(cluster_path).stem
-            fu.log(' ', self.out_log)
-            fu.log('------------ Iteration #%s --------------' % (idx + 1), self.out_log)
-            fu.log('Cluster member: %s' % cluster_name, self.out_log)
+            fu.log(" ", self.out_log)
+            fu.log(
+                "------------ Iteration #%s --------------" % (idx + 1), self.out_log
+            )
+            fu.log("Cluster member: %s" % cluster_name, self.out_log)
 
             # Load and Parse PDB
             clusterPDB = {}
             clusterPDB = parser.get_structure(cluster_name, cluster_path)[0]
 
             # Use only the first chain
-            for cluster_chain in clusterPDB.get_chains():
+            for cluster_chain in clusterPDB.get_chains():  # type: ignore
                 clusterPDB = cluster_chain
 
             # Looking for ligands
             clusterPDB_ligands = get_ligand_residues(clusterPDB)
             if (len(clusterPDB_ligands)) == 0:
-                fu.log('No ligands found that could guide the binding site search. Ignoring this member: %s' % cluster_name, self.out_log)
+                fu.log(
+                    "No ligands found that could guide the binding site search. Ignoring this member: %s"
+                    % cluster_name,
+                    self.out_log,
+                )
                 continue
 
             # Selecting the largest ligand, if more than one
@@ -185,15 +254,27 @@ def launch(self) -> int:
                         if lig.get_resname() == self.ligand:
                             clusterPDB_ligand = lig
                             lig_atoms_num = len(lig.get_list())
-                            fu.log('Ligand found: %s  (%s atoms)' % (lig.get_resname(), lig_atoms_num), self.out_log)
+                            fu.log(
+                                "Ligand found: %s  (%s atoms)"
+                                % (lig.get_resname(), lig_atoms_num),
+                                self.out_log,
+                            )
                 else:
-                    fu.log('Ligand %s not found in %s cluster member, skipping this cluster' % (self.ligand, cluster_name), self.out_log)
+                    fu.log(
+                        "Ligand %s not found in %s cluster member, skipping this cluster"
+                        % (self.ligand, cluster_name),
+                        self.out_log,
+                    )
                     continue
             else:
                 if len(clusterPDB_ligands) > 1:
                     for lig_res in clusterPDB_ligands:
                         lig_res_atoms_num = len(lig_res.get_list())
-                        fu.log('Ligand found: %s  (%s atoms)' % (lig_res.get_resname(), lig_res_atoms_num), self.out_log)
+                        fu.log(
+                            "Ligand found: %s  (%s atoms)"
+                            % (lig_res.get_resname(), lig_res_atoms_num),
+                            self.out_log,
+                        )
                         if lig_res_atoms_num > lig_atoms_num:
                             clusterPDB_ligand = lig_res
                             lig_atoms_num = lig_res_atoms_num
@@ -201,7 +282,11 @@ def launch(self) -> int:
                     clusterPDB_ligand = clusterPDB_ligands[0]
                     lig_atoms_num = len(clusterPDB_ligands[0].get_list())
 
-            fu.log('Member accepted. Valid ligand found: %s (%s atoms)' % (clusterPDB_ligand.get_resname(), lig_atoms_num), self.out_log)
+            fu.log(
+                "Member accepted. Valid ligand found: %s (%s atoms)"
+                % (clusterPDB_ligand.get_resname(), lig_atoms_num),  # type: ignore
+                self.out_log,
+            )
 
             # Mapping residues by sequence alignment to match structPDB-clusterPDB paired residues
 
@@ -209,13 +294,25 @@ def launch(self) -> int:
             clusterPDB_seq = get_pdb_sequence(clusterPDB)
 
             # Pairwise align
-            aln, residue_map = align_sequences(structPDB_seq, clusterPDB_seq, self.matrix_name, self.gap_open, self.gap_extend)
-            fu.log('Matching residues to input PDB structure. Alignment is:\n%s' % (aln[1]), self.out_log)
+            aln, residue_map = align_sequences(
+                structPDB_seq,
+                clusterPDB_seq,
+                self.matrix_name,
+                self.gap_open,
+                self.gap_extend,
+            )
+            fu.log(
+                "Matching residues to input PDB structure. Alignment is:\n%s"
+                % (aln[1]),
+                self.out_log,
+            )
 
             # Calculate (gapless) sequence identity
-            seq_identity, gap_seq_identity = calculate_alignment_identity(aln[0], aln[1])
-            fu.log('Sequence identity (%%): %s' % (seq_identity), self.out_log)
-            fu.log('Gap less identity (%%): %s' % (gap_seq_identity), self.out_log)
+            seq_identity, gap_seq_identity = calculate_alignment_identity(
+                aln[0], aln[1]
+            )
+            fu.log("Sequence identity (%%): %s" % (seq_identity), self.out_log)
+            fu.log("Gap less identity (%%): %s" % (gap_seq_identity), self.out_log)
 
             # Selecting aligned CA atoms from first model, first chain
 
@@ -224,28 +321,47 @@ def launch(self) -> int:
 
             for struct_res in residue_map:
                 try:
-                    cluster_atoms.append(clusterPDB[residue_map[struct_res]]['CA'])
-                    struct_atoms.append(get_residue_by_id(structPDB, struct_res)['CA'])
+                    cluster_atoms.append(clusterPDB[residue_map[struct_res]]["CA"])
+                    struct_atoms.append(get_residue_by_id(structPDB, struct_res)["CA"])
                 except KeyError:
-                    fu.log('Cannot find CA atom for residue %s  (input PDB  %s)' % (get_residue_by_id(structPDB, struct_res).get_resname(), struct_res), self.out_log)
+                    fu.log(
+                        "Cannot find CA atom for residue %s  (input PDB  %s)"
+                        % (
+                            get_residue_by_id(structPDB, struct_res).get_resname(),
+                            struct_res,
+                        ),
+                        self.out_log,
+                    )
                     pass
 
             if len(cluster_atoms) == 0:
-                fu.log(self.__class__.__name__ + ': Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member.' % (cluster_name, structure_name), self.out_log)
-                raise SystemExit(self.__class__.__name__ + ': Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member.' % (cluster_name, structure_name))
+                fu.log(
+                    self.__class__.__name__
+                    + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
+                    % (cluster_name, structure_name),
+                    self.out_log,
+                )
+                raise SystemExit(
+                    self.__class__.__name__
+                    + ": Cannot find CA atoms (1st model, 1st chain) in cluster member %s when aligning against %s. Ignoring this member."
+                    % (cluster_name, structure_name)
+                )
             else:
-                fu.log('Superimposing %s aligned protein residues' % (len(cluster_atoms)), self.out_log)
+                fu.log(
+                    "Superimposing %s aligned protein residues" % (len(cluster_atoms)),
+                    self.out_log,
+                )
 
