kbkit 1.0.15__tar.gz

kbkit-1.0.15/.gitignore

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kbkit-1.0.15/LICENSE

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+MIT License
+
+Copyright (c) 2025 Allison Peroutka
+
+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.

kbkit-1.0.15/PKG-INFO

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+Metadata-Version: 2.4
+Name: kbkit
+Version: 1.0.15
+Summary: KBKit: Kirkwood-Buff Analysis Toolkit
+Author: Allison Peroutka
+License: MIT License
+        
+        Copyright (c) 2025 Allison Peroutka
+        
+        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.
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: babel<3,>=2.17.0
+Requires-Dist: click<9,>=8.2.1
+Requires-Dist: furo<2026,>=2025.7.19
+Requires-Dist: gromacs<0.0.1,>=0.0.0
+Requires-Dist: ipykernel<7,>=6.30.1
+Requires-Dist: matplotlib<4,>=3.10.5
+Requires-Dist: mdanalysis
+Requires-Dist: mpltern<2,>=1.0.4
+Requires-Dist: mypy
+Requires-Dist: natsort<9,>=8.4.0
+Requires-Dist: nbsphinx<0.10,>=0.9.6
+Requires-Dist: numpy<3,>=2.3.2
+Requires-Dist: pandas<3,>=2.3.1
+Requires-Dist: pandoc<3,>=2.4
+Requires-Dist: pathlib<2,>=1.0.1
+Requires-Dist: pint<0.25
+Requires-Dist: plotly<7,>=6.3.0
+Requires-Dist: pytest-cov>=6.2.1
+Requires-Dist: pytest>=8.4.1
+Requires-Dist: rdkit<2026,>=2025.3.5
+Requires-Dist: scipy<2,>=1.16.1
+Requires-Dist: seaborn<0.14,>=0.13.2
+Requires-Dist: sphinx
+Requires-Dist: sphinx-copybutton<0.6,>=0.5.2
+Requires-Dist: sphinx-gallery<0.20,>=0.19.0
+Requires-Dist: sphinx-rtd-theme<4,>=3.0.2
+Requires-Dist: stubs>=1.0.0
+Requires-Dist: sympy<2,>=1.14.0
+Requires-Dist: tree-format<0.2,>=0.1.2
+Requires-Dist: types-requests
+Requires-Dist: uncertainties<4,>=3.2.3
+Description-Content-Type: text/markdown
+
+# KBKit: Kirkwood-Buff Analysis Toolkit
+
+[![License](https://img.shields.io/github/license/aperoutka/kbkit)](https://github.com/aperoutka/kbkit/blob/master/LICENSE)
+[![PyPI version](https://img.shields.io/pypi/v/kbkit.svg)](https://pypi.org/project/kbkit/)
+[![Powered by: Pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Coverage Status](https://coveralls.io/repos/github/aperoutka/kbkit/badge.svg?branch=main)](https://coveralls.io/github/aperoutka/kbkit?branch=main)
+[![docs](http://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://kbkit.readthedocs.io/)
+![python 3.12](https://img.shields.io/badge/Python-3.12%2B-blue)
+
+**KBKit** is a Python package for automated Kirkwood-Buff (KB) analysis of molecular simulation data. It provides tools to parse simulation outputs, compute Kirkwood-Buff integrals, and extract thermodynamic properties for binary and multicomponent systems. **KBKit** supports flexible workflows, including:
+
+* Parsing and processing of simulation data (e.g., RDFs, densities)
+* Calculation of KB integrals and related thermodynamic quantities
+* Integration of activity coefficient derivatives (numerical or polynomial)
+* Automated pipelines for batch analysis
+* Calculation of static structure factor and X-ray intensities in the limit of q &rarr; 0
+* Visualization tools for KB integrals, thermodynamic properties, and static structure factors
+
+**KBKit** is designed for researchers in computational chemistry, soft matter, and statistical mechanics who need robust, reproducible KB analysis from simulation data. The package is modular, extensible, and integrates easily with Jupyter notebooks and Python scripts.
+
+## Installation
+
+### Quick install via PyPI
+
+```python
+pip install kbkit
+```
+
+### Developer install (recommended for contributors or conda users)
+
+Clone the GitHub repository and use the provided Makefile to set up your development environment:
+
+```python
+git clone https://github.com/aperoutka/kbkit.git
+cd kbkit
+make setup-dev
+```
+
+This one-liner creates the `kbkit-dev` conda environment, installs `kbkit` in editable mode, and runs the test suite.
+
+To install without running tests:
+
+```python
+make dev-install
+```
+
+To build and install the package into a clean user environment:
+
+```python
+make setup-user
+```
+
+For a full list of available commands:
+
+```python
+make help
+```
+
+## File Organization
+
+For running `kbkit.Pipeline` or its dependencies, the following file structure is required: a structured directory layout that separates mixed systems from pure components. 
