pythonQEPest 2.0.0a2__py3-none-any.whl

pythonqepest-2.0.0a2.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: pythonQEPest
+Version: 2.0.0a2
+Summary: Java QEPest but written in Python
+Author: Lina
+Author-email: knocker767@gmail.com
+Requires-Python: >=3.12,<3.15
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: gui
+Provides-Extra: rdkit
+Requires-Dist: pydantic (==2.12.5)
+Requires-Dist: pyperclip (>=1.11.0,<2.0.0) ; extra == "gui"
+Requires-Dist: python-dotenv (>=1.2.1,<2.0.0)
+Requires-Dist: rdkit (>=2024.3.1,<2026.0.0) ; extra == "rdkit"
+Description-Content-Type: text/markdown
+
+# pythonQEPest
+
+[![pythonQEPest](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml/badge.svg)](https://github.com/PonyLianna/pythonQEPest/actions/workflows/python-package.yml)
+
+
+Python implementation of QEPest (Quantitative Estimation of Pesticide), a program for scoring molecules as herbicides (QEH), insecticides (QEI), and fungicides (QEF).
+
+Originally published in: [J Cheminform - QEPest](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-014-0042-6)
+Original Program Link is [here](https://static-content.springer.com/esm/art%3A10.1186%2Fs13321-014-0042-6/MediaObjects/13321_2014_42_MOESM2_ESM.zip)  
+
+## Features
+
+- Calculate pesticide scores for herbicidal, insecticidal, and fungicidal activity
+- Command-line interface (CLI)
+- Graphical User Interface (GUI)
+- Support for JSON and TXT output formats
+
+### Pre-built binaries
+
+Download ready-to-use executables from [Releases](https://github.com/PonyLianna/pythonQEPest/releases):
+
+| Platform | Download |
+|----------|----------|
+| Windows CLI | [main.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/main.exe) |
+| Windows GUI | [gui.exe](https://github.com/PonyLianna/pythonQEPest/releases/download/v2.0.0-alpha/gui.exe) |
+
+
+## Installation
+
+```bash
+pip install pythonQEPest
+```
+
+Or from source:
+
+```bash
+git clone https://github.com/PonyLianna/pythonQEPest.git
+cd pythonQEPest
+poetry install
+```
+
+### With GUI support
+
+```bash
+pip install pythonQEPest[gui]
+# or
+poetry install --extras ui
+```
+
+
+## Quick Start
+
+### CLI
+
+```bash
+pythonqepest -i data.txt -o result.txt
+pythonqepest --input data.txt --format json
+pythonqepest -v  # show version
+```
+
+### GUI
+
+```bash
+pythonqepest-gui
+# or
+python -m pythonQEPest.gui.gui
+```
+
+### Python API
+
+```python
+from pythonQEPest import QEPest, QEPestInput
+
+# Create input data
+qepest = QEPest()
+qepest.initialize_coefficients()
+qepest.initialize_normalisers()
+
+# From individual values
+inp = QEPestInput(
+    name="mol1",
+    mol_weight=240.2127,
+    log_p=3.2392,
+    hbond_acceptors=5,
+    hbond_donors=1,
+    rotatable_bonds=4,
+    aromatic_rings=1
+)
+
+result = qepest.compute_params(inp)
+
+print(result.name)       # mol1
+print(result.data.qe_herb)   # 0.8511
+print(result.data.qe_insect) # 0.5339
+print(result.data.qe_fung)   # 0.6224
+
+# Convert to array
+print(result.to_array())  # ["mol1", 0.6224, 0.8511, 0.5339]
+```
+
+## Input Format
+
+The input file should be a tab-separated text file with the following columns:
+
+| Column | Description |
+|--------|-------------|
+| Name   | Molecule name |
+| MW     | Molecular weight (g/mol) |
+| LogP   | Hydrophobicity (octanol-water partition coefficient) |
+| HBA    | Number of hydrogen bond acceptors |
+| HBD    | Number of hydrogen bond donors |
+| RB     | Number of rotatable bonds |
+| arR    | Number of aromatic rings |
+
+Example `data.txt`:
+
+```
+Name	MW	LogP	HBA	HBD	RB	arR
+mol1	240.2127	3.2392	5	1	4	1
+mol2	249.091	3.0273	3	1	5	1
+mol3	308.354	2.1086	1	0	7	1
+```
+
+## Output Format
+
+### TXT (default output for CLI)
+
+```
+Name	QEF	QEH	QEI
+mol1	0.6224	0.8511	0.5339
+mol2	0.7310	0.9750	0.6913
+```
+
+### JSON
+
+```json
+[
+  {"name": "mol1", "qe_fung": 0.6224, "qe_herb": 0.8511, "qe_insect": 0.5339},
+  {"name": "mol2", "qe_fung": 0.731, "qe_herb": 0.975, "qe_insect": 0.6913}
+]
+```
+
+## Configuration
+
+### Custom Coefficients
+
+```python
+from pythonQEPest import QEPest
+
+custom_coefficients = {
+    "herb": [
+        (70.77, 283.0, 84.97, -1.185),
+        (93.81, 3.077, 1.434, 0.6164),
+        # ... 6 tuples total
+    ],
+    "insect": [...],
+    "fung": [...]
+}
+
+qepest = QEPest(coefficients=custom_coefficients)
+```
+
+### Custom Normalisers
+
+```python
+from pythonQEPest import QEPest
+from pythonQEPest.dto.normalisation.Normaliser import Normaliser
+
+qepest = QEPest(normalisers={"herb": Normaliser(...), ...})
+```
+
+## CLI Options
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `-i`, `--input` | Input file path | data.txt |
+| `-o`, `--output` | Output file path | data.out.txt |
+| `-f`, `--format` | Output format (json, txt) | txt |
+| `-v`, `--version` | Show version | - |
+
+## Development
+
+### Run tests
+
+```bash
+poetry run pytest
+```
+
+### Build
+
+```bash
+# CLI executable
+poetry run poe build-simple
+
+# GUI executable
+poetry run poe build-gui
+```
+

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pythonqepest-2.0.0a2.dist-info/entry_points.txt

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+[console_scripts]
+pythonqepest=pythonQEPest.cli.cli:main
+
+[gui_scripts]
+pythonqepest-gui=pythonQEPest.gui.gui:main
+