sp-fitting-models 1.3.3__tar.gz

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sp_fitting_models-1.3.3/Cargo.toml

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+[package]
+name = "sp_fitting_models"
+version = "1.3.3"
+edition = "2021"
+readme = "README.md"
+
+[lib]
+name = "_core"
+# "cdylib" is necessary to produce a shared library for Python to import from.
+crate-type = ["cdylib"]
+
+[dependencies]
+# "extension-module" tells pyo3 we want to build an extension module (skips linking against libpython.so)
+# "abi3-py39" tells pyo3 (and maturin) to build using the stable ABI with minimum Python version 3.9
+pyo3 = { version = "0.22.4", features = ["extension-module", "abi3-py39"] }

sp_fitting_models-1.3.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: sp-fitting-models
+Version: 1.3.3
+Requires-Dist: lmfit>=1.3.4
+Requires-Dist: matplotlib>=3.10.8
+Requires-Dist: numba>=0.64.0
+Requires-Dist: numpy>=2.4.2
+Requires-Dist: pyright>=1.1.408
+Requires-Dist: pytest>=9.0.2
+Summary: For fitting spectroscopic data to cooperative and isodesmic models of supramolecular polymerization.
+Author-email: Yuhei Yamada <tamanisikaminai@gmail.com>
+Requires-Python: >=3.13
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# sp-fitting-models
+
+[English README](README.en.md)
+
+超分子ポリマーのフィッティングモデルライブラリ
+
+A Python library for fitting supramolecular polymerization data with various thermodynamic models.
+
+## 概要 / Overview
+
+このライブラリは、超分子ポリマー形成データを解析するための数理モデルを提供します。特に温度依存的な会合挙動を定量的に解析し、熱力学パラメータ（エンタルピー、エントロピー）を推定することができます。
+
+This library provides mathematical models for analyzing supramolecular polymerization data. It enables quantitative analysis of temperature-dependent aggregation behavior and estimation of thermodynamic parameters (enthalpy, entropy).
+
+## 特徴 / Features
+
+- **複数のモデルに対応**
+  - **Isodesmicモデル**: すべての会合定数が等しい単純な会合モデル
+  - **Cooperativeモデル**: 核形成と伸長で異なる定数を持つ協同的会合モデル
+  - **Mixedモデル**: IsodesmicとCooperativeの2経路が競合するモデル
+
+- **温度依存性の解析**
+  - van't Hoff式に基づく温度依存的な会合定数の計算
+  - ΔH（エンタルピー変化）とΔS（エントロピー変化）の推定
+
+- **フィッティング機能**
+  - lmfitライブラリを使用した実験データへのフィッティング
+  - 複数濃度データの同時フィッティング(グローバルフィット)に対応
+
+
+## インストール / Installation
+
+```bash
+uv add https://github.com/IndigoCarmine/sp_fitting_models.git
+```
+
+## 使用方法 / Usage
+
+### 基本的な使用例
+
+```python
+import numpy as np
+import matplotlib.pyplot as plt
+from sp_fitting_models.models import temp_cooperative_model
+
+# Temperature range
+temps = np.linspace(280, 400, 200)  # 280-400 K
+
+# Thermodynamic parameters
+deltaH = -96000      # Enthalpy change (J/mol)
+deltaS = -180        # Entropy change (J/(mol·K))
+deltaHnuc = 100000   # Nucleation penalty (J/mol)
+c_tot = 5e-6         # Total concentration (M)
+
+# Calculate aggregation
+agg = temp_cooperative_model(
+    Temp=temps,
+    deltaH=deltaH,
+    deltaS=deltaS,
+    deltaHnuc=deltaHnuc,
+    c_tot=c_tot,
+    scaler=1.0
+)
+
+# Plot
+plt.plot(temps - 273.15, agg)
+plt.xlabel('Temperature (°C)')
+plt.ylabel('Aggregation')
+plt.show()
+```
+
+### データフィッティング
+
+```python
+import lmfit as lm
+from sp_fitting_models.data import TempVsAggData
+from sp_fitting_models.fitting import objective_temp_cooperative
+
+# Prepare your experimental data
+data_list = [
+    TempVsAggData(temp=temps1, agg=agg1, concentration=c1),
+    TempVsAggData(temp=temps2, agg=agg2, concentration=c2),
+]
+
+# Set up parameters
+params = lm.Parameters()
+params.add('deltaH', value=-100000, min=-200000, max=0)
+params.add('deltaS', value=-180, min=-400, max=0)
+params.add('deltaHnuc', value=50000, min=0, max=200000)
+params.add('scaler', value=1.0, min=0.5, max=1.5)