+This organization enables automated parsing, reproducible KB integrals, and scalable analysis across chemical systems.
+
+* NOTE: **KBKit** currently only supports parsing for *GROMACS* files.
+
+An example of file structure:
+```python
+kbi_dir/
+├── project/
+│   └── system/
+│       ├── rdf_dir/
+│       │   ├── mol1_mol1.xvg
+│       │   ├── mol1_mol2.xvg
+│       │   └── mol1_mol2.xvg
+│       ├── system_npt.edr
+│       ├── system_npt.gro
+│       └── system.top
+└── pure_components/
+    └── molecule1/
+        ├── molecule1_npt.edr
+        └── molecule1.top
+```
+
+**Requirements:**
+
+* Each system to be analyzed must include:
+    * rdf_dir/ containing .xvg RDF files for all pairwise interactions
+        * Both molecule IDs in RDF calculation *MUST BE* in filename
+    * either .top topology file or .gro structure file (.gro is recommended)
+    * .edr energy file
+* Each pure component must include:
+    * either .top topology file or .gro structure file (.gro is recommended)
+    * .edr energy file
+    * all other files (optional)
+
+## Examples
+
+Below are several examples on various ways to implement **KBKit**.
+See examples for a more complete example on the ethanol/water binary system.
+
+### Calculating Kirkwood-Buff integrals on a single RDF
+
+```python
+import os
+from kbkit.analysis import KBIntegrator
+from kbkit.systems import SystemProperties
+
+syspath = "./examples/test_data/ethanol_water_26C/sys_405"
+rdf_path = os.path.join(sys_path, "kbi_rdf_files_gmx25", "rdf_ETHOL_SPCEW.xvg")
+
+# create integrator object from single RDF file
+integrator = KBIntegrator(
+    rdf_file=rdf_path,
+    system_properties=SystemProperties(sys_path),
+    use_fixed_rmin=False,
+)
+
+# calculate KBI in thermodynamic limit
+kbi = integrator.kbi_limit(mol_j="SPCEW")
+```
+
+### Run an automated pipeline for batch analysis
+
+```python
+from kbkit import Pipeline
+
+# Set up and run the pipeline
+pipe = Pipeline(
+    base_path="./examples/test_data/ethanol_water_26C", # directory with system data
+    pure_path="./examples/test_data/pure_components",   # directory with pure component data
+    pure_systems=["ETHOL_300", "SPCEW_300"],            # list of pure systems
+    ensemble="npt",                                     # ensemble type: npt or nvt
+    gamma_integration_type="numerical",                 # integration method
+    verbose=False                                       # logging verbosity
+)
+
+# run kbkit pipeline
+pipe.run()
+
+# Access the results properties
+# stored in dataclass (ThermoProperty); attributes: name, value, units
+# example for excess energy
+ge_obj = pipe.get("ge")
+print("GE summary: ", ge_array.shape)
+
+# Convert units from kJ/mol -> kcal/mol
+# default units will be those from GROMACS
+pipe.convert_units("ge", "kcal/mol")
+
+# make figures for select thermodynamic properties
+pipe.plot(
+    molecule_map={"ETHOL": "ethanol", "SPCEW": "water"}, # dictionary mapping MD names to label names
+    x_mol="ETHOL"                                        # MD name of molecule for x-axis
+)
+```
+
+### Parse GROMACS files
+
+```python
+import os
+from kbkit.parsers import TopFileParser, EdrFileParser, GroFileParser
+
+syspath = "./examples/test_data/ethanol_water_26C/sys_405"
+top_file = os.path.join(syspath, "sys_405.top")
+gro_file = os.path.join(syspath, "sys_405.gro")
+edr_file = os.path.join(syspath, "sys_405_npt.edr")
+
+# determines molecules present in simulation and their counts
+top_parser = TopFileParser(top_file)
+print("molecule dict: ", top_parser.molecule_counts)
+print("molecule names: ", top_parser.molecules)
+print("total molecule number: ", top_parser.total_molecules)
+
+# determines electron count for each molecule type
+gro_parser = GroFileParser(gro_file)
+print("electron dict: ", gro_parser.electron_count)
+print("box volume: ", gro_parser.compute_box_volume())
+
+# computes energy properties by calling gmx energy
+edr_parser = EdrFileParser(edr_file)
+print("List of available properties: ", edr_parser.available_properties())
+print("Density array over simulation time: ", edr_parser.extract_timeseries("density"))
+print("Average density with std deviation: ", edr_parser.average_property("density", return_std=True))
+```
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [jevandezande/pixi-cookiecutter](https://github.com/jevandezande/pixi-cookiecutter) project template.