             # Align against input structure
 
             si = Bio.PDB.Superimposer()
             si.set_atoms(struct_atoms, cluster_atoms)
-            si.apply(clusterPDB.get_atoms())
-            fu.log('RMSD: %s' % (si.rms), self.out_log)
+            si.apply(clusterPDB.get_atoms())  # type: ignore
+            fu.log("RMSD: %s" % (si.rms), self.out_log)
 
             # Save transformed structure (and ligand)
-            clusterPDB_ligand_aligned = clusterPDB[clusterPDB_ligand.get_id()]
-            fu.log('Saving transformed ligand coordinates', self.out_log)
+            clusterPDB_ligand_aligned = clusterPDB[clusterPDB_ligand.get_id()]  # type: ignore
+            fu.log("Saving transformed ligand coordinates", self.out_log)
 
             clusterPDB_ligands_aligned.append(clusterPDB_ligand_aligned)
 
@@ -256,17 +372,26 @@ def launch(self) -> int:
             if clusterPDB_ligands_num > self.max_num_ligands:
                 break
 
-        fu.log(' ', self.out_log)
-        fu.log('----------------------------------------', self.out_log)
-        fu.log('All transformed ligand coordinates saved, getting binding site residues', self.out_log)
+        fu.log(" ", self.out_log)
+        fu.log("----------------------------------------", self.out_log)
+        fu.log(
+            "All transformed ligand coordinates saved, getting binding site residues",
+            self.out_log,
+        )
 
         # Select binding site atoms as those around cluster superimposed ligands
 
-        fu.log('Defining binding site residues as those %sÅ around the %s cluster superimposed ligands' % (self.radius, clusterPDB_ligands_num), self.out_log)
+        fu.log(
+            "Defining binding site residues as those %sÅ around the %s cluster superimposed ligands"
+            % (self.radius, clusterPDB_ligands_num),
+            self.out_log,
+        )
 
         # select Atoms from aligned ligands
         clusterPDB_ligands_aligned2 = [res for res in clusterPDB_ligands_aligned]
-        clusterPDB_ligands_aligned_atoms = Bio.PDB.Selection.unfold_entities(clusterPDB_ligands_aligned2, 'A')
+        clusterPDB_ligands_aligned_atoms = Bio.PDB.Selection.unfold_entities(
+            clusterPDB_ligands_aligned2, "A"
+        )
 
         # select Atoms from input PDB structure
         structPDB_atoms = [atom for atom in structPDB.get_atoms()]
@@ -276,18 +401,22 @@ def launch(self) -> int:
         structPDB_neighbors = Bio.PDB.NeighborSearch(structPDB_atoms)
         for ligand_atom in clusterPDB_ligands_aligned_atoms:
             # look for PDB atoms 5A around each ligand atom
-            k_l = structPDB_neighbors.search(ligand_atom.coord, self.radius, 'R')
+            k_l = structPDB_neighbors.search(ligand_atom.coord, self.radius, "R")
             for k in k_l:
                 structPDB_bs_residues_raw[k.get_id()] = k.get_full_id()
 
         # Save binding site to PDB
 
         io = Bio.PDB.PDBIO()
-        fu.log('Writing binding site residues into %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log)
+        fu.log(
+            "Writing binding site residues into %s"
+            % (self.io_dict["out"]["output_pdb_path"]),
+            self.out_log,
+        )
 
         # unselect input PDB atoms not in binding site
         structPDB_bs_atoms = 0
-        p = re.compile('H_|W_|W')
+        p = re.compile("H_|W_|W")
         residue_ids_to_remove = []
         for res in structPDB.get_residues():
             if res.id not in structPDB_bs_residues_raw.keys():
@@ -312,10 +441,9 @@ def launch(self) -> int:
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir", ""),
-            str(unique_dir)
-        ])
+        self.tmp_files.extend(
+            [self.stage_io_dict.get("unique_dir", ""), str(unique_dir)]
+        )
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -323,37 +451,63 @@ def launch(self) -> int:
         return 0
 
 
-def bindingsite(input_pdb_path: str, input_clusters_zip: str, output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
+def bindingsite(
+    input_pdb_path: str,
+    input_clusters_zip: str,
+    output_pdb_path: str,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Execute the :class:`BindingSite <utils.bindingsite.BindingSite>` class and
     execute the :meth:`launch() <utils.bindingsite.BindingSite.launch>` method."""
 
-    return BindingSite(input_pdb_path=input_pdb_path,
-                       input_clusters_zip=input_clusters_zip,
-                       output_pdb_path=output_pdb_path,
-                       properties=properties, **kwargs).launch()
+    return BindingSite(
+        input_pdb_path=input_pdb_path,
+        input_clusters_zip=input_clusters_zip,
+        output_pdb_path=output_pdb_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Finds the binding site of the input_pdb file based on the ligands' location of similar structures (members of the sequence identity cluster)", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('--config', required=False, help='Configuration file')
+    parser = argparse.ArgumentParser(
+        description="Finds the binding site of the input_pdb file based on the ligands' location of similar structures (members of the sequence identity cluster)",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument("--config", required=False, help="Configuration file")
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_pdb_path', required=True, help='Path to the PDB structure where the binding site is to be found. Accepted formats: pdb.')
-    required_args.add_argument('--input_clusters_zip', required=True, help='Path to the ZIP file with all the PDB members of the identity cluster. Accepted formats: zip.')
-    required_args.add_argument('--output_pdb_path', required=True, help='Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.')
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "--input_pdb_path",
+        required=True,
+        help="Path to the PDB structure where the binding site is to be found. Accepted formats: pdb.",
+    )
+    required_args.add_argument(
+        "--input_clusters_zip",
+        required=True,
+        help="Path to the ZIP file with all the PDB members of the identity cluster. Accepted formats: zip.",
+    )
+    required_args.add_argument(
+        "--output_pdb_path",
+        required=True,
+        help="Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.",
+    )
 
     args = parser.parse_args()
     args.config = args.config or "{}"
     properties = settings.ConfReader(config=args.config).get_prop_dic()
 
