cosmopharm 0.0.31__tar.gz → 0.1.0__tar.gz

{cosmopharm-0.0.31 → cosmopharm-0.1.0}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2024 Ivan Antolovic <Ivan.Antolovic@tu-berlin.de>, Martin Klajmon <Martin.Klajmon@vscht.cz>
-
-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
+MIT License
+
+Copyright (c) 2024 Ivan Antolovic <Ivan.Antolovic@tu-berlin.de>, Martin Klajmon <Martin.Klajmon@vscht.cz>
+
+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.

{cosmopharm-0.0.31 → cosmopharm-0.1.0}/PKG-INFO

@@ -1,150 +1,150 @@
-Metadata-Version: 2.1
-Name: cosmopharm
-Version: 0.0.31
-Summary: Predictive modeling for drug-polymer compatibility in pharmaceutical formulations using COSMO-SAC.
-Home-page: https://github.com/ivanantolo/cosmopharm,
-Author: Ivan Antolovic
-Author-email: Ivan.Antolovic@tu-berlin.de
-Maintainer: Martin Klajmon
-Maintainer-email: Martin.Klajmon@vscht.cz
-License: MIT
-Keywords: Drug-Polymer Compatibility,Amorphous Solid Dispersions,Pharmaceutical Formulation,COSMO-SAC Model,Solubility Prediction,Miscibility Analysis,Phase Behavior Prediction,Pharmaceutical Sciences,Drug Formulation Research,Polymer Science,Predictive Modeling in Pharma,Drug Development Tools,Biopharmaceuticals
-Classifier: Development Status :: 3 - Alpha
-Classifier: Intended Audience :: Science/Research
-Classifier: Intended Audience :: Healthcare Industry
-Classifier: Intended Audience :: Developers
-Classifier: Intended Audience :: Education
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3 :: Only
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: numpy>=1.15
-Requires-Dist: pandas>=1.0
-Requires-Dist: scipy>=1.4
-Requires-Dist: openpyxl>=3.0
-Provides-Extra: examples
-Requires-Dist: matplotlib>=3.0; extra == "examples"
-
-# COSMOPharm
-
-Welcome to the COSMOPharm package, accompanying [our paper in *Molecular Pharmaceutics*](https://doi.org/10.1021/acs.molpharmaceut.4c00342). This project and its associated publication offer insights and a practical toolkit for researching drug-polymer and drug-solvent systems, aiming to provide the scientific community with the means to reproduce our findings and further the development of COSMO-SAC-based models.
-
-<p align="center">
-  <!-- <img src="https://github.com/usnistgov/COSMOSAC/raw/master/JCTC2020.PNG" alt="TOC Figure" width="500"> -->
-  <img src="https://raw.githubusercontent.com/ivanantolo/cosmopharm/main/TOC.png" alt="TOC Figure">
-</p>
-
-## About 
-
-COSMOPharm is a Python package designed to streamline the predictive modeling of drug-polymer compatibility, crucial for the development of pharmaceutical amorphous solid dispersions. Apart from that, it can also be used for the miscibility/solubility of drugs with/in common solvents. Leveraging the COSMO-SAC (Conductor-like Screening Model Segment Activity Coefficient) model, COSMOPharm offers a robust platform for scientists and researchers to predict solubility, miscibility, and phase behavior in drug formulation processes.
-
-## Features
-
-- **Compatibility Prediction**: Utilize open-source COSMO-SAC model for prediction of drug-polymer compatibility.
-- **Solubility Calculation**: Calculate drug-polymer solubilities to guide the selection of suitable polymers for drug formulations.
-- **Miscibility and Phase Behavior Analysis**: Analyze the miscibility of drug-polymer pairs and understand their phase behavior under various conditions.
-- **User-friendly Interface**: Easy-to-use functions and comprehensive documentation to facilitate research and development in pharmaceutical sciences.
-
-## Installation
-
-Install COSMOPharm with pip:
-
-`pip install cosmopharm`
-
-Ensure you have installed the `cCOSMO` library as per instructions on the [COSMOSAC GitHub page](https://github.com/usnistgov/COSMOSAC).