kbkit-1.0.15/README.md

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+# KBKit: Kirkwood-Buff Analysis Toolkit
+
+[![License](https://img.shields.io/github/license/aperoutka/kbkit)](https://github.com/aperoutka/kbkit/blob/master/LICENSE)
+[![PyPI version](https://img.shields.io/pypi/v/kbkit.svg)](https://pypi.org/project/kbkit/)
+[![Powered by: Pixi](https://img.shields.io/badge/Powered_by-Pixi-facc15)](https://pixi.sh)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Coverage Status](https://coveralls.io/repos/github/aperoutka/kbkit/badge.svg?branch=main)](https://coveralls.io/github/aperoutka/kbkit?branch=main)
+[![docs](http://img.shields.io/badge/docs-latest-brightgreen.svg?style=flat)](https://kbkit.readthedocs.io/)
+![python 3.12](https://img.shields.io/badge/Python-3.12%2B-blue)
+
+**KBKit** is a Python package for automated Kirkwood-Buff (KB) analysis of molecular simulation data. It provides tools to parse simulation outputs, compute Kirkwood-Buff integrals, and extract thermodynamic properties for binary and multicomponent systems. **KBKit** supports flexible workflows, including:
+
+* Parsing and processing of simulation data (e.g., RDFs, densities)
+* Calculation of KB integrals and related thermodynamic quantities
+* Integration of activity coefficient derivatives (numerical or polynomial)
+* Automated pipelines for batch analysis
+* Calculation of static structure factor and X-ray intensities in the limit of q → 0
+* Visualization tools for KB integrals, thermodynamic properties, and static structure factors
+
+**KBKit** is designed for researchers in computational chemistry, soft matter, and statistical mechanics who need robust, reproducible KB analysis from simulation data. The package is modular, extensible, and integrates easily with Jupyter notebooks and Python scripts.
+
+## Installation
+
+### Quick install via PyPI
+
+```python
+pip install kbkit
+```
+
+### Developer install (recommended for contributors or conda users)
+
+Clone the GitHub repository and use the provided Makefile to set up your development environment:
+
+```python
+git clone https://github.com/aperoutka/kbkit.git
+cd kbkit
+make setup-dev
+```
+
+This one-liner creates the `kbkit-dev` conda environment, installs `kbkit` in editable mode, and runs the test suite.
+
+To install without running tests:
+
+```python
+make dev-install
+```
+
+To build and install the package into a clean user environment:
+
+```python
+make setup-user
+```
+
+For a full list of available commands:
+
+```python
+make help
+```
+
+## File Organization
+
+For running `kbkit.Pipeline` or its dependencies, the following file structure is required: a structured directory layout that separates mixed systems from pure components. 
+This organization enables automated parsing, reproducible KB integrals, and scalable analysis across chemical systems.
+
+* NOTE: **KBKit** currently only supports parsing for *GROMACS* files.
+
+An example of file structure:
+```python
+kbi_dir/
+├── project/
+│   └── system/
+│       ├── rdf_dir/
+│       │   ├── mol1_mol1.xvg
+│       │   ├── mol1_mol2.xvg
+│       │   └── mol1_mol2.xvg
+│       ├── system_npt.edr
+│       ├── system_npt.gro
+│       └── system.top
+└── pure_components/
+    └── molecule1/
+        ├── molecule1_npt.edr
+        └── molecule1.top
+```
+
+**Requirements:**
+
+* Each system to be analyzed must include:
+    * rdf_dir/ containing .xvg RDF files for all pairwise interactions
+        * Both molecule IDs in RDF calculation *MUST BE* in filename
+    * either .top topology file or .gro structure file (.gro is recommended)
