cosmopharm 0.0.27__tar.gz → 0.0.29__tar.gz

cosmopharm-0.0.29/.github/workflows/python-publish.yml

@@ -0,0 +1,41 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Fetch all history and tags
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

cosmopharm-0.0.29/.gitignore

@@ -0,0 +1,189 @@
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+conda-recipe/
+*.rst
+docs/*
+!docs/README_pypi.md
+#README_pypi.md
+figs
+~$*
+releases
+advanced_usage.py
+minimal_working_example.py
+COSMOSAC
+figures
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python

cosmopharm-0.0.29/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "profiles/pharmaceuticals"]
+	path = profiles/pharmaceuticals
+	url = https://github.com/klajmonm/pharmaceuticals

cosmopharm-0.0.29/CITATION.cff

@@ -0,0 +1,52 @@
+cff-version: 1.2.0
+message: "If you use COSMOPharm for your research, please cite the associated research article as follows."
+
+# Preferred citation for the associated research article
+preferred-citation:
+  type: article
+  authors:
+    - family-names: Antolovic
+      given-names: Ivan
+    - family-names: Vrabec
+      given-names: Jadran
+    - family-names: Klajmon
+      given-names: Martin
+  title: "COSMOPharm: Drug--Polymer Compatibility of Pharmaceutical Amorphous Solid Dispersions from COSMO-SAC"
+  journal: "Molecular Pharmaceutics"
+  doi: "10.1021/acs.molpharmaceut.3c12345"
+  year: 2024
+  month: 3
+  start: 1
+  end: 10
+  issue: 1
+  volume: 1
+
+# Citation information for the COSMOPharm software
+title: "COSMOPharm Tool: Computational Analysis of Drug-Polymer Compatibility"
+version: "1.0.0"
+doi: "10.5281/zenodo.10792203" # Replace with actual DOI if available
+date-released: 2024-03-28
+url: "https://github.com/ivanantolo/cosmopharm"
+authors:
+  - family-names: Antolović
+    given-names: Ivan
+    affiliation: "Thermodynamics, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany"
+    email: ivan.antolovic@tu-berlin.de
+  - family-names: Vrabec
+    given-names: Jadran
+    affiliation: "Thermodynamics, Technische Universität Berlin, Ernst-Reuter-Platz 1, 10587 Berlin, Germany"
+  - family-names: Klajmon
+    given-names: Martin
+    affiliation: "Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czechia"
+    email: martin.klajmon@vscht.cz
+keywords:
+  - chemical-engineering
+  - phase-behavior
+  - cosmo-sac
+  - solubility-prediction
+  - pharmaceutical-science
+  - pharmaceutical-development
+  - drug-polymer-compatibility
+  - miscibility-analysis
+  - amorphous-solid-dispersions
+  - cosmopharm

{cosmopharm-0.0.27/src/cosmopharm.egg-info → cosmopharm-0.0.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cosmopharm
-Version: 0.0.27
+Version: 0.0.29
 Summary: Predictive modeling for drug-polymer compatibility in pharmaceutical formulations using COSMO-SAC.
 Home-page: https://github.com/ivanantolo/cosmopharm,
 Author: Ivan Antolovic