-
-## Quick Start
-
-Get started with COSMOPharm using the minimal example below, which demonstrates how to calculate the solubility of a drug in a polymer. This example succinctly showcases the use of COSMOPharm for solubility calculations:
-
-
-```python
-import matplotlib.pyplot as plt
-import cCOSMO
-from cosmopharm import SLE, COSMOSAC
-from cosmopharm.utils import create_components, read_params
-
-# Define components
-names = ['SIM','PLGA50']
-params_file = "data/sle/table_params.xlsx"
-
-# Load parameters and create components
-parameters = read_params(params_file)
-mixture = create_components(names, parameters)
-
-# Initialize COSMO-SAC model - replace paths with your local paths to COSMO profiles
-db = cCOSMO.DelawareProfileDatabase(
-    "./profiles/_import_methods/UD/complist.txt",
-    "./profiles/_import_methods/UD/sigma3/")
-
-for name in names:
-    iden = db.normalize_identifier(name)
-    db.add_profile(iden)
-COSMO = cCOSMO.COSMO3(names, db)
-
-# Setup the COSMO-SAC model with components
-actmodel = COSMOSAC(COSMO, mixture=mixture)
-
-# Calculate solubility (SLE)
-sle = SLE(actmodel=actmodel)
-solubility = sle.solubility(mix='real')
-
-# Output the solubility
-print(solubility[['T', 'w', 'x']].to_string(index=False))
-
-# Plot results
-plt.plot(*solubility[['w','T']].values.T,'.-', label='Solubility (w)')
-
-# Settings
-plt.xlim(0,1)
-plt.ylim(300,500)
-# Adding title and labels
-plt.title('Solubility vs. Temperature')
-plt.ylabel("T / K")
-xlabel = {'w':'Weight', 'x':'Mole'}
-plt.xlabel(f"Weight fraction {mixture[0].name}")
-plt.legend()
-# Save the figure to a PNG or PDF file
-plt.savefig('solubility_plot.png')  # Saves the plot as a PNG file
-# plt.savefig('solubility_plot.pdf')  # Saves the plot as a PDF file
-plt.show()
-```
-
-For a more comprehensive demonstration, including advanced functionalities and plotting results, please see the [example_usage.py](https://github.com/ivanantolo/cosmopharm/blob/main/example_usage.py) script in this repository. This detailed example walks through the process of setting up COSMOPharm, initializing models, and visualizing the results of solubility and miscibility calculations.
-
-## Contributing
-
-Contributions are welcome! Please refer to our [GitHub repository](https://github.com/ivanantolo/cosmopharm) for more information.
-
-## Citation
-
-We appreciate citations to our work as they help acknowledge and spread our research contributions. If you use COSMOPharm in your research, please cite the associated paper as follows:
-
-```bibtex
-@article{Antolovic2024COSMOPharm,
-  title={COSMOPharm: Drug--Polymer Compatibility of Pharmaceutical Amorphous Solid Dispersions from COSMO-SAC},
-  author={Antolovic, Ivan and Vrabec, Jadran and Klajmon, Martin},
-  journal={Molecular Pharmaceutics},
-  year={2024},
-  volume={1}, # Will be adjusted accordingly
-  issue={1}, # Will be adjusted accordingly
-  month={3}, # Will be adjusted accordingly
-  pages={1--10},  # Will be adjusted accordingly
-  doi={10.1021/acs.molpharmaceut.3c12345} # Will be adjusted accordingly
-}
-```
-
-## License
-
-COSMOPharm is released under the MIT License. For more details, see the [LICENSE](https://github.com/ivanantolo/cosmopharm/LICENSE) file.
+Metadata-Version: 2.1
+Name: cosmopharm
+Version: 0.1.0
+Summary: Predictive modeling for drug-polymer compatibility in pharmaceutical formulations using COSMO-SAC.
+Home-page: https://github.com/ivanantolo/cosmopharm,
+Author: Ivan Antolovic
+Author-email: Ivan.Antolovic@tu-berlin.de
+Maintainer: Martin Klajmon
+Maintainer-email: Martin.Klajmon@vscht.cz
+License: MIT
+Keywords: Drug-Polymer Compatibility,Amorphous Solid Dispersions,Pharmaceutical Formulation,COSMO-SAC Model,Solubility Prediction,Miscibility Analysis,Phase Behavior Prediction,Pharmaceutical Sciences,Drug Formulation Research,Polymer Science,Predictive Modeling in Pharma,Drug Development Tools,Biopharmaceuticals
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.15
+Requires-Dist: pandas>=1.0
+Requires-Dist: scipy>=1.4
+Requires-Dist: openpyxl>=3.0
+Provides-Extra: examples
+Requires-Dist: matplotlib>=3.0; extra == "examples"
+
+# COSMOPharm
+
+Welcome to the COSMOPharm package, accompanying [our paper in *Molecular Pharmaceutics*](https://doi.org/10.1021/acs.molpharmaceut.4c00342). This project and its associated publication offer insights and a practical toolkit for researching drug-polymer and drug-solvent systems, aiming to provide the scientific community with the means to reproduce our findings and further the development of COSMO-SAC-based models.