     # Specific call of each building block
-    bindingsite(input_pdb_path=args.input_pdb_path,
-                input_clusters_zip=args.input_clusters_zip,
-                output_pdb_path=args.output_pdb_path,
-                properties=properties)
+    bindingsite(
+        input_pdb_path=args.input_pdb_path,
+        input_clusters_zip=args.input_clusters_zip,
+        output_pdb_path=args.output_pdb_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_vs/utils/box.py b/biobb_vs/utils/box.py
index c900dd4..6de1bed 100755
--- a/biobb_vs/utils/box.py
+++ b/biobb_vs/utils/box.py
@@ -1,15 +1,22 @@
 #!/usr/bin/env python3
 
 """Module containing the Box class and the command line interface."""
+
 import argparse
+from pathlib import PurePath
 from typing import Optional
+
 import numpy as np
-from pathlib import PurePath
-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_vs.utils.common import check_input_path, check_output_path, get_box_coordinates
+
+from biobb_vs.utils.common import (
+    check_input_path,
+    check_output_path,
+    get_box_coordinates,
+)
 
 
 class Box(BiobbObject):
@@ -50,8 +57,9 @@ class Box(BiobbObject):
 
     """
 
-    def __init__(self, input_pdb_path, output_pdb_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(
+        self, input_pdb_path, output_pdb_path, properties=None, **kwargs
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -61,12 +69,12 @@ def __init__(self, input_pdb_path, output_pdb_path,
         # Input/Output files
         self.io_dict = {
             "in": {"input_pdb_path": input_pdb_path},
-            "out": {"output_pdb_path": output_pdb_path}
+            "out": {"output_pdb_path": output_pdb_path},
         }
 
         # Properties specific for BB
-        self.offset = float(properties.get('offset', 2.0))
-        self.box_coordinates = float(properties.get('box_coordinates', False))
+        self.offset = float(properties.get("offset", 2.0))
+        self.box_coordinates = float(properties.get("box_coordinates", False))
         self.properties = properties
 
         # Check the properties
@@ -74,9 +82,20 @@ def __init__(self, input_pdb_path, output_pdb_path,
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.io_dict["in"]["input_pdb_path"] = check_input_path(self.io_dict["in"]["input_pdb_path"], "input_pdb_path", self.out_log, self.__class__.__name__)
-        self.io_dict["out"]["output_pdb_path"] = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, self.out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.io_dict["in"]["input_pdb_path"] = check_input_path(
+            self.io_dict["in"]["input_pdb_path"],
+            "input_pdb_path",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["out"]["output_pdb_path"] = check_output_path(
+            self.io_dict["out"]["output_pdb_path"],
+            "output_pdb_path",
+            False,
+            self.out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -91,11 +110,21 @@ def launch(self) -> int:
         self.stage_files()
 
         # check if cavity (pdb) or pocket (pqr)
-        input_type = PurePath(self.io_dict["in"]["input_pdb_path"]).suffix.lstrip('.')
-        if input_type == 'pdb':
-            fu.log('Loading residue PDB selection from %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
+        input_type = PurePath(self.io_dict["in"]["input_pdb_path"]).suffix.lstrip(".")
+        if input_type == "pdb":
+            fu.log(
+                "Loading residue PDB selection from %s"
+                % (self.io_dict["in"]["input_pdb_path"]),
+                self.out_log,
+                self.global_log,
+            )
         else:
-            fu.log('Loading pocket PQR selection from %s' % (self.io_dict["in"]["input_pdb_path"]), self.out_log, self.global_log)
+            fu.log(
+                "Loading pocket PQR selection from %s"
+                % (self.io_dict["in"]["input_pdb_path"]),
+                self.out_log,
+                self.global_log,
+            )
 
         # get input_pdb_path atoms coordinates
         selection_atoms_num = 0
@@ -113,43 +142,80 @@ def launch(self) -> int:
         # Compute binding site box size
 
         # compute box center
-        selection_box_center = [np.average(x_coordslist), np.average(y_coordslist), np.average(z_coordslist)]
-        fu.log('Binding site center (Angstroms): %10.3f%10.3f%10.3f' % (selection_box_center[0], selection_box_center[1], selection_box_center[2]), self.out_log, self.global_log)
+        selection_box_center = [
+            np.average(x_coordslist),
+            np.average(y_coordslist),
+            np.average(z_coordslist),
+        ]
+        fu.log(
+            "Binding site center (Angstroms): %10.3f%10.3f%10.3f"
+            % (
+                selection_box_center[0],
+                selection_box_center[1],
+                selection_box_center[2],
+            ),
+            self.out_log,
+            self.global_log,
+        )
 
         # compute box size
-        selection_coords_max = np.amax([x_coordslist, y_coordslist, z_coordslist], axis=1)
+        selection_coords_max = np.amax(
+            [x_coordslist, y_coordslist, z_coordslist], axis=1
+        )
         selection_box_size = selection_coords_max - selection_box_center
         if self.offset:
-            fu.log('Adding %.1f Angstroms offset' % (self.offset), self.out_log, self.global_log)
+            fu.log(
+                "Adding %.1f Angstroms offset" % (self.offset),
+                self.out_log,
+                self.global_log,
+            )
             selection_box_size = [c + self.offset for c in selection_box_size]
-        fu.log('Binding site size (Angstroms):   %10.3f%10.3f%10.3f' % (selection_box_size[0], selection_box_size[1], selection_box_size[2]), self.out_log, self.global_log)
+        fu.log(
+            "Binding site size (Angstroms):   %10.3f%10.3f%10.3f"
+            % (selection_box_size[0], selection_box_size[1], selection_box_size[2]),
+            self.out_log,
+            self.global_log,
+        )
 