cosmopharm-0.0.29/basic_usage.py

@@ -0,0 +1,81 @@
+"""
+Solubility & Miscibility calculations CLI
+"""
+
+import argparse
+import cCOSMO
+from cosmopharm import SLE, LLE, COSMOSAC
+from cosmopharm.utils import create_components, read_params
+try:
+    import matplotlib.pyplot as plt
+except ImportError:
+    raise ImportError(
+        "This script requires matplotlib. Please install it with "
+        "'pip install matplotlib'."
+    )
+
+def parse_args():
+    parser = argparse.ArgumentParser(description='Solubility & Miscibility Calculations CLI')
+    parser.add_argument('--names', nargs=2, default=['SIM', 'PLGA50'], help='Names of components e.g. SIM PLGA50')
+    parser.add_argument('--params_file', type=str, default="data/sle/table_params.xlsx", help='Path to parameters file')
+    parser.add_argument('--profile_path', type=str, default="./profiles/_import_methods/UD/", help='Path to COSMO profiles')
+    parser.add_argument('--fraction', type=str, default='w', choices=['w', 'x'], help='Fraction type for plotting (w = weight, x = mole)')
+    parser.add_argument('--output', type=str, default='basic_usage.png', help='Output file name for the plot')
+    return parser.parse_args()
+
+def main():
+    args = parse_args()
+
+    # Create components and add parameters for SLE calculation
+    parameters = read_params(args.params_file)
+    components = create_components(args.names, parameters)
+    api, polymer = components[:2]
+
+    # Initialize COSMO-SAC model
+    db = cCOSMO.DelawareProfileDatabase(
+        f"{args.profile_path}/complist.txt",
+        f"{args.profile_path}/sigma3/")
+
+    for name in args.names:
+        iden = db.normalize_identifier(name)
+        db.add_profile(iden)
+    COSMO = cCOSMO.COSMO3(args.names, db)
+
+    # Add extended functionality to COSMO-SAC model (e.g. free volume, .. etc.)
+    actmodel = COSMOSAC(COSMO, mixture=components)
+    actmodel.combinatorial = 'FV'  # Free-Volume (FV), Staverman-Guggenheim (SG)
+    actmodel.dispersion = True  # Turn on/off the dispersion (optional)
+
+    # Calculate SLE (solubility)
+    sle = SLE(actmodel=actmodel)
+    ideal = sle.solubility(mix_type='ideal', show_progress=True)  # ideal mixture (gamma=1)
+    real = sle.solubility(mix_type='real', show_progress=True)  # real mixture (gamma=COSMO)
+
+    # Calculate LLE (miscibility)
+    lle = LLE(actmodel=actmodel)
+    options = dict(max_gap=0.1, dT=30, exponent=2.1, max_gap_type='weight')
+    miscibility = lle.miscibility(T=310, **options)
+
+    # =============================================================================
+    # Plot results
+    # =============================================================================
+    plt.figure()
+    plt.plot(*ideal[[args.fraction, 'T']].values.T, 'r.-', label='SLE (ideal)')
+    plt.plot(*real[[args.fraction, 'T']].values.T, 'k.-', label='SLE (real)')
+    plt.plot(miscibility[args.fraction+'L1'], miscibility['T'], 'k.--', mfc='w', label='LLE')
+    plt.plot(miscibility[args.fraction+'L2'], miscibility['T'], 'k.--', mfc='w')
+
+    plt.xlim(0, 1)
+    plt.ylim(300, 500)
+    plt.title(f"{api} + {polymer}")
+    plt.ylabel("T / K")
+    xlabel = {'w': 'Weight', 'x': 'Mole'}
+    plt.xlabel(f"{xlabel[args.fraction]} fraction {api}")
+    plt.legend()
+
+    # Save the figure to a file
+    plt.savefig(args.output)
+    plt.show()
+
+if __name__ == "__main__":
+    main()

cosmopharm-0.0.29/data/sle/README.md

@@ -0,0 +1,18 @@
+# COSMOPharm Data Sources
+
+This document details the sources for the free-volume-related parameters (`v298`, `v_hc`) of APIs that are not covered in [our *Mol. Pharm.* paper](https://doi.org/10.1021/acs.molpharmaceut.4c00342). These specific parameters are included in the `table_params.xlsx` file. For the sources of other parameters, please refer to the above *Mol. Pharm.* paper or the publication by [Klajmon (2022)](https://doi.org/10.1021/acs.molpharmaceut.2c00573).
+
+## Sources for `v298`
+
+- **CBZ (Carbamazepine)**
+  - Liquid densities from [molecular dynamics simulations](https://doi.org/10.1021/acs.molpharmaceut.2c00573) extrapolated to 298 K.
+
+- **RBV (Ribavirin) and VST (Valsartan)**
+  - As in case of GSF and SIM, estimated using a quantitative structure–property relationship (QSPR) approach implemented in the [Amsterdam Modeling Suite](https://www.scm.com/), version 2022.101. Should be taken with caution.
+ 
+## Sources for `v_hc`
+
+- **All APIs**
+  - `v_hc` based on Bondi atomic radii and calculated using the fast method proposed by [Zhao *et al.*](https://doi.org/10.1021/jo034808o)
+
+Please make sure to refer to the `table_params.xlsx` for the detailed parameters and their respective values.

