biointerface 0.1.0__tar.gz

biointerface-0.1.0/AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Alessandro Pandolfi <alessandro.pandolfi@protonmail.com>
+
+Contributors
+------------
+
+None yet. Why not be the first?

biointerface-0.1.0/CONTRIBUTING.rst

@@ -0,0 +1,137 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/MorfeoRenai/biointerface/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub 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"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+BioInterface could always use more documentation, whether as part of the
+official BioInterface docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/MorfeoRenai/biointerface/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+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::
+
+    $ git clone git@github.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::
+
+    $ mkvirtualenv biointerface
+    $ cd biointerface/
+    $ python setup.py develop
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass flake8 and the
+   tests, including testing other Python versions with tox::
+
+    $ 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 GitHub::
+
+    $ 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.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+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.
+
+Tips
+----
+
+To run a subset of tests::
+
+$ pytest tests.test_biointerface
+
+
+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::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.
+
+Code of Conduct
+---------------
+
+Please note that this project is released with a `Contributor Code of Conduct`_.
+By participating in this project you agree to abide by its terms.
+
+.. _`Contributor Code of Conduct`: CODE_OF_CONDUCT.rst

biointerface-0.1.0/HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.1.0 (2025-02-08)
+------------------
+
+* First release on PyPI.

biointerface-0.1.0/LICENSE

@@ -0,0 +1,22 @@
+MIT License
+
+Copyright (c) 2025, Alessandro Pandolfi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

biointerface-0.1.0/MANIFEST.in

@@ -0,0 +1,11 @@
+include AUTHORS.rst
+include CONTRIBUTING.rst
+include HISTORY.rst
+include LICENSE
+include README.rst
+
+recursive-include tests *
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

biointerface-0.1.0/PKG-INFO

@@ -0,0 +1,64 @@
+Metadata-Version: 2.2
+Name: biointerface
+Version: 0.1.0
+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>
+License: MIT license
+Project-URL: bugs, https://gitlab.com/MorfeoRenai/biointerface/-/issues
+Project-URL: changelog, https://gitlab.com/MorfeoRenai/biointerface/-/blob/main/HISTORY.rst
+Project-URL: homepage, https://gitlab.com/MorfeoRenai/biointerface
+Classifier: Programming Language :: Python :: 3
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: pdbnucleicacids>=0.2.0
+Provides-Extra: dev
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+============
+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://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.
+
+
+* Free software: MIT license
+* Documentation: https://biointerface.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+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-0.1.0/README.rst

@@ -0,0 +1,41 @@
+============
+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://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.
+
+
+* Free software: MIT license
+* Documentation: https://biointerface.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+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-0.1.0/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = biointerface
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

biointerface-0.1.0/docs/authors.rst

@@ -0,0 +1 @@
+.. include:: ../AUTHORS.rst

biointerface-0.1.0/docs/conf.py

@@ -0,0 +1,162 @@
+#!/usr/bin/env python
+#
+# biointerface documentation build configuration file, created by
+# sphinx-quickstart on Fri Jun  9 13:47:02 2017.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('..'))
+
+import biointerface
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# 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.viewcode']
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'BioInterface'
+copyright = "2025, Alessandro Pandolfi"
+author = "Alessandro Pandolfi"
+
+# 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 = biointerface.__version__
+# The full version, including alpha/beta/rc tags.
+release = biointerface.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+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']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+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
+# documentation.
+#
+# html_theme_options = {}
+
+# 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']
+
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'biointerfacedoc'
+
+
+# -- 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',
+}
+
+# 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, 'biointerface.tex',
+     'BioInterface Documentation',
+     'Alessandro Pandolfi', 'manual'),
+]
+
+
+# -- 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, 'biointerface',
+     'BioInterface Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (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'),
+]
+
+
+