         # compute volume
         vol = np.prod(selection_box_size) * 2**3
-        fu.log('Volume (cubic Angstroms): %.0f' % (vol), self.out_log, self.global_log)
+        fu.log("Volume (cubic Angstroms): %.0f" % (vol), self.out_log, self.global_log)
 
         # add box details as PDB remarks
-        remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (selection_box_center[0], selection_box_center[1], selection_box_center[2])
-        remarks += " SIZE:%10.3f%10.3f%10.3f" % (selection_box_size[0], selection_box_size[1], selection_box_size[2])
+        remarks = "REMARK BOX CENTER:%10.3f%10.3f%10.3f" % (
+            selection_box_center[0],
+            selection_box_center[1],
+            selection_box_center[2],
+        )
+        remarks += " SIZE:%10.3f%10.3f%10.3f" % (
+            selection_box_size[0],
+            selection_box_size[1],
+            selection_box_size[2],
+        )
 
         selection_box_coords_txt = ""
         # add (optional) box coordinates as 8 ATOM records
         if self.box_coordinates:
-            fu.log('Adding box coordinates', self.out_log, self.global_log)
-            selection_box_coords_txt = get_box_coordinates(selection_box_center, selection_box_size)
+            fu.log("Adding box coordinates", self.out_log, self.global_log)
+            selection_box_coords_txt = get_box_coordinates(
+                selection_box_center, selection_box_size
+            )
 
-        with open(self.io_dict["out"]["output_pdb_path"], 'w') as f:
+        with open(self.io_dict["out"]["output_pdb_path"], "w") as f:
             f.seek(0, 0)
-            f.write(remarks.rstrip('\r\n') + '\n' + selection_box_coords_txt)
+            f.write(remarks.rstrip("\r\n") + "\n" + selection_box_coords_txt)
 
-        fu.log('Saving output PDB file (with box setting annotations): %s' % (self.io_dict["out"]["output_pdb_path"]), self.out_log, self.global_log)
+        fu.log(
+            "Saving output PDB file (with box setting annotations): %s"
+            % (self.io_dict["out"]["output_pdb_path"]),
+            self.out_log,
+            self.global_log,
+        )
 
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir", "")
-        ])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -157,34 +223,55 @@ def launch(self) -> int:
         return 0
 
 
-def box(input_pdb_path: str, output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
+def box(
+    input_pdb_path: str,
+    output_pdb_path: str,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Execute the :class:`Box <utils.box.Box>` class and
     execute the :meth:`launch() <utils.box.Box.launch>` method."""
 
-    return Box(input_pdb_path=input_pdb_path,
-               output_pdb_path=output_pdb_path,
-               properties=properties, **kwargs).launch()
+    return Box(
+        input_pdb_path=input_pdb_path,
+        output_pdb_path=output_pdb_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('--config', required=False, help='Configuration file')
+    parser = argparse.ArgumentParser(
+        description="Sets the center and the size of a rectangular parallelepiped box around a set of residues from a given PDB or a pocket from a given PQR.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument("--config", required=False, help="Configuration file")
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_pdb_path', required=True, help='PDB file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr.')
-    required_args.add_argument('--output_pdb_path', required=True, help='PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.')
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "--input_pdb_path",
+        required=True,
+        help="PDB file containing a selection of residue numbers or PQR file containing the pocket. Accepted formats: pdb, pqr.",
+    )
+    required_args.add_argument(
+        "--output_pdb_path",
+        required=True,
+        help="PDB including the annotation of the box center and size as REMARKs. Accepted formats: pdb.",
+    )
 
     args = parser.parse_args()
     args.config = args.config or "{}"
     properties = settings.ConfReader(config=args.config).get_prop_dic()
 
     # Specific call of each building block
-    box(input_pdb_path=args.input_pdb_path,
+    box(
+        input_pdb_path=args.input_pdb_path,
         output_pdb_path=args.output_pdb_path,
-        properties=properties)
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_vs/utils/extract_model_pdbqt.py b/biobb_vs/utils/extract_model_pdbqt.py
index 94c4ba7..613b2b1 100755
--- a/biobb_vs/utils/extract_model_pdbqt.py
+++ b/biobb_vs/utils/extract_model_pdbqt.py
@@ -1,26 +1,28 @@
 #!/usr/bin/env python3
 
 """Module containing the ExtractModelPDBQT class and the command line interface."""
+
 import argparse
-from typing import Optional
+import warnings
 from pathlib import PurePath
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
+from Bio import BiopythonDeprecationWarning
 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_vs.utils.common import check_input_path, check_output_path
 
-from Bio import BiopythonDeprecationWarning
-import warnings
 with warnings.catch_warnings():
     warnings.simplefilter("ignore", BiopythonDeprecationWarning)
-    import Bio.PDB
-    import Bio.pairwise2
     # try:
     #    import Bio.SubsMat.MatrixInfo
     # except ImportError:
-
     import Bio.Align.substitution_matrices
+    import Bio.pairwise2
+    import Bio.PDB
 
 
 class ExtractModelPDBQT(BiobbObject):
@@ -60,8 +62,9 @@ class ExtractModelPDBQT(BiobbObject):
 
     """
 
-    def __init__(self, input_pdbqt_path, output_pdbqt_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(
+        self, input_pdbqt_path, output_pdbqt_path, properties=None, **kwargs
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -71,11 +74,11 @@ def __init__(self, input_pdbqt_path, output_pdbqt_path,
         # Input/Output files
         self.io_dict = {
             "in": {"input_pdbqt_path": input_pdbqt_path},
-            "out": {"output_pdbqt_path": output_pdbqt_path}
+            "out": {"output_pdbqt_path": output_pdbqt_path},
         }
 