cosmopharm-0.0.29/data/sle/experimental/GSF_PVPK12.dat

@@ -0,0 +1,5 @@
+463.15	0.378	1
+453.15	0.277	1
+443.15	0.219	1
+
+# GSF / PVPK12

cosmopharm-0.0.29/data/sle/experimental/GSF_PVPK25.dat

@@ -0,0 +1,4 @@
+478.15	0.463	1
+468.15	0.331	1
+
+# GSF / PVPK25

cosmopharm-0.0.29/data/sle/experimental/GSF_PVPK30.dat

@@ -0,0 +1,4 @@
+473.15	0.342	1
+463.15	0.224	1
+
+# GSF / PVPK30

cosmopharm-0.0.29/data/sle/experimental/GSF_PVPVAc64.dat

@@ -0,0 +1,5 @@
+473.15	0.316	1
+463.15	0.234	1
+453.15	0.149	1
+
+# GSF / PVPVAc64

cosmopharm-0.0.29/data/sle/experimental/IBP_EUD.dat

@@ -0,0 +1,9 @@
+348.25	0.9	1
+347.95	0.7	1
+347.65	0.5	1
+346.95	0.33	1
+346.55	0.25	1
+346.25	0.2	1
+345.55	0.1	1
+
+# IBP / EUD

cosmopharm-0.0.29/data/sle/experimental/IBP_PLGA50.dat

@@ -0,0 +1,4 @@
+348.55	0.5	1
+348.25	0.3	1
+
+# IBP / PLGA50

cosmopharm-0.0.29/data/sle/experimental/IBP_PLGA75.dat

@@ -0,0 +1,5 @@
+348.05	0.7	1
+347.95	0.5	1
+347.85	0.3	1
+
+# IBP / PLGA75

cosmopharm-0.0.29/data/sle/experimental/IBP_PVA.dat

@@ -0,0 +1,8 @@
+348.25	0.975	1
+348.05	0.95	1
+348.05	0.925	1
+347.65	0.9	1
+347.95	0.875	1
+347.45	0.85	1
+
+# IBP / PVA

cosmopharm-0.0.29/data/sle/experimental/IBP_PVPK12.dat

@@ -0,0 +1,9 @@
+347.15	0.9	1
+342.95	0.8	1
+340.65	0.702	1
+338.15	0.672	1
+333.15	0.647	1
+328.15	0.632	1
+323.15	0.611	1
+
+# IBP / PVPK12

cosmopharm-0.0.29/data/sle/experimental/IMC_EUD.dat

@@ -0,0 +1,3 @@
+433.35	0.8097	1
+
+# IMC / EUD

cosmopharm-0.0.29/data/sle/experimental/IMC_PLGA50.dat

@@ -0,0 +1,7 @@
+433.15	0.9	1
+432.45	0.8	1
+431.75	0.7	1
+431.05	0.6	1
+427.15	0.5	1
+
+# IMC / PLGA50

cosmopharm-0.0.29/data/sle/experimental/IMC_PLGA75.dat

@@ -0,0 +1,7 @@
+433.25	0.9	1
+432.25	0.8	1
+431.75	0.7	1
+429.75	0.6	1
+426.25	0.5	1
+
+# IMC / PLGA75

cosmopharm-0.0.29/data/sle/experimental/IMC_PVA.dat

@@ -0,0 +1,11 @@
+433.15	0.903	1
+432.65	0.806	1
+432.45	0.707	1
+431.65	0.609	1
+430.25	0.509	1
+429.35	0.409	1
+423.15	0.31	1
+413.15	0.204	1
+403.15	0.148	1
+
+# IMC / PVA