+
+<p align="center">
+  <!-- <img src="https://github.com/usnistgov/COSMOSAC/raw/master/JCTC2020.PNG" alt="TOC Figure" width="500"> -->
+  <img src="https://github.com/usnistgov/COSMOSAC/raw/master/JCTC2020.PNG" alt="TOC Figure">
+</p>
+
+## About 
+
+COSMOPharm is a Python package designed to streamline the predictive modeling of drug-polymer compatibility, crucial for the development of pharmaceutical amorphous solid dispersions. Apart from that, it can also be used for the miscibility/solubility of drugs with/in common solvents. Leveraging the COSMO-SAC (Conductor-like Screening Model Segment Activity Coefficient) model, COSMOPharm offers a robust platform for scientists and researchers to predict solubility, miscibility, and phase behavior in drug formulation processes.
+
+## Features
+
+- **Compatibility Prediction**: Utilize open-source COSMO-SAC model for prediction of drug-polymer compatibility.
+- **Solubility Calculation**: Calculate drug-polymer solubilities to guide the selection of suitable polymers for drug formulations.
+- **Miscibility and Phase Behavior Analysis**: Analyze the miscibility of drug-polymer pairs and understand their phase behavior under various conditions.
+- **User-friendly Interface**: Easy-to-use functions and comprehensive documentation to facilitate research and development in pharmaceutical sciences.
+
+## Installation
+
+Install COSMOPharm with pip:
+
+`pip install cosmopharm`
+
+Ensure you have installed the `cCOSMO` library as per instructions on the [COSMOSAC GitHub page](https://github.com/usnistgov/COSMOSAC).
+
+## Quick Start
+
+Get started with COSMOPharm using the minimal example below, which demonstrates how to calculate the solubility of a drug in a polymer. This example succinctly showcases the use of COSMOPharm for solubility calculations:
+
+
+```python
+import matplotlib.pyplot as plt
+import cCOSMO
+from cosmopharm import SLE, COSMOSAC
+from cosmopharm.utils import create_components, read_params
+
+# Define components
+names = ['SIM','PLGA50']
+params_file = "data/sle/table_params.xlsx"
+
+# Load parameters and create components
+parameters = read_params(params_file)
+mixture = create_components(names, parameters)
+
+# Initialize COSMO-SAC model - replace paths with your local paths to COSMO profiles
+db = cCOSMO.DelawareProfileDatabase(
+    "./profiles/_import_methods/UD/complist.txt",
+    "./profiles/_import_methods/UD/sigma3/")
+
+for name in names:
+    iden = db.normalize_identifier(name)
+    db.add_profile(iden)
+COSMO = cCOSMO.COSMO3(names, db)
+
+# Setup the COSMO-SAC model with components
+actmodel = COSMOSAC(COSMO, mixture=mixture)
+
+# Calculate solubility (SLE)
+sle = SLE(actmodel=actmodel)
+solubility = sle.solubility(mix='real')
+
+# Output the solubility
+print(solubility[['T', 'w', 'x']].to_string(index=False))
+
+# Plot results
+plt.plot(*solubility[['w','T']].values.T,'.-', label='Solubility (w)')
+
+# Settings
+plt.xlim(0,1)
+plt.ylim(300,500)
+# Adding title and labels
+plt.title('Solubility vs. Temperature')
+plt.ylabel("T / K")
+xlabel = {'w':'Weight', 'x':'Mole'}
+plt.xlabel(f"Weight fraction {mixture[0].name}")
+plt.legend()
+# Save the figure to a PNG or PDF file
+plt.savefig('solubility_plot.png')  # Saves the plot as a PNG file
+# plt.savefig('solubility_plot.pdf')  # Saves the plot as a PDF file
+plt.show()
+```
+
+For a more comprehensive demonstration, including advanced functionalities and plotting results, please see the [example_usage.py](https://github.com/ivanantolo/cosmopharm/blob/main/example_usage.py) script in this repository. This detailed example walks through the process of setting up COSMOPharm, initializing models, and visualizing the results of solubility and miscibility calculations.
+
+## Contributing
+
+Contributions are welcome! Please refer to our [GitHub repository](https://github.com/ivanantolo/cosmopharm) for more information.
+
+## Citation
+
+We appreciate citations to our work as they help acknowledge and spread our research contributions. If you use COSMOPharm in your research, please cite the associated paper as follows:
+
+```bibtex
+@article{Antolovic2024COSMOPharm,
+  title={COSMOPharm: Drug--Polymer Compatibility of Pharmaceutical Amorphous Solid Dispersions from COSMO-SAC},
+  author={Antolovic, Ivan and Vrabec, Jadran and Klajmon, Martin},
+  journal={Molecular Pharmaceutics},
+  year={2024},
+  volume={1}, # Will be adjusted accordingly
+  issue={1}, # Will be adjusted accordingly
+  month={3}, # Will be adjusted accordingly
+  pages={1--10},  # Will be adjusted accordingly
+  doi={10.1021/acs.molpharmaceut.3c12345} # Will be adjusted accordingly
+}
+```
+
+## License
+
+COSMOPharm is released under the MIT License. For more details, see the [LICENSE](https://github.com/ivanantolo/cosmopharm/LICENSE) file.