biointerface-0.1.0/docs/contributing.rst

@@ -0,0 +1 @@
+.. include:: ../CONTRIBUTING.rst

biointerface-0.1.0/docs/history.rst

@@ -0,0 +1 @@
+.. include:: ../HISTORY.rst

biointerface-0.1.0/docs/index.rst

@@ -0,0 +1,20 @@
+Welcome to BioInterface's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   readme
+   installation
+   usage
+   modules
+   contributing
+   authors
+   history
+
+Indices and tables
+==================
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

biointerface-0.1.0/docs/installation.rst

@@ -0,0 +1,51 @@
+.. highlight:: shell
+
+============
+Installation
+============
+
+
+Stable release
+--------------
+
+To install BioInterface, run this command in your terminal:
+
+.. code-block:: console
+
+    $ pip install biointerface
+
+This is the preferred method to install BioInterface, as it will always install the most recent stable release.
+
+If you don't have `pip`_ installed, this `Python installation guide`_ can guide
+you through the process.
+
+.. _pip: https://pip.pypa.io
+.. _Python installation guide: http://docs.python-guide.org/en/latest/starting/installation/
+
+
+From sources
+------------
+
+The sources for BioInterface can be downloaded from the `Github repo`_.
+
+You can either clone the public repository:
+
+.. code-block:: console
+
+    $ git clone git://github.com/MorfeoRenai/biointerface
+
+Or download the `tarball`_:
+
+.. code-block:: console
+
+    $ curl -OJL https://github.com/MorfeoRenai/biointerface/tarball/master
+
+Once you have a copy of the source, you can install it with:
+
+.. code-block:: console
+
+    $ python setup.py install
+
+
+.. _Github repo: https://github.com/MorfeoRenai/biointerface
+.. _tarball: https://github.com/MorfeoRenai/biointerface/tarball/master

biointerface-0.1.0/docs/make.bat

@@ -0,0 +1,36 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=biointerface
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

biointerface-0.1.0/docs/readme.rst

@@ -0,0 +1 @@
+.. include:: ../README.rst

biointerface-0.1.0/docs/usage.rst

@@ -0,0 +1,7 @@
+=====
+Usage
+=====
+
+To use BioInterface in a project::
+
+    import biointerface