         # Properties specific for BB
-        self.model = properties.get('model', 1)
+        self.model = properties.get("model", 1)
         self.properties = properties
 
         # Check the properties
@@ -83,9 +86,20 @@ def __init__(self, input_pdbqt_path, output_pdbqt_path,
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.io_dict["in"]["input_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_pdbqt_path"], "input_pdbqt_path", out_log, self.__class__.__name__)
-        self.io_dict["out"]["output_pdbqt_path"] = check_output_path(self.io_dict["out"]["output_pdbqt_path"], "output_pdbqt_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.io_dict["in"]["input_pdbqt_path"] = check_input_path(
+            self.io_dict["in"]["input_pdbqt_path"],
+            "input_pdbqt_path",
+            out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["out"]["output_pdbqt_path"] = check_output_path(
+            self.io_dict["out"]["output_pdbqt_path"],
+            "output_pdbqt_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -102,41 +116,60 @@ def launch(self) -> int:
         if self.restart:
             output_file_list = [self.io_dict["out"]["output_pdbqt_path"]]
             if fu.check_complete_files(output_file_list):
-                fu.log('Restart is enabled, this step: %s will the skipped' % self.step, self.out_log, self.global_log)
+                fu.log(
+                    "Restart is enabled, this step: %s will the skipped" % self.step,
+                    self.out_log,
+                    self.global_log,
+                )
                 return 0
 
         structure_name = PurePath(self.io_dict["in"]["input_pdbqt_path"]).name
         parser = Bio.PDB.PDBParser(QUIET=True)
-        structPDB = parser.get_structure(structure_name, self.io_dict["in"]["input_pdbqt_path"])
+        structPDB = parser.get_structure(
+            structure_name, self.io_dict["in"]["input_pdbqt_path"]
+        )
 
         models = []
         for model in structPDB.get_models():
             models.append(model.id + 1)
 
         if self.model not in models:
-            fu.log(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]), self.out_log)
-            raise SystemExit(self.__class__.__name__ + ': Selected model %d not found in %s structure.' % (self.model, self.io_dict["in"]["input_pdbqt_path"]))
+            fu.log(
+                self.__class__.__name__
+                + ": Selected model %d not found in %s structure."
+                % (self.model, self.io_dict["in"]["input_pdbqt_path"]),
+                self.out_log,
+            )
+            raise SystemExit(
+                self.__class__.__name__
+                + ": Selected model %d not found in %s structure."
+                % (self.model, self.io_dict["in"]["input_pdbqt_path"])
+            )
 
         save = False
         lines = 0
-        with open(self.io_dict["in"]["input_pdbqt_path"], "r") as input_pdb, open(self.io_dict["out"]["output_pdbqt_path"], "w") as output_pdb:
+        with open(self.io_dict["in"]["input_pdbqt_path"], "r") as input_pdb, open(
+            self.io_dict["out"]["output_pdbqt_path"], "w"
+        ) as output_pdb:
             for line in input_pdb:
-                if line.startswith('MODEL') and line.split()[1] == str(self.model):
+                if line.startswith("MODEL") and line.split()[1] == str(self.model):
                     save = True
-                if line.startswith('ENDMDL'):
+                if line.startswith("ENDMDL"):
                     save = False
-                if save and not line.startswith('MODEL'):
+                if save and not line.startswith("MODEL"):
                     lines = lines + 1
                     output_pdb.write(line)
 
-        fu.log('Saving model %d to %s' % (self.model, self.io_dict["out"]["output_pdbqt_path"]), self.out_log)
+        fu.log(
+            "Saving model %d to %s"
+            % (self.model, self.io_dict["out"]["output_pdbqt_path"]),
+            self.out_log,
+        )
 
         # Copy files to host
         self.copy_to_host()
 
-        self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir", "")
-        ])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -144,34 +177,55 @@ def launch(self) -> int:
         return 0
 
 
-def extract_model_pdbqt(input_pdbqt_path: str, output_pdbqt_path: str, properties: Optional[dict] = None, **kwargs) -> int:
+def extract_model_pdbqt(
+    input_pdbqt_path: str,
+    output_pdbqt_path: str,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Execute the :class:`ExtractModelPDBQT <utils.extract_model_pdbqt.ExtractModelPDBQT>` class and
     execute the :meth:`launch() <utils.extract_model_pdbqt.ExtractModelPDBQT.launch>` method."""
 
-    return ExtractModelPDBQT(input_pdbqt_path=input_pdbqt_path,
-                             output_pdbqt_path=output_pdbqt_path,
-                             properties=properties, **kwargs).launch()
+    return ExtractModelPDBQT(
+        input_pdbqt_path=input_pdbqt_path,
+        output_pdbqt_path=output_pdbqt_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Extracts a model from a PDBQT file with several models.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('--config', required=False, help='Configuration file')
+    parser = argparse.ArgumentParser(
+        description="Extracts a model from a PDBQT file with several models.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument("--config", required=False, help="Configuration file")
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_pdbqt_path', required=True, help='Input PDBQT file. Accepted formats: pdbqt.')
-    required_args.add_argument('--output_pdbqt_path', required=True, help='Output PDBQT file. Accepted formats: pdbqt.')
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "--input_pdbqt_path",
+        required=True,
+        help="Input PDBQT file. Accepted formats: pdbqt.",
+    )
+    required_args.add_argument(
+        "--output_pdbqt_path",
+        required=True,
+        help="Output PDBQT file. Accepted formats: pdbqt.",
+    )
 
     args = parser.parse_args()
     args.config = args.config or "{}"
     properties = settings.ConfReader(config=args.config).get_prop_dic()
 