cosmopharm-0.0.29/data/sle/experimental/IMC_PVPK12.dat

@@ -0,0 +1,11 @@
+432.55	0.953	1
+431.15	0.9058	1
+427.15	0.8582	1
+421.55	0.8103	1
+413.15	0.7164	1
+408.15	0.6846	1
+403.15	0.6584	1
+398.15	0.6422	1
+393.15	0.6312	1
+
+# IMC / PVPK12

cosmopharm-0.0.29/data/sle/experimental/IMC_PVPVAc64.dat

@@ -0,0 +1,14 @@
+432.25	0.9	1
+425.85	0.8	1
+418.05	0.7	1
+423.15	0.737	1
+418.15	0.681	1
+413.15	0.639	1
+408.15	0.611	1
+403.15	0.579	1
+398.15	0.551	1
+393.15	0.54	1
+388.15	0.506	1
+383.15	0.472	1
+
+# IMC / PVPVAc64

cosmopharm-0.0.29/data/sle/experimental/NIF_PVPK12.dat

@@ -0,0 +1,8 @@
+433.15	0.659	1
+428.15	0.589	1
+423.15	0.542	1
+418.15	0.502	1
+413.15	0.468	1
+408.15	0.441	1
+
+# NIF / PVPK12

cosmopharm-0.0.29/data/sle/experimental/NIF_PVPK25.dat

@@ -0,0 +1,7 @@
+433.15	0.662	1
+428.15	0.591	1
+423.15	0.528	1
+418.15	0.479	1
+413.15	0.451	1
+
+# NIF / PVPK25

cosmopharm-0.0.29/data/sle/experimental/NIF_PVPK30.dat

@@ -0,0 +1,5 @@
+433.15	0.638	1
+428.15	0.584	1
+423.15	0.547	1
+
+# NIF / PVPK30

cosmopharm-0.0.29/data/sle/experimental/NIF_PVPVAc64.dat

@@ -0,0 +1,7 @@
+433.15	0.612	1
+428.15	0.561	1
+423.15	0.515	1
+418.15	0.484	1
+413.15	0.454	1
+
+# NIF / PVPVAc64

cosmopharm-0.0.29/data/sle/experimental/NPX_EUD.dat

@@ -0,0 +1,3 @@
+426.25	0.5154	1
+
+# NPX / EUD

cosmopharm-0.0.29/data/sle/experimental/NPX_PLGA50.dat

@@ -0,0 +1,7 @@
+429.05	0.9	1
+428.35	0.8	1
+427.15	0.7	1
+424.75	0.5	1
+411.95	0.3	1
+
+# NPX / PLGA50

cosmopharm-0.0.29/data/sle/experimental/NPX_PLGA75.dat

@@ -0,0 +1,7 @@
+428.65	0.9	1
+428.25	0.8	1
+427.95	0.7	1
+423.25	0.5	1
+414.85	0.3	1
+
+# NPX / PLGA75

cosmopharm-0.0.29/data/sle/experimental/NPX_PVA.dat

@@ -0,0 +1,10 @@
+428.45	0.806	1
+425.25	0.509	1
+422.15	0.409	1
+416.95	0.308	1
+413.15	0.228	1
+408.15	0.206	1
+403.15	0.164	1
+393.15	0.129	1
+
+# NPX / PVA

cosmopharm-0.0.29/data/sle/experimental/NPX_PVPK12.dat

@@ -0,0 +1,8 @@
+413.15	0.675	1
+403.15	0.626	1
+393.15	0.585	1
+388.15	0.566	1
+383.15	0.546	1
+378.15	0.532	1
+
+# NPX / PVPK12

cosmopharm-0.0.29/data/sle/experimental/NPX_PVPK25.dat

@@ -0,0 +1,8 @@
+408.15	0.698	1
+403.15	0.668	1
+398.15	0.644	1
+393.15	0.620	1
+388.15	0.602	1
+383.15	0.585	1
+
+# NPX / PVPK25

cosmopharm-0.0.29/data/sle/experimental/NPX_PVPK30.dat

@@ -0,0 +1,7 @@
+418.15	0.770	1
+413.15	0.726	1
+408.15	0.694	1
+403.15	0.664	1
+393.15	0.616	1
+
+# NPX / PVPK30