+
+# Fit
+minner = lm.Minimizer(objective_temp_cooperative, params, fcn_args=(data_list,))
+result = minner.minimize()
+
+print(lm.fit_report(result))
+```
+
+### インタラクティブな可視化
+
+```bash
+# Run the interactive mixed model example
+python examples/interactive_mixed.py
+```
+
+スライダーを使用してパラメータを変更し、リアルタイムで会合曲線の変化を観察できます。
+
+### Windowsアプリとしてビルド (uv + PyInstaller)
+
+`examples/interactive_mixed.py` をコンソールなしの Windows GUI アプリとしてビルドできます。
+
+```powershell
+./scripts/build_interactive_mixed.ps1
+```
+
+または `cmd.exe` から:
+
+```bat
+build_interactive_mixed.bat
+```
+
+生成物:
+
+- `dist/interactive_mixed/interactive_mixed.exe`
+
+このスクリプトは次を自動で行います。
+
+1. `uv sync` で依存関係とローカルパッケージを同期
+2. `uv run --with pyinstaller ...` で GUI アプリをビルド
+
+## プロジェクト構造 / Project Structure
+
+```
+sp_fitting_models/
+├── src/
+│   └── sp_fitting_models/
+│       ├── __init__.py
+│       ├── data.py              # Data structures
+│       ├── models/              # Model implementations
+│       │   ├── __init__.py
+│       │   ├── isodesmic.py     # Isodesmic models
+│       │   ├── cooperative.py   # Cooperative models
+│       │   ├── mixed.py         # Mixed models
+│       │   └── utils.py         # Utility functions
+│       └── fitting/             # Fitting utilities
+│           ├── __init__.py
+│           └── objective.py     # Objective functions for lmfit
+├── tests/                       # Test files
+│   ├── test_isodesmic.py
+│   ├── test_cooperative.py
+│   ├── test_mixed.py
+│   └── test_fitting.py
+├── examples/                    # Example scripts
+│   ├── basic_usage.py
+│   └── interactive_mixed.py
+├── pyproject.toml
+└── README.md
+```
+
+## モデルの説明 / Model Description
+
+### Isodesmicモデル
+
+すべての会合ステップが同じ平衡定数Kを持つモデルです。シグモイド型の会合曲線を示します。
+
+$$K = \exp\left(-\frac{\Delta H}{RT} + \frac{\Delta S}{R}\right)$$
+
+次のような平衡状態です。
+供給されるモノマーは省略してあります。：
+$$M \stackrel{K}{\rightleftarrows}
+ M_2\stackrel{K}{\rightleftarrows}
+ M_3 \stackrel{K}{\rightleftarrows} ...$$
+
+### Cooperativeモデル
+
+核形成と伸長で異なる平衡定数を持つモデルです。非シグモイド型の会合曲線を示します。核形成ペナルティσにより協同性が表現されます。
+
+$$\sigma = \exp\left(-\frac{\Delta H_{nuc}}{RT}\right)$$
+
+$$ K = \exp\left(-\frac{\Delta H}{RT} + \frac{\Delta S}{R}\right)$$
+
+$$ K_{nuc} = \sigma K $$
+次のような平衡状態です。
+$$M \stackrel{K_{nuc}}{\rightleftarrows}
+ M_2\stackrel{K}{\rightleftarrows}
+ M_3 \stackrel{K}{\rightleftarrows} ...$$
+
+
+### Mixedモデル
+
+IsodesmicとCooperativeの2つの経路が同じモノマープールを共有して競合するモデルです。実験系で複数の会合機構が同時に起こる場合に適用できます。
+
+次のような平衡状態を考えています。
+$$M \stackrel{K_{nuc}}{\rightleftarrows}
+ M_2\stackrel{K}{\rightleftarrows}
+ M_3 \stackrel{K}{\rightleftarrows} ...$$
+$$ \searrow \nwarrow^{K_{iso}}
+ M_2\stackrel{K_{iso}}{\rightleftarrows}
+  M_3 \stackrel{K_{iso}}{\rightleftarrows} ...$$
+（MDではこれ以上きれいに書けませんでした...）
+## テスト / Testing
+
+```bash
+# Run all tests
+python -m pytest tests/
+
+# Run specific test
+python tests/test_cooperative.py
+```
+
+## サンプル / Examples
+
+```bash
+# Basic usage examples
+python examples/basic_usage.py
+
+# Interactive mixed model visualization
+python examples/interactive_mixed.py
+```
+
+## 依存関係 / Dependencies
+
+- Python >= 3.13
+- numpy >= 2.4.2
+- numba >= 0.64.0
+- lmfit >= 1.3.4
+- matplotlib >= 3.10.8
+
+## 引用　/Citation
+
+書いていただけるなら嬉しいですが、必ずしも論文で言及する必要はありません。
+ご自由にお使いください。
+
+I would be grateful if you could cite this library in your publications, but it is not mandatory. Please feel free to use it as you see fit.
+
+
+## 作成者 / Author
+山田悠平　(Yuhei Yamada, Orcid: [0009-0003-9780-4135](https://orcid.org/0009-0003-9780-4135), google scholar: [Yuhei Yamada](https://scholar.google.co.jp/citations?user=mRKL6CYAAAAJ))