     # Specific call of each building block
-    extract_model_pdbqt(input_pdbqt_path=args.input_pdbqt_path,
-                        output_pdbqt_path=args.output_pdbqt_path,
-                        properties=properties)
+    extract_model_pdbqt(
+        input_pdbqt_path=args.input_pdbqt_path,
+        output_pdbqt_path=args.output_pdbqt_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_vs/vina/__init__.py b/biobb_vs/vina/__init__.py
index 956f788..dbc831c 100644
--- a/biobb_vs/vina/__init__.py
+++ b/biobb_vs/vina/__init__.py
@@ -1,3 +1,4 @@
 from . import autodock_vina_run
+
 name = "vina"
 __all__ = ["autodock_vina_run"]
diff --git a/biobb_vs/vina/autodock_vina_run.py b/biobb_vs/vina/autodock_vina_run.py
index fd8e255..2811888 100755
--- a/biobb_vs/vina/autodock_vina_run.py
+++ b/biobb_vs/vina/autodock_vina_run.py
@@ -1,12 +1,15 @@
 #!/usr/bin/env python3
 
 """Module containing the AutoDockVinaRun class and the command line interface."""
+
 import argparse
-from typing import Optional
 import os
-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_vs.vina.common import check_input_path, check_output_path
 
 
@@ -64,8 +67,16 @@ class AutoDockVinaRun(BiobbObject):
 
     """
 
-    def __init__(self, input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box_path, output_pdbqt_path,
-                 output_log_path=None, properties=None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_ligand_pdbqt_path,
+        input_receptor_pdbqt_path,
+        input_box_path,
+        output_pdbqt_path,
+        output_log_path=None,
+        properties=None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -74,17 +85,24 @@ def __init__(self, input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box
 
         # Input/Output files
         self.io_dict = {
-            "in": {"input_ligand_pdbqt_path": input_ligand_pdbqt_path, "input_receptor_pdbqt_path": input_receptor_pdbqt_path, "input_box_path": input_box_path},
-            "out": {"output_pdbqt_path": output_pdbqt_path, "output_log_path": output_log_path}
+            "in": {
+                "input_ligand_pdbqt_path": input_ligand_pdbqt_path,
+                "input_receptor_pdbqt_path": input_receptor_pdbqt_path,
+                "input_box_path": input_box_path,
+            },
+            "out": {
+                "output_pdbqt_path": output_pdbqt_path,
+                "output_log_path": output_log_path,
+            },
         }
 
         # Properties specific for BB
-        self.cpu = properties.get('cpu', 1)
-        self.exhaustiveness = properties.get('exhaustiveness', 8)
-        self.num_modes = properties.get('num_modes', 9)
-        self.min_rmsd = properties.get('min_rmsd', 1)
-        self.energy_range = properties.get('energy_range', 3)
-        self.binary_path = properties.get('binary_path', 'vina')
+        self.cpu = properties.get("cpu", 1)
+        self.exhaustiveness = properties.get("exhaustiveness", 8)
+        self.num_modes = properties.get("num_modes", 9)
+        self.min_rmsd = properties.get("min_rmsd", 1)
+        self.energy_range = properties.get("energy_range", 3)
+        self.binary_path = properties.get("binary_path", "vina")
         self.properties = properties
 
         # Check the properties
@@ -92,22 +110,61 @@ def __init__(self, input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.io_dict["in"]["input_ligand_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_ligand_pdbqt_path"], "input_ligand_pdbqt_path", self.out_log, self.__class__.__name__)
-        self.io_dict["in"]["input_receptor_pdbqt_path"] = check_input_path(self.io_dict["in"]["input_receptor_pdbqt_path"], "input_receptor_pdbqt_path", self.out_log, self.__class__.__name__)
-        self.io_dict["in"]["input_box_path"] = check_input_path(self.io_dict["in"]["input_box_path"], "input_box_path", self.out_log, self.__class__.__name__)
-        self.io_dict["out"]["output_pdbqt_path"] = check_output_path(self.io_dict["out"]["output_pdbqt_path"], "output_pdbqt_path", False, self.out_log, self.__class__.__name__)
-        self.io_dict["out"]["output_log_path"] = check_output_path(self.io_dict["out"]["output_log_path"], "output_log_path", True, self.out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.io_dict["in"]["input_ligand_pdbqt_path"] = check_input_path(
+            self.io_dict["in"]["input_ligand_pdbqt_path"],
+            "input_ligand_pdbqt_path",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["in"]["input_receptor_pdbqt_path"] = check_input_path(
+            self.io_dict["in"]["input_receptor_pdbqt_path"],
+            "input_receptor_pdbqt_path",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["in"]["input_box_path"] = check_input_path(
+            self.io_dict["in"]["input_box_path"],
+            "input_box_path",
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["out"]["output_pdbqt_path"] = check_output_path(
+            self.io_dict["out"]["output_pdbqt_path"],
+            "output_pdbqt_path",
+            False,
+            self.out_log,
+            self.__class__.__name__,
+        )
+        self.io_dict["out"]["output_log_path"] = check_output_path(
+            self.io_dict["out"]["output_log_path"],
+            "output_log_path",
+            True,
+            self.out_log,
+            self.__class__.__name__,
+        )
 
     def calculate_box(self, box_file_path):
-        with open(box_file_path, 'r') as box_file:
+        with open(box_file_path, "r") as box_file:
             for line in box_file:
                 line = line.rstrip(os.linesep)
                 if line.startswith("REMARK BOX CENTER"):
                     fields = line.split()
                     center = fields[3:6]
                     size = fields[-3:]
-                    return list(map(str, [center[0], center[1], center[2], size[0], size[1], size[2]]))
+                    return list(
+                        map(
+                            str,
+                            [
+                                center[0],
+                                center[1],
+                                center[2],
+                                size[0],
+                                size[1],
+                                size[2],
+                            ],
+                        )
+                    )
             return list(map(str, [0, 0, 0, 0, 0, 0]))
 
     @launchlogger
@@ -123,26 +180,44 @@ def launch(self) -> int:
         self.stage_files()
 
         # calculating box position and size
-        x0, y0, z0, sidex, sidey, sidez = self.calculate_box(self.io_dict["in"]["input_box_path"])
+        x0, y0, z0, sidex, sidey, sidez = self.calculate_box(
+            self.io_dict["in"]["input_box_path"]
+        )
 
