cosmopharm 0.0.23__py3-none-any.whl → 0.0.23.1__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-0.0.23.1.dist-info/METADATA

@@ -0,0 +1,117 @@
+Metadata-Version: 2.1
+Name: cosmopharm
+Version: 0.0.23.1
+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 *J. Chem. Theory Comput.*](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 for predictive modeling of drug-polymer compatibility and drug-solubility in common solvents. It leverages the COSMO-SAC (Conductor-like Screening Model Segment Activity Coefficient) model, offering a robust platform for solubility, miscibility, and phase behavior prediction in drug formulation processes.
+
+## Features
+
+- **Compatibility Prediction**: Predict drug-polymer compatibility using the open-source COSMO-SAC model.
+- **Solubility Calculation**: Guide polymer selection for drug formulations by calculating drug-polymer solubilities.
+- **Miscibility and Phase Behavior Analysis**: Understand drug-polymer miscibility and phase behavior under various conditions.
+- **User-friendly Interface**: Facilitate research with easy-to-use functions and comprehensive documentation.
+
+## 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
+
+This minimal example demonstrates how to use COSMOPharm to calculate solubility and miscibility of a drug with a polymer:
+
+```python
+import cCOSMO
+from cosmopharm import SLE, COSMOSAC
+from cosmopharm.utils import create_components, read_params
+
+# Define components - replace 'DrugName' and 'PolymerName' with your actual component names
+names = ['DrugName', 'PolymerName']
+params_file = "path/to/your/params.xlsx"
+
+# Load parameters and create components
+parameters = read_params(params_file)
+components = create_components(names, parameters)
+
+# Initialize COSMO-SAC model - replace paths with your local paths to COSMO profiles
+db = cCOSMO.DelawareProfileDatabase(
+    "path/to/your/complist/complist.txt",
+    "path/to/your/profiles/")
+
+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
+model = COSMOSAC(COSMO, components=components)
+
+# Calculate solubility (SLE)
+sle = SLE(solute=components[0], solvent=components[1], actmodel=model)
+solubility = sle.solubility(mix='real')
+
+# Output the solubility
+print(solubility[['T', 'w', 'x']].to_string(index=False))
+```
+
+Replace 'DrugName', 'PolymerName', and file paths with your actual data and files. This example provides a straightforward demonstration of calculating the real solubility of a drug in a polymer using COSMOPharm.
+
+## Contributing
+
+Contributions are welcome! Please refer to our [GitHub repository](https://github.com/ivanantolo/cosmopharm) for more information.
+
+## Citation
+
+If you use COSMOPharm in your research, kindly cite our work. Citation details are available in [CITATION.md](https://github.com/ivanantolo/cosmopharm/CITATION.md).
+
+## License
+
+COSMOPharm is released under the MIT License. For more details, see the [LICENSE](https://github.com/ivanantolo/cosmopharm/LICENSE) file.

cosmopharm-0.0.23.1.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
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-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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