biointerface 0.1.0__tar.gz → 0.2.2__tar.gz

{biointerface-0.1.0 → biointerface-0.2.2}/CONTRIBUTING.rst

@@ -15,7 +15,7 @@ Types of Contributions
 Report Bugs
 ~~~~~~~~~~~
 
-Report bugs at https://github.com/MorfeoRenai/biointerface/issues.
+Report bugs at https://gitlab.com/MorfeoRenai/biointerface/-/issues.
 
 If you are reporting a bug, please include:
 
@@ -26,13 +26,13 @@ If you are reporting a bug, please include:
 Fix Bugs
 ~~~~~~~~
 
-Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+Look through the Gitlab issues for bugs. Anything tagged with "bug" and "help
 wanted" is open to whoever wants to implement it.
 
 Implement Features
 ~~~~~~~~~~~~~~~~~~
 
-Look through the GitHub issues for features. Anything tagged with "enhancement"
+Look through the Gitlab issues for features. Anything tagged with "enhancement"
 and "help wanted" is open to whoever wants to implement it.
 
 Write Documentation
@@ -45,7 +45,7 @@ articles, and such.
 Submit Feedback
 ~~~~~~~~~~~~~~~
 
-The best way to send feedback is to file an issue at https://github.com/MorfeoRenai/biointerface/issues.
+The best way to send feedback is to file an issue at https://gitlab.com/MorfeoRenai/biointerface/-/issues.
 
 If you are proposing a feature:
 
@@ -57,42 +57,49 @@ If you are proposing a feature:
 Get Started!
 ------------
 
-Ready to contribute? Here's how to set up `biointerface` for local development.
+Ready to contribute? Here's how to set up BioInterface for local development.
 
-1. Fork the `biointerface` repo on GitHub.
-2. Clone your fork locally::
+1. Fork the BioInterface repo on Gitlab.
+2. Clone your fork locally:
 
-    $ git clone git@github.com:your_name_here/biointerface.git
+.. code-block:: console
 
-3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development::
+    $ git clone git@gitlab.com:your_name_here/biointerface.git
+
+3. Install your local copy into a virtualenv. Assuming you have
+   virtualenvwrapper installed, this is how you set up your fork for local
+   development:
+
+.. code-block:: console
 
     $ mkvirtualenv biointerface
     $ cd biointerface/
-    $ python setup.py develop
+    $ make requirements-dev
 
-4. Create a branch for local development::
+4. Create a branch for local development:
 
-    $ git checkout -b name-of-your-bugfix-or-feature
+.. code-block:: console
 
-   Now you can make your changes locally.
+    $ git checkout -b name-of-your-bugfix-or-feature
 
 5. When you're done making changes, check that your changes pass flake8 and the
-   tests, including testing other Python versions with tox::
+   tests, including testing other Python versions with tox:
+
+.. code-block:: console
 
     $ make lint
     $ make test
-    Or
     $ make test-all
 
-   To get flake8 and tox, just pip install them into your virtualenv.
+6. Commit your changes and push your branch to Gitlab:
 
-6. Commit your changes and push your branch to GitHub::
+.. code-block:: console
 
     $ git add .
     $ git commit -m "Your detailed description of your changes."
     $ git push origin name-of-your-bugfix-or-feature
 
-7. Submit a pull request through the GitHub website.
+7. Submit a pull request through the Gitlab website.
 
 Pull Request Guidelines
 -----------------------
@@ -103,16 +110,17 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.com/MorfeoRenai/biointerface/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13,
+   and for PyPy. Make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
 
-To run a subset of tests::
+To run a subset of tests:
+
+.. code-block:: console
 
-$ pytest tests.test_biointerface
+    $ pytest tests.test_biointerface
 
 
 Deploying
@@ -120,13 +128,14 @@ Deploying
 
 A reminder for the maintainers on how to deploy.
 Make sure all your changes are committed (including an entry in HISTORY.rst).
-Then run::
+Then run:
+
+.. code-block:: console
 
-$ bump2version patch # possible: major / minor / patch
-$ git push
-$ git push --tags
+    $ bump-my-version patch # possible: major / minor / patch
+    $ git push
+    $ git push --tags
 
-Travis will then deploy to PyPI if tests pass.
 
