pythonQEPest 2.0.0a2__tar.gz

pythonqepest-2.0.0a2/PKG-INFO

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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
+```
+

pythonqepest-2.0.0a2/README.md

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+# 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
+```

pythonqepest-2.0.0a2/pyproject.toml

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+[project]
+name = "pythonQEPest"
+version = "2.0.0a2"
+description = "Java QEPest but written in Python"
+readme = "README.md"
+requires-python = ">=3.12,<3.15"
+authors = [{ name = "Lina", email = "knocker767@gmail.com" }]
+dependencies = ["pydantic==2.12.5", "python-dotenv>=1.2.1,<2.0.0"]
+
+[project.optional-dependencies]
+gui = ["pyperclip>=1.11.0,<2.0.0"]
+rdkit = ["rdkit (>=2024.3.1,<2026.0.0)"]
+
+[project.scripts]
+pythonqepest = "pythonQEPest.cli.cli:main"
+
+[project.gui-scripts]
+pythonqepest-gui = "pythonQEPest.gui.gui:main"
+
+[tool.poetry]
+packages = [{ include = "pythonQEPest" }]
+
+[dependency-groups]
+dev = [
+    "pytest (>=9.0.0)",
+    "pre-commit (>=4.3.0,<5.0.0)",
+    "pyinstaller (>=6.18.0,<7.0.0)",
+    "poethepoet[poetry_plugin] (>=0.39.0)",
+    "pytest-cov (>=7.0.0,<8.0.0)",
+    "twine (>=6.2.0,<7.0.0)",
+]
+
+[build-system]
+requires = ["poetry-core>=1.0.0", "setuptools>=40.8.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.flake8]
+max-line-length = 88
+extend-ignore = ["E203", "W503"]
+exclude = [".venv", ".git", "__pycache__", "build", "dist"]
+
+[tool.poe.tasks]
+test = "pytest"
+build-simple = "pyinstaller --onefile pythonQEPest/main.py"
+build-gui = "pyinstaller --onefile --noconsole pythonQEPest/gui/gui.py"
+publish-pypy = "twine upload --repository pythonQEPest dist/*"

pythonqepest-2.0.0a2/pythonQEPest/.env.example

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+LOG_LEVEL="INFO"
+LOG_FILE_LOCATION="logs/app.log"
+
+APP_DEBUG_ENABLE="false"

pythonqepest-2.0.0a2/pythonQEPest/__init__.py

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+from pythonQEPest.core import QEPest
+from pythonQEPest.dto import QEPestData
+from pythonQEPest.dto import QEPestInput
+from pythonQEPest.dto import QEPestOutput
+
+__all__ = [
+    "QEPest",
+    "QEPestData",
+    "QEPestInput",
+    "QEPestOutput",
+]

pythonqepest-2.0.0a2/pythonQEPest/cli/__init__.py

@@ -0,0 +1,7 @@
+def main():
+    from pythonQEPest.cli.cli import main as _main
+
+    return _main()
+
+
+__all__ = ["main"]

pythonqepest-2.0.0a2/pythonQEPest/cli/cli.py

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+from __future__ import annotations
+
+import argparse
+import logging
+from importlib.metadata import PackageNotFoundError, version
+from pathlib import Path
+from typing import Sequence
+
+from pythonQEPest.dto import QEPestFile
+from pythonQEPest.services.QEPestFileService import QEPestFileService
+
+logger = logging.getLogger(__name__)
+
+
+def _resolve_package_version() -> str:
+    try:
+        return version("pythonQEPest")
+    except PackageNotFoundError:
+        pass
+
+    try:
+        import tomllib  # py3.11+
+
+        pyproject = Path(__file__).resolve().parents[2] / "pyproject.toml"
+        data = tomllib.loads(pyproject.read_text(encoding="utf-8"))
+        return data["project"]["version"]
+    except Exception:
+        return "0+unknown"
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        prog="pythonqepest",
+        description="Compute QEPest scores from a tab-separated input file.",
+    )
+    parser.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"%(prog)s {_resolve_package_version()}",
+        help="Show program's version number.",
+    )
+    parser.add_argument(
+        "-i",
+        "--input",
+        default="data.txt",
+        help="Path to input tab-separated file with "
+        + "QEPest descriptors (default: data.txt).",
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        default="data.out.txt",
+        help="Path to output tab-separated file with "
+        + "QEPest descriptors (default: data.txt.out).",
+    )
+
+    parser.add_argument(
+        "-f",
+        "--format",
+        default="txt",
+        help="Format to output file with QEPest (json, txt).",
+    )
+
+    parser.add_argument(
+        "--smiles",
+        action="store_true",
+        help="Input file contains SMILES strings "
+        "(one per line) instead of descriptors.",
+    )
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    from dotenv import load_dotenv
+
+    from pythonQEPest.core.qepest import QEPest
+    from pythonQEPest.logger import init_logger
+
+    args = build_parser().parse_args(argv)
+
+    load_dotenv()
+    init_logger()
+
+    logger.debug("CLI initiated")
+    logger.info(f"CLI args: {argv}")
+
+    service = QEPestFileService(
+        qepest=QEPest(),
+        qepest_file=QEPestFile(
+            input_file=args.input,
+            output_file=args.output,
+            format=args.format,
+            smiles=args.smiles,
+        ),
+    )
+
+    service.read_file_and_compute_params()
+
+    return 0 if not service.error else 1

