Initial commit.

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# VSCode
+.vscode/

BBB_calculator/BBB_score.py

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+"""Provides a BBB score calculator.
+
+See: BBB_score.
+"""
+
+
+def aro_r_term(aro_r):
+    if aro_r == 0:
+        return 0.336376
+    elif aro_r == 1:
+        return 0.816016
+    elif aro_r == 2:
+        return 1
+    elif aro_r == 3:
+        return 0.691115
+    elif aro_r == 4:
+        return 0.199399
+    elif aro_r > 4:
+        return 0
+    else:
+        raise ValueError('invalid aro_r input number')
+
+
+def ha_term(ha):
+    if ha > 5 and ha <= 45:
+        return 1/0.624231*(0.0000443*ha**3 - 0.004556*ha**2 + 0.12775*ha - 0.463)
+    elif ha <= 5 or ha > 45:
+        return 0
+    else:
+        raise ValueError('invalid ha number')
+
+
+def mwhbn_term(mw, hbd, hba):
+    if mw <= 0:
+        raise ValueError('invalid mw number')
+    if hbd < 0:
+        raise ValueError('invalid hbd number')
+    if hba < 0:
+        raise ValueError('invalid hba number')
+    mwhbn = (hbd + hba)/mw**0.5
+    if 0.05 <= mwhbn and mwhbn < 0.45:
+        return 1/0.72258*(26.733*mwhbn**3 - 31.495*mwhbn**2 + 9.5202*mwhbn - 0.1358)
+    elif mwhbn <= 0.05 or mwhbn > 0.45:
+        return 0
+    else: 
+        raise ValueError('invalid mwhbn number')
+
+
+def tpsa_term(tpsa):
+    if tpsa > 0 and tpsa <= 120:
+        return 1/0.9598*(-0.0067*tpsa + 0.9598)
+    elif tpsa == 0 or tpsa > 120:
+        return 0
+    else:
+        raise ValueError('invalid tpsa number')
+
+
+def pka_term(pka):
+    if pka > 3 and pka < 11:
+        return 1/0.597488*(0.00045068*pka**4 - 0.0116331*pka**3 + 0.18618*pka**2 - 0.71043*pka + 0.8579)
+    elif pka <= 3 or pka > 11:
+        return 0
+    else:
+        raise ValueError('invalif pka number')
+
+
+def BBB_score(aro_r, ha, mw, hbd, hba, tpsa, pka):
+    """BBB_score does the calculation from the gupta 2019 J Med Chem paper.
+
+    Args:
+        aro_r (int): The number of aromatic rings.
+        ha (int):  number of heavy atoms.
+        mw (float): molecular weight.
+        hbd (int): number of hydrogen bond donors.
+        hba (int): number of hydrogen bond acceptora.
+        tpsa (float): total polar surface area.
+        pka (float): pKa value.
+    
+    Returns:
+        float: The bbb score.
+
+    .. J. Med. Chem. 2019, 62, 21, 9824-9836:
+        https://doi.org/10.1021/acs.jmedchem.9b01220
+    """
+    aro_r_term_value = aro_r_term(aro_r)
+    ha_term_value = ha_term(ha)
+    mwhbn_term_value = mwhbn_term(mw, hbd, hba)
+    tpsa_term_value = tpsa_term(tpsa)
+    pka_term_value = pka_term(pka)
+    return aro_r_term_value + ha_term_value + 1.5*mwhbn_term_value + 2*tpsa_term_value + 0.5*pka_term_value

BBB_calculator/__init__.py

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+"""Implements a BBB score and related helper utilities.
+
+Provides the following sub-packages:
+- BBB_calculator: Provides a BBB score calculator.
+"""
+
+from BBB_calculator.BBB_score import BBB_score

LICENSE.txt

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+MIT License
+
+Copyright (c) 2020 Keira Garland
+
+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.

README.md

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+# BBB_calculator
+
+Implements the blood brain barrier score described in the following paper
+
+J. Med. Chem. 2019, 62, 21, 9824-9836
+https://doi.org/10.1021/acs.jmedchem.9b01220
+
+## Install
+
+```
+pip install BBB_calculator
+```
+
+## Use
+
+```
+from BBB_calculator import BBB_score
+
+score = BBB_score(1, 20, 300.29, 1, 7, 122.46, 2.86)
+print(score)
+# Prints: 1.815645...
+```

setup.cfg

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+[metadata]
+description-file = README.md

setup.py

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+from distutils.core import setup
+setup(
+  name = 'BBB_calculator',
+  packages = ['BBB_calculator'],
+  version = '1.0',
+  license='MIT',
+  description = 'Implements the blood brain barrier score described in: J. Med. Chem. 2019, 62, 21, 9824-9836',
+  author = 'Keira Garland',
+  author_email = '[email protected]',
+  url = 'https://github.com/frequencykg/BBB_calculator',
+  download_url = 'https://github.com/frequencykg/BBB_calculator/archive/v_10.tar.gz',
+  keywords = ['BBB', 'brain', 'medchem', 'calculator'],
+  install_requires=[],
+  classifiers=[
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Developers',
+    'Topic :: Software Development :: Build Tools',
+    'License :: OSI Approved :: MIT License',   # Again, pick a license
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.4',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Programming Language :: Python :: 3.8',
+  ],
+)

test_BBB_calc.py

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+import pytest
+from BBB_calculator.BBB_score import aro_r_term
+from BBB_calculator.BBB_score import ha_term
+from BBB_calculator.BBB_score import mwhbn_term
+from BBB_calculator.BBB_score import tpsa_term
+from BBB_calculator.BBB_score import pka_term
+from BBB_calculator import BBB_score
+
+
+def test_aro_r_term():
+    assert aro_r_term(2) == 1
+
+
+def test_ha_term():
+    assert ha_term(10) == pytest.approx(0.645914, 0.001)
+
+
+def test_mwhbn_term():
+    assert mwhbn_term(200, 2, 2) == pytest.approx(0.888784, 0.001)
+
+
+def test_tpsa_term():
+    assert tpsa_term(130) == 0
+
+
+def test_pka_term():
+    assert pka_term(2) == 0
+
+
+def test_bbb_score():
+    assert BBB_score(1, 20, 300.29, 1, 7, 122.46, 2.86) == pytest.approx(1.815645, 0.001)