         # in case ligand or receptor end with END, remove last line
         # check_input_autodock(self.io_dict["in"]["input_ligand_pdbqt_path"], self.out_log)
         # check_input_autodock(self.io_dict["in"]["input_receptor_pdbqt_path"], self.out_log)
 
         # create cmd
-        self.cmd = [self.binary_path,
-                    '--ligand', self.stage_io_dict["in"]["input_ligand_pdbqt_path"],
-                    '--receptor', self.stage_io_dict["in"]["input_receptor_pdbqt_path"],
-                    '--center_x=' + x0, '--center_y=' + y0, '--center_z=' + z0,
-                    '--size_x=' + sidex, '--size_y=' + sidey, '--size_z=' + sidez,
-                    '--cpu', str(self.cpu),
-                    '--exhaustiveness', str(self.exhaustiveness),
-                    '--num_modes', str(self.num_modes),
-                    '--min_rmsd', str(self.min_rmsd),
-                    '--energy_range', str(self.energy_range),
-                    '--out', self.stage_io_dict["out"]["output_pdbqt_path"],
-                    '--verbosity', '1',
-                    '>', self.stage_io_dict["out"]["output_log_path"]]
+        self.cmd = [
+            self.binary_path,
+            "--ligand",
+            self.stage_io_dict["in"]["input_ligand_pdbqt_path"],
+            "--receptor",
+            self.stage_io_dict["in"]["input_receptor_pdbqt_path"],
+            "--center_x=" + x0,
+            "--center_y=" + y0,
+            "--center_z=" + z0,
+            "--size_x=" + sidex,
+            "--size_y=" + sidey,
+            "--size_z=" + sidez,
+            "--cpu",
+            str(self.cpu),
+            "--exhaustiveness",
+            str(self.exhaustiveness),
+            "--num_modes",
+            str(self.num_modes),
+            "--min_rmsd",
+            str(self.min_rmsd),
+            "--energy_range",
+            str(self.energy_range),
+            "--out",
+            self.stage_io_dict["out"]["output_pdbqt_path"],
+            "--verbosity",
+            "1",
+            ">",
+            self.stage_io_dict["out"]["output_log_path"],
+        ]
 
         # Run Biobb block
         self.run_biobb()
@@ -151,9 +226,7 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # remove temporary folder(s)
-        self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir", "")
-        ])
+        self.tmp_files.extend([self.stage_io_dict.get("unique_dir", "")])
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -161,43 +234,79 @@ def launch(self) -> int:
         return self.return_code
 
 
-def autodock_vina_run(input_ligand_pdbqt_path: str, input_receptor_pdbqt_path: str, input_box_path: str, output_pdbqt_path: str, output_log_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
+def autodock_vina_run(
+    input_ligand_pdbqt_path: str,
+    input_receptor_pdbqt_path: str,
+    input_box_path: str,
+    output_pdbqt_path: str,
+    output_log_path: Optional[str] = None,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Execute the :class:`AutoDockVinaRun <vina.autodock_vina_run.AutoDockVinaRun>` class and
     execute the :meth:`launch() <vina.autodock_vina_run.AutoDockVinaRun.launch>` method."""
 
-    return AutoDockVinaRun(input_ligand_pdbqt_path=input_ligand_pdbqt_path,
-                           input_receptor_pdbqt_path=input_receptor_pdbqt_path,
-                           input_box_path=input_box_path,
-                           output_pdbqt_path=output_pdbqt_path,
-                           output_log_path=output_log_path,
-                           properties=properties, **kwargs).launch()
+    return AutoDockVinaRun(
+        input_ligand_pdbqt_path=input_ligand_pdbqt_path,
+        input_receptor_pdbqt_path=input_receptor_pdbqt_path,
+        input_box_path=input_box_path,
+        output_pdbqt_path=output_pdbqt_path,
+        output_log_path=output_log_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Prepares input ligand for an Autodock Vina Virtual Screening.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('--config', required=False, help='Configuration file')
+    parser = argparse.ArgumentParser(
+        description="Prepares input ligand for an Autodock Vina Virtual Screening.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument("--config", required=False, help="Configuration file")
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_ligand_pdbqt_path', required=True, help='Path to the input PDBQT ligand. Accepted formats: pdbqt.')
-    required_args.add_argument('--input_receptor_pdbqt_path', required=True, help='Path to the input PDBQT receptor. Accepted formats: pdbqt.')
-    required_args.add_argument('--input_box_path', required=True, help='Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.')
-    required_args.add_argument('--output_pdbqt_path', required=True, help='Path to the output PDBQT file. Accepted formats: pdbqt.')
-    parser.add_argument('--output_log_path', required=False, help='Path to the log file. Accepted formats: log.')
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "--input_ligand_pdbqt_path",
+        required=True,
+        help="Path to the input PDBQT ligand. Accepted formats: pdbqt.",
+    )
+    required_args.add_argument(
+        "--input_receptor_pdbqt_path",
+        required=True,
+        help="Path to the input PDBQT receptor. Accepted formats: pdbqt.",
+    )
+    required_args.add_argument(
+        "--input_box_path",
+        required=True,
+        help="Path to the PDB containig the residues belonging to the binding site. Accepted formats: pdb.",
+    )
+    required_args.add_argument(
+        "--output_pdbqt_path",
+        required=True,
+        help="Path to the output PDBQT file. Accepted formats: pdbqt.",
+    )
+    parser.add_argument(
+        "--output_log_path",
+        required=False,
+        help="Path to the log file. Accepted formats: log.",
+    )
 
     args = parser.parse_args()
     args.config = args.config or "{}"
     properties = settings.ConfReader(config=args.config).get_prop_dic()
 