biointerface-0.1.0/pyproject.toml

@@ -0,0 +1,185 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "biointerface"
+version = "0.1.0"
+description = "BioInterface is a python package capable of extracting Protein-DNA interfaces from PDB/mmCif structures."
+readme = "README.rst"
+authors = [
+  {name = "Alessandro Pandolfi", email = "alessandro.pandolfi@protonmail.com"}
+]
+maintainers = [
+  {name = "Alessandro Pandolfi", email = "alessandro.pandolfi@protonmail.com"}
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+license = {text = "MIT license"}
+dependencies = [
+    "pandas",
+    "biopython",
+    "pdbnucleicacids >= 0.2.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "coverage",  # testing
+    "mypy",  # linting
+    "pytest",  # testing
+    "ruff"  # linting
+]
+
+[project.urls]
+
+bugs = "https://gitlab.com/MorfeoRenai/biointerface/-/issues"
+changelog = "https://gitlab.com/MorfeoRenai/biointerface/-/blob/main/HISTORY.rst"
+homepage = "https://gitlab.com/MorfeoRenai/biointerface"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.package-data]
+"*" = ["*.*"]
+
+
+
+
+# Mypy
+# ----
+
+[tool.mypy]
+files = "."
+
+# Use strict defaults
+strict = true
+warn_unreachable = true
+warn_no_return = true
+
+[[tool.mypy.overrides]]
+# Don't require test functions to include types
+module = "tests.*"
+allow_untyped_defs = true
+disable_error_code = "attr-defined"
+
+
+
+
+# pytest
+# ----
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = "-rA"
+testpaths = [
+    "tests"
+]
+
+
+
+
+# bump-my-version
+# ----
+
+[tool.bumpversion]
+current_version = "0.1.0"
+parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
+serialize = ["{major}.{minor}.{patch}"]
+search = "{current_version}"
+replace = "{new_version}"
+regex = false
+ignore_missing_version = false
+ignore_missing_files = false
+tag = false
+sign_tags = false
+tag_name = "v{new_version}"
+tag_message = "Bump version: {current_version} → {new_version}"
+allow_dirty = false
+commit = true
+message = "Bump version: {current_version} → {new_version}"
+commit_args = ""
+setup_hooks = []
+pre_commit_hooks = []
+post_commit_hooks = []
+
+[[tool.bumpversion.files]]
+filename = "PDBNucleicAcids/__init__.py"
+search = "{current_version}"
+replace = "{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "HISTORY.rst"
+search = "{current_version}"
+replace = "{new_version}"
+
+[[tool.bumpversion.files]]
+filename = "pyproject.toml"
+search = "{current_version}"
+replace = "{new_version}"
+
+
+
+
+# ruff
+# ----
+
+[tool.ruff]
+# Set the maximum line length to 79.
+line-length = 79
+show-fixes = true
+
+[tool.ruff.lint]
+# Add the `line-too-long` rule to the enforced rule set. By default, Ruff omits rules that
+# overlap with the use of a formatter, like Black, but we can override this behavior by
+# explicitly adding the rule.
+extend-select = ["E501"]
+
+
+
+
+# tox
+# ----
+
+[tool.tox]
+#requires = ["tox>=4.19"]
+requires = ["tox"]
+# Elenco delle versioni di Python con cui testare
+envlist = ["py38", "py39", "py310", "py311", "py312", "py313"]
+
+[tool.tox.env_run_base]  # Configurazione generale per tutti gli ambienti di test
+description = "Run the tests with pytest"
+deps = [
+    #"pytest-cov",  # Esempio di dipendenza per la coverage dei test
+    "-r requirements-dev.txt"  # Se hai un file requirements per lo sviluppo
+]
+commands = [["pytest"]]
+
+#[tool.tox.env.type]
+#description = "run type check on code base"
+#deps = ["mypy==1.11.2", "types-cachetools>=5.5.0.20240820", "types-chardet>=5.0.4.6"]
+#commands = [["mypy", "src{/}tox"], ["mypy", "tests"]]
+
+[tool.tox.env.py38]
+description = "Run the tests on Python 3.8"
+
+[tool.tox.env.py39]
+description = "Run the tests on Python 3.9"
+
+[tool.tox.env.py310]
+description = "Run the tests on Python 3.10"
+
+[tool.tox.env.py311]
+description = "Run the tests on Python 3.11"
+
+[tool.tox.env.py312]
+description = "Run the tests on Python 3.12"
+
+[tool.tox.env.py313]
+description = "Run the tests on Python 3.13"
+
+# Esempio di configurazione per l'analisi statica del codice (opzionale)
+#[tool.tox.env.lint]
+#description = "Run linting"
+#deps = ["flake8"]
+#commands = ["flake8 src tests"]

biointerface-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

biointerface-0.1.0/src/biointerface/__init__.py

@@ -0,0 +1,5 @@
+"""Top-level package for BioInterface."""
+
+__author__ = """Alessandro Pandolfi"""
+__email__ = 'alessandro.pandolfi@protonmail.com'
+__version__ = '0.1.0'