 Code of Conduct
 ---------------

biointerface-0.2.2/HISTORY.rst

@@ -0,0 +1,14 @@
+=======
+History
+=======
+
+0.1.0 (2025-02-08)
+------------------
+
+* First release on PyPI.
+
+
+0.2.0 (2025-02-28)
+------------------
+
+* Feature: Interface class, with getter methods for atoms, dataframes etc

{biointerface-0.1.0 → biointerface-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: biointerface
-Version: 0.1.0
+Version: 0.2.2
 Summary: BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures.
 Author-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
 Maintainer-email: Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
@@ -14,7 +14,7 @@ License-File: LICENSE
 License-File: AUTHORS.rst
 Requires-Dist: pandas
 Requires-Dist: biopython
-Requires-Dist: pdbnucleicacids>=0.2.0
+Requires-Dist: pdbnucleicacids>=0.2
 Provides-Extra: dev
 Requires-Dist: coverage; extra == "dev"
 Requires-Dist: mypy; extra == "dev"
@@ -29,31 +29,86 @@ BioInterface
 .. image:: https://img.shields.io/pypi/v/biointerface.svg
         :target: https://pypi.python.org/pypi/biointerface
 
-.. image:: https://img.shields.io/travis/MorfeoRenai/biointerface.svg
-        :target: https://travis-ci.com/MorfeoRenai/biointerface
-
 .. image:: https://readthedocs.org/projects/biointerface/badge/?version=latest
         :target: https://biointerface.readthedocs.io/en/latest/?version=latest
         :alt: Documentation Status
 
+.. image:: https://gitlab.com/MorfeoRenai/biointerface/badges/main/coverage.svg
+        :target: https://gitlab.com/MorfeoRenai/biointerface/-/commits/main
+        :alt: Coverage Status
 
 .. image:: https://pyup.io/repos/github/MorfeoRenai/biointerface/shield.svg
      :target: https://pyup.io/repos/github/MorfeoRenai/biointerface/
      :alt: Updates
 
 
-
-BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures.
-
+BioInterface is a `Biopython <https://biopython.org/>`_ based package that extracts Protein-DNA
+interfaces in a PDB structures.
 
 * Free software: MIT license
 * Documentation: https://biointerface.readthedocs.io.
 
 
-Features
+Get Started
+-----------
+
+This is a little tutorial on how to use the BioInterface package.
+
+The official release is found in the Python Package Index (PyPI)
+
+.. code-block:: console
+
+    $ pip install biointerface
+
+You can extract a single Protein-DNA interface from a single protein chain.
+
+.. code-block:: python
+
+    from Bio.PDB.MMCIFParser import MMCIFParser
+    from biointerface import Interface, build_interfaces
+
+    # parse and build structure with Biopython
+    parser = MMCIFParser()
+    structure = parser.get_structure(
+        structure_id="1A02", filename="1a02-assembly1.cif"
+    )
+
+    # extract interface from a specific protein chain
+    face = Interface(
+        structure=structure,
+        protein_chain_id="F",
+        search_radius=5.0
+    )
+    face
+
+.. code-block:: console
+
+    <Interface chains=F:BA contacts=258 search_radius=5.0>
+
+Check the official documentation for more information.
+
+
+Feaures
+-------
+
+* Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;
+
+* Extract all Protein-DNA interfaces in a PDB structure;
+
+* Get all interacting residues in a interface;
+
+* Get all interacting atoms in a interface;
+
+* Interface data as ``pandas`` DataFrame;
+
+
+TODO
 --------
 
-* TODO
+* Extract continous bound DNA sequence
+
+* Proper tests (WIP)
+
 
 Credits
 -------

biointerface-0.2.2/README.rst

@@ -0,0 +1,96 @@
+============
+BioInterface
+============
+
+
+.. image:: https://img.shields.io/pypi/v/biointerface.svg
+        :target: https://pypi.python.org/pypi/biointerface
+
+.. image:: https://readthedocs.org/projects/biointerface/badge/?version=latest
+        :target: https://biointerface.readthedocs.io/en/latest/?version=latest
+        :alt: Documentation Status
+
+.. image:: https://gitlab.com/MorfeoRenai/biointerface/badges/main/coverage.svg
+        :target: https://gitlab.com/MorfeoRenai/biointerface/-/commits/main
+        :alt: Coverage Status
+
+.. image:: https://pyup.io/repos/github/MorfeoRenai/biointerface/shield.svg
+     :target: https://pyup.io/repos/github/MorfeoRenai/biointerface/
+     :alt: Updates
+
+
+BioInterface is a `Biopython <https://biopython.org/>`_ based package that extracts Protein-DNA
+interfaces in a PDB structures.
+
+* Free software: MIT license
+* Documentation: https://biointerface.readthedocs.io.
+
+
+Get Started
+-----------
+
+This is a little tutorial on how to use the BioInterface package.
+
+The official release is found in the Python Package Index (PyPI)
+
+.. code-block:: console
+
+    $ pip install biointerface
+
+You can extract a single Protein-DNA interface from a single protein chain.
+
+.. code-block:: python
+
+    from Bio.PDB.MMCIFParser import MMCIFParser
+    from biointerface import Interface, build_interfaces
+
+    # parse and build structure with Biopython
+    parser = MMCIFParser()
+    structure = parser.get_structure(
+        structure_id="1A02", filename="1a02-assembly1.cif"
+    )
+
+    # extract interface from a specific protein chain
+    face = Interface(
+        structure=structure,
+        protein_chain_id="F",
+        search_radius=5.0
+    )
+    face
+
+.. code-block:: console
+
+    <Interface chains=F:BA contacts=258 search_radius=5.0>
+
+Check the official documentation for more information.
+
+
+Feaures
+-------
+
+* Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;
+
+* Extract all Protein-DNA interfaces in a PDB structure;
+
+* Get all interacting residues in a interface;
+
+* Get all interacting atoms in a interface;
+
+* Interface data as ``pandas`` DataFrame;
+
+
+TODO
+--------
+
+* Extract continous bound DNA sequence
+
+* Proper tests (WIP)
+
+
+Credits
+-------
+
+This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+
+.. _Cookiecutter: https://github.com/audreyr/cookiecutter
+.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