+    * .edr energy file
+* Each pure component must include:
+    * either .top topology file or .gro structure file (.gro is recommended)
+    * .edr energy file
+    * all other files (optional)
+
+## Examples
+
+Below are several examples on various ways to implement **KBKit**.
+See examples for a more complete example on the ethanol/water binary system.
+
+### Calculating Kirkwood-Buff integrals on a single RDF
+
+```python
+import os
+from kbkit.analysis import KBIntegrator
+from kbkit.systems import SystemProperties
+
+syspath = "./examples/test_data/ethanol_water_26C/sys_405"
+rdf_path = os.path.join(sys_path, "kbi_rdf_files_gmx25", "rdf_ETHOL_SPCEW.xvg")
+
+# create integrator object from single RDF file
+integrator = KBIntegrator(
+    rdf_file=rdf_path,
+    system_properties=SystemProperties(sys_path),
+    use_fixed_rmin=False,
+)
+
+# calculate KBI in thermodynamic limit
+kbi = integrator.kbi_limit(mol_j="SPCEW")
+```
+
+### Run an automated pipeline for batch analysis
+
+```python
+from kbkit import Pipeline
+
+# Set up and run the pipeline
+pipe = Pipeline(
+    base_path="./examples/test_data/ethanol_water_26C", # directory with system data
+    pure_path="./examples/test_data/pure_components",   # directory with pure component data
+    pure_systems=["ETHOL_300", "SPCEW_300"],            # list of pure systems
+    ensemble="npt",                                     # ensemble type: npt or nvt
+    gamma_integration_type="numerical",                 # integration method
+    verbose=False                                       # logging verbosity
+)
+
+# run kbkit pipeline
+pipe.run()
+
+# Access the results properties
+# stored in dataclass (ThermoProperty); attributes: name, value, units
+# example for excess energy
+ge_obj = pipe.get("ge")
+print("GE summary: ", ge_array.shape)
+
+# Convert units from kJ/mol -> kcal/mol
+# default units will be those from GROMACS
+pipe.convert_units("ge", "kcal/mol")
+
+# make figures for select thermodynamic properties
+pipe.plot(
+    molecule_map={"ETHOL": "ethanol", "SPCEW": "water"}, # dictionary mapping MD names to label names
+    x_mol="ETHOL"                                        # MD name of molecule for x-axis
+)
+```
+
+### Parse GROMACS files
+
+```python
+import os
+from kbkit.parsers import TopFileParser, EdrFileParser, GroFileParser
+
+syspath = "./examples/test_data/ethanol_water_26C/sys_405"
+top_file = os.path.join(syspath, "sys_405.top")
+gro_file = os.path.join(syspath, "sys_405.gro")
+edr_file = os.path.join(syspath, "sys_405_npt.edr")
+
+# determines molecules present in simulation and their counts
+top_parser = TopFileParser(top_file)
+print("molecule dict: ", top_parser.molecule_counts)
+print("molecule names: ", top_parser.molecules)
+print("total molecule number: ", top_parser.total_molecules)
+
+# determines electron count for each molecule type
+gro_parser = GroFileParser(gro_file)
+print("electron dict: ", gro_parser.electron_count)
+print("box volume: ", gro_parser.compute_box_volume())
+
+# computes energy properties by calling gmx energy
+edr_parser = EdrFileParser(edr_file)
+print("List of available properties: ", edr_parser.available_properties())
+print("Density array over simulation time: ", edr_parser.extract_timeseries("density"))
+print("Average density with std deviation: ", edr_parser.average_property("density", return_std=True))
+```
+
+## Credits
+
+This package was created with [Cookiecutter](https://github.com/audreyr/cookiecutter) and the [jevandezande/pixi-cookiecutter](https://github.com/jevandezande/pixi-cookiecutter) project template.