hemopimod2 1.0__py3-none-any.whl

hemopimod2/__init__.py

@@ -0,0 +1,7 @@
+"""
+HemoPI-MOD2: Prediction of Hemolytic Potency (HC50)
+of Chemically Modified Peptides.
+"""
+
+__version__ = "1.0"
+__author__ = "Anand Singh Rathore"

hemopimod2/python_scripts/__init__.py

@@ -0,0 +1,3 @@
+"""
+Python scripts and utilities for HemoPI-MOD2.
+"""

hemopimod2/python_scripts/config/INSTALLATION.txt

@@ -0,0 +1,77 @@
+# 🛠️ Installation Guide for HemoPI-MOD2
+
+## 🔹 Standalone Installation
+
+HemoPI-MOD2 is written in **Python 3** and requires the following
+dependencies:
+
+### ✅ Required Libraries
+
+```bash
+python>=3.9
+```
+
+Core packages, needed by every model:
+
+```bash
+pip install scikit-learn==1.6.1
+pip install xgboost==3.2.0
+pip install "numpy>=1.23,<2.0"
+pip install pandas
+pip install joblib
+pip install scipy
+```
+
+Needed only for the Chemical (-m 2) and Structure (-m 3) models:
+
+```bash
+pip install rdkit
+pip install mordred==1.2.0
+pip install "networkx>=2.8,<3.0"
+```
+
+Or install everything at once:
+
+```bash
+pip install -r requirements.txt
+```
+
+## 🔹 Installation using environment.yml
+
+1. Create a new Conda environment:
+```bash
+conda env create -f environment.yml
+```
+2. Activate the environment:
+```bash
+conda activate HemoPI-MOD2
+```
+
+## ⚠️ Important Note-1
+
+- scikit-learn and xgboost are PINNED on purpose. The three model files in
+  models/ were fitted with scikit-learn 1.6.1, and chemical_model.pkl holds a
+  serialized XGBoost regressor. Loading either under a different version
+  prints a version warning and is not guaranteed to reproduce the published
+  numbers.
+
+## ⚠️ Important Note-2
+
+- The model files ship inside this package, in the models/ directory. Nothing
+  needs to be downloaded or extracted.
+- The Sequence model (-m 1) and the Design module (-j 2) run without RDKit and
+  Mordred. Install those two only if you need the Chemical or Structure model.
+
+## 🔹 Checking the installation
+
+```bash
+python HemoPI_MOD2.py -h
+python HemoPI_MOD2.py -i example_sequence.fasta -o output.csv
+```
+
+The second command should print a table of five peptides with their predicted
+HC50 values and write output.csv.
+
+---
+
+🚀 **You are now ready to use HemoPI-MOD2!**

hemopimod2/python_scripts/config/environment.yml

@@ -0,0 +1,17 @@
+name: HemoPI-MOD2
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - python=3.10
+  - numpy=1.26.4
+  - pandas=2.2.3
+  - scipy
+  - joblib=1.4.2
+  - scikit-learn=1.6.1
+  - rdkit
+  - networkx=2.8.8
+  - pip
+  - pip:
+      - xgboost==3.2.0
+      - mordred==1.2.0

hemopimod2/python_scripts/config/requirements.txt

@@ -0,0 +1,19 @@
+# HemoPI-MOD2 standalone — Python dependencies  (Python 3.9 or newer)
+#
+# scikit-learn and xgboost are PINNED on purpose. The three model files in
+# models/ were fitted with scikit-learn 1.6.1, and chemical_model.pkl holds a
+# serialized XGBoost regressor. Other versions usually load, but are not
+# guaranteed to reproduce the published numbers.
+
+numpy>=1.23,<2.0
+pandas>=1.5
+scipy>=1.9
+joblib>=1.2
+scikit-learn==1.6.1
+xgboost==3.2.0
+
+# Chemical (-m 2) and Structure (-m 3) models only.
+# Mordred 1.2.0 needs networkx<3.
+rdkit>=2022.9
+mordred==1.2.0
+networkx>=2.8,<3.0