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pythonQEPest

pythonQEPest PyPI Version

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 Original Program Link is here

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:

Platform Download
Windows CLI main.exe
Windows GUI gui.exe

Installation

pip install pythonQEPest

Or from source:

git clone https://github.com/PonyLianna/pythonQEPest.git
cd pythonQEPest
poetry install

With GUI support

pip install pythonQEPest[gui]
# or
poetry install --extras ui

Quick Start

CLI

pythonqepest -i data.txt -o result.txt
pythonqepest --input data.txt --format json
pythonqepest -v  # show version

GUI

pythonqepest-gui
# or
python -m pythonQEPest.gui.gui

Python API

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

[
  {"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

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

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

poetry run pytest

Build

# CLI executable
poetry run poe build-simple

# GUI executable
poetry run poe build-gui