pythonqepest-2.0.0a2/pythonQEPest/config/__init__.py

@@ -0,0 +1,11 @@
+from pythonQEPest.config.qepest_default import qepest_default
+from pythonQEPest.config.normalise import normalise_default
+from pythonQEPest.config.qepest_config import QEPestConfig
+from pythonQEPest.config.config_provider import ConfigProvider
+
+__all__ = [
+    "normalise_default",
+    "qepest_default",
+    "ConfigProvider",
+    "QEPestConfig",
+]

pythonqepest-2.0.0a2/pythonQEPest/config/config_provider.py

@@ -0,0 +1,9 @@
+from abc import ABC, abstractmethod
+
+from pythonQEPest.config.qepest_config import QEPestConfig
+
+
+class ConfigProvider(ABC):
+    @abstractmethod
+    def load(self) -> QEPestConfig:
+        pass

pythonqepest-2.0.0a2/pythonQEPest/config/normalise.py

@@ -0,0 +1,12 @@
+normalise_default = {
+    "herb": (69.5849922, 94.4228257, 120.4572352, 228.1589796, 89.7012502, 276.9634213),
+    "insect": (
+        78.2919965,
+        71.2829691,
+        133.9224801,
+        331.170104,
+        70.5540709,
+        193.0023343,
+    ),
+    "fung": (53.3719946, 52.773116, 73.7976536, 144.9887053, 41.4385926, 102.3024319),
+}

pythonqepest-2.0.0a2/pythonQEPest/config/qepest_config.py

@@ -0,0 +1,31 @@
+from typing import Optional
+
+from pydantic import BaseModel
+
+from pythonQEPest.dto.pest_type.PestTypeConfig import PestTypeConfig
+
+
+class QEPestConfig(BaseModel):
+    name: Optional[str] = "HerbInsectFung"
+    pest_types: list[PestTypeConfig]
+
+    def get_pest_names(self) -> list[str]:
+        return [pest.name for pest in self.pest_types]
+
+    def get_coefficients(
+        self, pest_name: str
+    ) -> list[tuple[float, float, float, float]]:
+        for pest in self.pest_types:
+            if pest.name == pest_name:
+                return pest.coefficients.as_set()
+
+        raise ValueError(f"Pest type '{pest_name}' not found")
+
+    def get_normaliser(
+        self, pest_name: str
+    ) -> tuple[float, float, float, float, float, float]:
+        for pest in self.pest_types:
+            if pest.name == pest_name:
+                return pest.normaliser
+
+        raise ValueError(f"Pest type '{pest_name}' not found")

pythonqepest-2.0.0a2/pythonQEPest/config/qepest_default.py

@@ -0,0 +1,26 @@
+qepest_default = {
+    "herb": [
+        (70.77, 283.0, 84.97, -1.185),  # mwH
+        (93.81, 3.077, 1.434, 0.6164),  # logpH
+        (117.6, 2.409, 1.567, 7.155),  # hbaH
+        (233.4, 0.4535, -1.48, 4.47),  # hbdH
+        (84.7, 4.758, -2.423, 5.437),  # rbH
+        (301.8, 1.101, 0.8869, -22.81),  # arRCH
+    ],
+    "insect": [
+        (76.38, 298.3, 83.64, 1.912),  # mwI
+        (74.27, 4.555, -2.193, -2.987),  # logpI
+        (139.4, 1.363, 1.283, 0.5341),  # hbaI
+        (670.6, -1.163, 0.7856, 0.7951),  # hbdI
+        (65.49, 6.219, -2.448, 5.318),  # rbI
+        (287.5, 0.305, 1.554, -88.64),  # arRCI
+    ],
+    "fung": [
+        (51.03, 314.2, -56.31, 2.342),  # mwF
+        (50.73, 3.674, -1.238, 2.067),  # logpF
+        (73.79, 1.841, 1.326, 0.5158),  # hbaF
+        (164.7, -0.9762, -2.027, 1.384),  # hbdF
+        (40.91, 1.822, 2.582, 0.6235),  # rbF
+        (134.4, 0.8383, 1.347, -31.17),  # arRCF
+    ],
+}

pythonqepest-2.0.0a2/pythonQEPest/core/__init__.py

@@ -0,0 +1,7 @@
+from .qepest import QEPest
+from .qepest_meta import QEPestMeta
+
+__all__ = [
+    "QEPestMeta",
+    "QEPest",
+]