cosmopharm 0.0.23__py3-none-any.whl → 0.0.23.2__py3-none-any.whl

cosmopharm/actmodels/cosmo.py

@@ -6,7 +6,12 @@ from typing import List, Union, Literal
 from .actmodel import ActModel
 from ..components import Component
 
+
 class COSMOSAC(ActModel):
+    # Handling invalid values for free volume calculation
+    class InvalidFreeVolumeParametersException(Exception):
+        pass
+
     def __init__(self,
                  COSMO: Union[cCOSMO.COSMO1, cCOSMO.COSMO3],
                  mixture: List[Component],
@@ -62,6 +67,8 @@ class COSMOSAC(ActModel):
         (can replace ln_gamma_comb of normal COSMO-SAC) - Kuo2013
         x, v_298, v_hc are 1D arrays (number of elements = number of components)
         """
+        # TODO: Make sure, that v_298 and v_hc are provided, else "FV" not possible
+        self.validate_free_volume_parameters()  # Ensure components are valid before proceeding
         v_298 = np.array([comp.v_298 for comp in self.mixture])
         v_hc = np.array([comp.v_hc for comp in self.mixture])
         vf = v_298-v_hc
@@ -121,3 +128,27 @@ class COSMOSAC(ActModel):
         """ Convenience function to quickly configure COSMO parameters """
         self._combinatorial = comb
         self._dispersion = dsp
+
+
+    def validate_free_volume_parameters(self):
+        # List of parameters to validate
+        parameters_to_check = ["v_298", "v_hc"]
+
+        for comp in self.mixture:
+            invalid_params = []  # List to accumulate names of invalid parameters for this component
+            for param in parameters_to_check:
+                value = getattr(comp, param, None)
+                # Check if value is None, not a number (np.nan), less than or equal to 0
+                if value is None or np.isnan(value) or value <= 0:
+                    invalid_params.append((param, value))  # Append parameter name and value tuple
+
+            # Check if any errors were found for this component
+            if invalid_params:
+                # If errors were found, construct the warning message
+                error_message = f"Invalid FV parameters for component {comp}: {invalid_params}"
+                raise self.InvalidFreeVolumeParametersException(error_message)
+
+            # Additionally check if v_298 and v_hc are equal
+            if comp.v_298 == comp.v_hc:
+                msg = f"v_298 and v_hc are equal for component {comp}: v_298={comp.v_298}, v_hc={comp.v_hc}"
+                raise self.InvalidFreeVolumeParametersException(msg)

cosmopharm/components.py

@@ -2,12 +2,13 @@ from typing import Optional
 from numbers import Number
 
 class Component:
-    def __init__(self, name: Optional[str] = None,
-                 Mw: Optional[Number] = None,
-                 T_fus: Optional[Number] = None,
-                 H_fus: Optional[Number] = None,
-                 Cp_fus_a_fit: Optional[Number] = None,
-                 Cp_fus_bT_fit: Optional[Number] = None,
+    def __init__(self,
+                 name: Optional[str] = None,
+                 Mw: Optional[Number] = None,  # Positive number expected
+                 T_fus: Optional[Number] = None,  # Positive number expected
+                 H_fus: Number = 0,
+                 Cp_fus_a_fit: Number = 0,
+                 Cp_fus_bT_fit: Number = 0,
                  v_298: Optional[Number] = None,
                  v_hc: Optional[Number] = None,
                  ):

cosmopharm/equilibrium/lle.py

@@ -123,4 +123,4 @@ class LLE:
         else:
             # If actmodel is neither an instance nor a subclass of ActModel
             err = "'actmodel' must be an instance or a subclass of 'ActModel'"
-            raise ValueError(err)
+            raise ValueError(err)

cosmopharm/equilibrium/sle.py

@@ -43,10 +43,14 @@ class SLE:
             args = self.set_args(args)
             init = self.set_x0(init)
             gen = self.solve_sle(args, init, solver)
-        res = [k for k in gen]
-        res = pd.DataFrame(res, columns=['T', 'x', 'vary', 'w'])
-        res = res[['T', 'w', 'x', 'vary']]
-        return res
+        try:
+            res = [k for k in gen]
+            res = pd.DataFrame(res, columns=['T', 'x', 'vary', 'w'])
+            res = res[['T', 'w', 'x', 'vary']]
+            return res
+        except self.actmodel.InvalidFreeVolumeParametersException as e:
+            print(f"Warning: {e}")  # Inform the user
+            return pd.DataFrame(columns=['T', 'w', 'x', 'vary'])
 
 
 # =============================================================================

cosmopharm/utils/helpers.py

@@ -21,8 +21,8 @@ def add_parameters(c, params):
     c.Mw = params['Mw']  # g/mol
     c.T_fus = params['T_fus'] if params['T_fus'] > 0 else np.nan  # K
     c.H_fus = params['H_fus'] * KILOJOULE_TO_JOULE  # J/mol
-    c.Cp_fus_A = params['Cp_fus_a_fit']  # J/(mol K)
-    c.Cp_fus_BT = params['Cp_fus_bT_fit']  # J/(mol K²)
+    c.Cp_fus_A = np.nan_to_num(params['Cp_fus_a_fit'])  # J/(mol K)
+    c.Cp_fus_BT = np.nan_to_num(params['Cp_fus_bT_fit'])  # J/(mol K²)
     c.v_298 = params['v298']  # cm³/mol
     c.v_hc = params['v_hc']  # cm³/mol
 

cosmopharm-0.0.23.2.dist-info/METADATA

@@ -0,0 +1,150 @@
+Metadata-Version: 2.1
+Name: cosmopharm
+Version: 0.0.23.2
+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://dx.doi.org/10.1021/acs.jctc.9b01016). 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.

cosmopharm-0.0.23.2.dist-info/RECORD

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cosmopharm-0.0.23.dist-info/METADATA

@@ -1,38 +0,0 @@
-Metadata-Version: 2.1
-Name: cosmopharm
-Version: 0.0.23
-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-0.0.23.dist-info/RECORD

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