biointerface-0.2.2/docs/biointerface.rst

@@ -0,0 +1,21 @@
+biointerface package
+====================
+
+Submodules
+----------
+
+biointerface.core module
+------------------------
+
+.. automodule:: biointerface.core
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Module contents
+---------------
+
+.. automodule:: biointerface
+   :members:
+   :show-inheritance:
+   :undoc-members:

{biointerface-0.1.0 → biointerface-0.2.2}/docs/conf.py

@@ -19,7 +19,8 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
+
+sys.path.insert(0, os.path.abspath(".."))
 
 import biointerface
 
@@ -31,22 +32,22 @@ import biointerface
 
 # 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.viewcode']
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode"]
 
 # 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']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = 'BioInterface'
+project = "BioInterface"
 copyright = "2025, Alessandro Pandolfi"
 author = "Alessandro Pandolfi"
 
@@ -69,10 +70,10 @@ language = None
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
@@ -83,7 +84,7 @@ todo_include_todos = False
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # 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
@@ -94,13 +95,13 @@ html_theme = 'alabaster'
 # 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"]
 
 
 # -- Options for HTMLHelp output ---------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biointerfacedoc'
+htmlhelp_basename = "biointerfacedoc"
 
 
 # -- Options for LaTeX output ------------------------------------------
@@ -109,15 +110,12 @@ 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',
@@ -127,9 +125,13 @@ latex_elements = {
 # (source start file, target name, title, author, documentclass
 # [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biointerface.tex',
-     'BioInterface Documentation',
-     'Alessandro Pandolfi', 'manual'),
+    (
+        master_doc,
+        "biointerface.tex",
+        "BioInterface Documentation",
+        "Alessandro Pandolfi",
+        "manual",
+    ),
 ]
 
 
@@ -138,9 +140,7 @@ latex_documents = [
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'biointerface',
-     'BioInterface Documentation',
-     [author], 1)
+    (master_doc, "biointerface", "BioInterface Documentation", [author], 1)
 ]
 
 
@@ -150,13 +150,14 @@ man_pages = [
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biointerface',
-     'BioInterface Documentation',
-     author,
-     'biointerface',
-     'One line description of project.',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "biointerface",
+        "BioInterface Documentation",
+        author,
+        "biointerface",
+        "BioInterface is a python package capable of extracting Protein-DNA \
+interfaces from BioPython PDB structures.",
+        "Miscellaneous",
+    ),
 ]
-
-
-

{biointerface-0.1.0 → biointerface-0.2.2}/docs/installation.rst

@@ -26,7 +26,7 @@ you through the process.
 From sources
 ------------
 
-The sources for BioInterface can be downloaded from the `Github repo`_.
+The sources for BioInterface can be downloaded from the `Gitlab repo`_.
 
 You can either clone the public repository:
 
@@ -38,14 +38,14 @@ Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl -OJL https://github.com/MorfeoRenai/biointerface/tarball/master
+    $ curl -OJL https://gitlab.com/MorfeoRenai/biointerface/tarball/main
 
 Once you have a copy of the source, you can install it with:
 
 .. code-block:: console
 
-    $ python setup.py install
+    $ make install
 
 
-.. _Github repo: https://github.com/MorfeoRenai/biointerface
-.. _tarball: https://github.com/MorfeoRenai/biointerface/tarball/master
+.. _Gitlab repo: https://gitlab.com/MorfeoRenai/biointerface
+.. _tarball: https://gitlab.com/MorfeoRenai/biointerface/tarball/main

biointerface-0.2.2/docs/modules.rst

@@ -0,0 +1,7 @@
+src
+===
+
+.. toctree::
+   :maxdepth: 4
+
+   biointerface