biointerface-0.1.0/src/biointerface/biointerface.py

@@ -0,0 +1,138 @@
+"""Extract interface."""
+
+from Bio.PDB.Polypeptide import PPBuilder
+from Bio.PDB.NeighborSearch import NeighborSearch
+from Bio.PDB import Structure, Model, Chain, Residue
+from Bio.PDB import MMCIFIO
+
+import pandas as pd
+
+from PDBNucleicAcids.NucleicAcid import NABuilder
+
+
+def get_interface(structure, protein_chain_id, search_radius, n_atoms):
+    """Extract interface."""
+    # get all the atoms from the nucleic acids, in most cases DNA
+    na_builder = NABuilder()
+    na_list = na_builder.build_nucleic_acids(structure)
+    na_atoms = []
+    for na in na_list:
+        na_atoms.extend(na.get_atoms())
+    na_atoms = list(set(na_atoms))
+
+    # get all the atoms from the protein chain
+    protein_chain = structure[0][protein_chain_id]
+    pp_builder = PPBuilder()
+    pp = pp_builder.build_peptides(protein_chain)[0]
+    pp_atoms = []
+    for pp in pp_builder.build_peptides(protein_chain):
+        for res in pp:
+            pp_atoms.extend(res.get_atoms())
+    pp_atoms = list(set(pp_atoms))
+
+    # Crea una lista con tutti gli atomi di DNA e proteina
+    all_atoms = na_atoms + pp_atoms
+
+    # Usa NeighborSearch per trovare gli atomi vicini entro una certa
+    # distanza
+    ns = NeighborSearch(all_atoms)
+
+    # Cerca gli atomi vicini entro un raggio di 4 Å tra DNA e proteina
+    all_contacts = ns.search_all(search_radius)
+
+    # Filtra solo i contatti, ovvero le coppied di atomi,
+    # che hanno un atomo di DNA
+    temp = [
+        (atom1, atom2)
+        for atom1, atom2 in all_contacts
+        if (atom1 in na_atoms or atom2 in na_atoms)
+    ]
+
+    # Filtra solo i contatti tra DNA e proteina
+    contacts = [
+        (atom1, atom2)
+        for atom1, atom2 in temp
+        if (atom1 in na_atoms and atom2 in pp_atoms)
+    ] + [
+        (atom2, atom1)
+        for atom1, atom2 in temp
+        if (atom1 in pp_atoms and atom2 in na_atoms)
+    ]
+    # temp è utile per greedyness, prima prendi il DNA, che ha meno
+    # atomi, escludendo quelli intra-proteina
+    # poi escludi anche quelli intra-DNA
+    # inoltre ci assicuriamo che la col 0 contenga gli atomi di DNA e
+    # che col 1 contenga gli atomi di proteine
+    # Ce ne assicuriamo invertendo atom1 e atom2 nella seconda lista
+
+    # dataframe
+    contacts_df = pd.DataFrame(contacts, columns=["na_atoms", "pp_atoms"])
+
+    # distance column
+    # Atom - Atom = distance in armstrong
+    contacts_df["dist"] = contacts_df.apply(
+        lambda row: row["na_atoms"] - row["pp_atoms"], axis=1
+    )
+
+    # grouping: minimum distance for every protein atom, then sorted
+    dist = contacts_df.groupby(by="pp_atoms")["dist"].min().sort_values()
+
+    # take the n top smallest distances
+    # atoms as indexes
+    dist = dist.head(n_atoms)  # Series of floats
+    interface_atoms = dist.index.tolist()  # index of Atom objects, to list
+
+    return interface_atoms
+
+
+def export_atom_list(structure_id, atom_list, out_filepath):
+    # not in Path but in string
+    out_filepath = str(out_filepath)
+
+    new_structure = Structure.Structure(structure_id)
+    for atom in atom_list:
+        _add_atom_to_new_structure(atom, new_structure)
+
+    # Prepare IO object
+    io = MMCIFIO()
+    io.set_structure(new_structure)
+
+    # Esporta la nuova struttura in un file PDB
+    # necessita di string type filepath
+    io.save(out_filepath)
+
+
+def _add_atom_to_new_structure(atom, new_structure):
+    model_id = (
+        atom.get_parent().get_parent().get_parent().id
+    )  # Ottieni l'ID del modello
+    chain_id = atom.get_parent().get_parent().id  # Ottieni l'ID della catena
+    residue_id = atom.get_parent().id  # Ottieni l'ID del residuo
+    resname = atom.get_parent().resname  # Nome del residuo
+
+    # Controlla se il modello esiste già nel nuovo modello
+    if model_id in [model.id for model in new_structure]:
+        new_model = new_structure[model_id]
+    else:
+        new_model = Model.Model(model_id)
+        new_structure.add(new_model)
+
+    # Controlla se la catena esiste già nel nuovo modello
+    if chain_id in [chain.id for chain in new_model]:
+        new_chain = new_model[chain_id]
+    else:
+        new_chain = Chain.Chain(chain_id)
+        new_model.add(new_chain)
+
+    # Controlla se il residuo esiste già nella nuova catena
+    if residue_id in [res.id for res in new_chain]:
+        new_residue = new_chain[residue_id]
+    else:
+        new_residue = Residue.Residue(
+            residue_id, resname, atom.get_parent().segid
+        )
+        new_chain.add(new_residue)
+
+    # Copia l'atomo e aggiungilo al residuo
+    new_atom = atom.copy()
+    new_residue.add(new_atom)