     # Specific call of each building block
-    autodock_vina_run(input_ligand_pdbqt_path=args.input_ligand_pdbqt_path,
-                      input_receptor_pdbqt_path=args.input_receptor_pdbqt_path,
-                      input_box_path=args.input_box_path,
-                      output_pdbqt_path=args.output_pdbqt_path,
-                      output_log_path=args.output_log_path,
-                      properties=properties)
+    autodock_vina_run(
+        input_ligand_pdbqt_path=args.input_ligand_pdbqt_path,
+        input_receptor_pdbqt_path=args.input_receptor_pdbqt_path,
+        input_box_path=args.input_box_path,
+        output_pdbqt_path=args.output_pdbqt_path,
+        output_log_path=args.output_log_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_vs/vina/common.py b/biobb_vs/vina/common.py
index 79fec69..07ae02a 100644
--- a/biobb_vs/vina/common.py
+++ b/biobb_vs/vina/common.py
@@ -1,57 +1,77 @@
-""" Common functions for package biobb_vs.vina """
+"""Common functions for package biobb_vs.vina"""
+
 from pathlib import Path, PurePath
-from biobb_common.tools import file_utils as fu
 
+from biobb_common.tools import file_utils as fu
 
 # CHECK PARAMETERS
 
+
 def check_input_path(path, argument, out_log, classname):
-    """ Checks input file """
+    """Checks input file"""
     if not Path(path).exists():
-        fu.log(classname + ': Unexisting %s file, exiting' % argument, out_log)
-        raise SystemExit(classname + ': Unexisting %s file' % argument)
+        fu.log(classname + ": Unexisting %s file, exiting" % argument, out_log)
+        raise SystemExit(classname + ": Unexisting %s file" % argument)
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
-        fu.log(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument), out_log)
-        raise SystemExit(classname + ': Format %s in %s file is not compatible' % (file_extension[1:], argument))
+        fu.log(
+            classname
+            + ": Format %s in %s file is not compatible"
+            % (file_extension[1:], argument),
+            out_log,
+        )
+        raise SystemExit(
+            classname
+            + ": Format %s in %s file is not compatible"
+            % (file_extension[1:], argument)
+        )
     return path
 
 
 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():
-        fu.log(classname + ': Unexisting  %s folder, exiting' % argument, out_log)
-        raise SystemExit(classname + ': Unexisting  %s folder' % argument)
+        fu.log(classname + ": Unexisting  %s folder, exiting" % argument, out_log)
+        raise SystemExit(classname + ": Unexisting  %s folder" % argument)
     file_extension = PurePath(path).suffix
     if not is_valid_file(file_extension[1:], argument):
-        fu.log(classname + ': Format %s in  %s file is not compatible' % (file_extension[1:], argument), out_log)
-        raise SystemExit(classname + ': Format %s in  %s file is not compatible' % (file_extension[1:], argument))
+        fu.log(
+            classname
+            + ": Format %s in  %s file is not compatible"
+            % (file_extension[1:], argument),
+            out_log,
+        )
+        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 """
+    """Checks if file format is compatible"""
     formats = {
-        'input_ligand_path': ['pdb'],
-        'output_ligand_path': ['pdbqt'],
-        'input_receptor_path': ['pdb'],
-        'output_receptor_path': ['pdbqt'],
-        'input_ligand_pdbqt_path': ['pdbqt'],
-        'input_receptor_pdbqt_path': ['pdbqt'],
-        'input_box_path': ['pdb'],
-        'output_pdbqt_path': ['pdbqt'],
-        'output_log_path': ['log']
+        "input_ligand_path": ["pdb"],
+        "output_ligand_path": ["pdbqt"],
+        "input_receptor_path": ["pdb"],
+        "output_receptor_path": ["pdbqt"],
+        "input_ligand_pdbqt_path": ["pdbqt"],
+        "input_receptor_pdbqt_path": ["pdbqt"],
+        "input_box_path": ["pdb"],
+        "output_pdbqt_path": ["pdbqt"],
+        "output_log_path": ["log"],
     }
     return ext in formats[argument]
 
 
 def check_mgltools_path(mgltools_path, out_log, classname):
-    """ Checks the path of mgltools """
+    """Checks the path of mgltools"""
     if not Path(mgltools_path).exists():
-        fu.log(classname + ': Unexisting mgltools_path, exiting', out_log)
-        raise SystemExit(classname + ': Unexisting mgltools_path, exiting')
+        fu.log(classname + ": Unexisting mgltools_path, exiting", out_log)
+        raise SystemExit(classname + ": Unexisting mgltools_path, exiting")
     return mgltools_path
 
 
diff --git a/setup.py b/setup.py
index 2cb91b4..28c107d 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_vs",
-    version="4.2.0",
+    version="5.0.0",
     author="Biobb developers",
     author_email="genis.bayarri@irbbarcelona.org",
     description="Biobb_vs is the Biobb module collection to perform virtual screening studies.",
@@ -15,12 +15,12 @@
     url="https://github.com/bioexcel/biobb_vs",
     project_urls={
         "Documentation": "http://biobb-vs.readthedocs.io/en/latest/",
-        "Bioexcel": "https://bioexcel.eu/"
+        "Bioexcel": "https://bioexcel.eu/",
     },
-    packages=setuptools.find_packages(exclude=['docs', 'test']),
-    package_data={'biobb_vs': ['py.typed']},
-    install_requires=['biobb_common==4.2.0'],
-    python_requires='>=3.8',
+    packages=setuptools.find_packages(exclude=["docs", "test"]),
+    package_data={"biobb_vs": ["py.typed"]},
+    install_requires=["biobb_common==5.0.0"],
+    python_requires=">=3.9",
     entry_points={
         "console_scripts": [
             "fpocket_filter = biobb_vs.fpocket.fpocket_filter:main",
@@ -30,16 +30,15 @@
             "box_residues = biobb_vs.utils.box_residues:main",
             "box = biobb_vs.utils.box:main",
             "extract_model_pdbqt = biobb_vs.utils.extract_model_pdbqt:main",
-            "autodock_vina_run = biobb_vs.vina.autodock_vina_run:main"
+            "autodock_vina_run = biobb_vs.vina.autodock_vina_run:main",
         ]
     },
-    classifiers=(
-        "Development Status :: 3 - Alpha",
-        "Programming Language :: Python :: 3.8",
+    classifiers=[
+        "Development Status :: 5 - Production/Stable",
         "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
-    ),
+        "Operating System :: Unix",
+    ],
 )