biointerface-0.1.0/src/biointerface.egg-info/PKG-INFO

@@ -0,0 +1,64 @@
+Metadata-Version: 2.2
+Name: biointerface
+Version: 0.1.0
+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>
+License: MIT license
+Project-URL: bugs, https://gitlab.com/MorfeoRenai/biointerface/-/issues
+Project-URL: changelog, https://gitlab.com/MorfeoRenai/biointerface/-/blob/main/HISTORY.rst
+Project-URL: homepage, https://gitlab.com/MorfeoRenai/biointerface
+Classifier: Programming Language :: Python :: 3
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: pandas
+Requires-Dist: biopython
+Requires-Dist: pdbnucleicacids>=0.2.0
+Provides-Extra: dev
+Requires-Dist: coverage; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+============
+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://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.
+
+
+* Free software: MIT license
+* Documentation: https://biointerface.readthedocs.io.
+
+
+Features
+--------
+
+* TODO
+
+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-0.1.0/src/biointerface.egg-info/SOURCES.txt

@@ -0,0 +1,26 @@
+AUTHORS.rst
+CONTRIBUTING.rst
+HISTORY.rst
+LICENSE
+MANIFEST.in
+README.rst
+pyproject.toml
+docs/Makefile
+docs/authors.rst
+docs/conf.py
+docs/contributing.rst
+docs/history.rst
+docs/index.rst
+docs/installation.rst
+docs/make.bat
+docs/readme.rst
+docs/usage.rst
+src/biointerface/__init__.py
+src/biointerface/biointerface.py
+src/biointerface.egg-info/PKG-INFO
+src/biointerface.egg-info/SOURCES.txt
+src/biointerface.egg-info/dependency_links.txt
+src/biointerface.egg-info/requires.txt
+src/biointerface.egg-info/top_level.txt
+tests/__init__.py
+tests/test_biointerface.py

biointerface-0.1.0/src/biointerface.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

biointerface-0.1.0/src/biointerface.egg-info/requires.txt

@@ -0,0 +1,9 @@
+pandas
+biopython
+pdbnucleicacids>=0.2.0
+
+[dev]
+coverage
+mypy
+pytest
+ruff

biointerface-0.1.0/src/biointerface.egg-info/top_level.txt

@@ -0,0 +1 @@
+biointerface

biointerface-0.1.0/tests/__init__.py

@@ -0,0 +1 @@
+"""Unit test package for biointerface."""

biointerface-0.1.0/tests/test_biointerface.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+"""Tests for `biointerface` package."""
+
+import pytest
+
+
+from biointerface import biointerface
+
+
+@pytest.fixture
+def response():
+    """Sample pytest fixture.
+
+    See more at: http://doc.pytest.org/en/latest/fixture.html
+    """
+    # import requests
+    # return requests.get('https://github.com/audreyr/cookiecutter-pypackage')
+
+
+def test_content(response):
+    """Sample pytest test function with the pytest fixture as an argument."""
+    # from bs4 import BeautifulSoup
+    # assert 'GitHub' in BeautifulSoup(response.content).title.string