Improve import

.github/dependabot.yml

@@ -1,6 +1,12 @@
 version: 2
+registries:
+  pytorch-cuda:
+    type: python-index
+    url: https://download.pytorch.org/whl/cu121 #so Dependabot retrieves cuda wheels for torch
 updates:
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
       interval: "weekly"
+    registries: ["pytorch-cuda"]
+

.github/release-drafter.yml

@@ -0,0 +1,31 @@
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+  - title: '🚀 Features'
+    labels:
+      - 'feature'
+      - 'enhancement'
+  - title: '🐛 Bug Fixes'
+    labels:
+      - 'fix'
+      - 'bugfix'
+      - 'bug'
+  - title: '🧰 Maintenance'
+    label: 'chore'
+change-template: '- $TITLE @$AUTHOR (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+template: |
+  ## Changes
+
+  $CHANGES

.github/workflows/release-drafter.yml

@@ -0,0 +1,43 @@
+name: Release Drafter
+
+on:
+  push:
+    # branches to consider in the event; optional, defaults to all
+    branches:
+      - main
+      - master
+
+  # pull_request event is required only for autolabeler
+  pull_request:
+    # Only following types are handled by the action, but one can default to all as well
+    types: [opened, reopened, synchronize]
+  # pull_request_target event is required for autolabeler to support PRs from forks
+  pull_request_target:
+    types: [opened, reopened, synchronize]
+
+permissions:
+  contents: read
+
+jobs:
+  update_release_draft:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+      # write permission is required for autolabeler
+      # otherwise, read permission is required at least
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      # (Optional) GitHub Enterprise requires GHE_HOST variable set
+      #- name: Set GHE_HOST
+      #  run: |
+      #    echo "GHE_HOST=${GITHUB_SERVER_URL##https:\/\/}" >> $GITHUB_ENV
+
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v6
+        # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+        # with:
+        #   config-name: my-config.yml
+        #   disable-autolabeler: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/unittest.yml

@@ -3,16 +3,8 @@ name: Unit Tests & Coverage
 on:
   push:
     branches: [main]
-    paths:
-      - "ionerdss/**"
-      - "tests/**"
-      - ".github/workflows/unittest.yml"
   pull_request:
     branches: [main]
-    paths:
-      - "ionerdss/**"
-      - "tests/**"
-      - ".github/workflows/unittest.yml"
 
 #Stop redundant CI runs for superseded commits
 concurrency:
@@ -41,26 +33,23 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip                       # built‑in dependency+wheel cache
-          cache-dependency-path: env/requirements.txt
+          cache-dependency-path: env/requirements-dev.txt
 
       #Extra cache layer: pre‑built wheels in ~/.cache/pip so can work between OS/versions
       - name: Cache compiled pip wheels
         uses: actions/cache@v4             
         with:
           path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('env/requirements.txt') }}
+          key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('env/requirements-dev.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-${{ matrix.python-version }}
             ${{ runner.os }}-pip-
 
       # Qt/OpenGL runtime (Linux only; no‑op elsewhere as stated in the action repo, mac shouldn't need it)
       - uses: tlambert03/setup-qt-libs@v1
 
-      - name: Install project dependencies
-        run: pip install -r env/requirements.txt
-
-      - name: Install package in editable mode
-        run: pip install -e .[tests] # optional pytest/pytest-cov deps as defined in toml file
+      - name: Install package in editable mode with test dependencies
+        run: pip install -e .[test]
 
       - name: Configure headless Qt
         run: echo "QT_QPA_PLATFORM=offscreen" >> $GITHUB_ENV   #avoids xcb/display errors, according to the web

.gitignore

@@ -78,7 +78,6 @@ celerybeat.pid
 .venv
 
 venv/
-ENV/
 env.bak/
 venv.bak/
 
@@ -112,3 +111,7 @@ cython_debug/
 ~*
 *~
 .DS_Store
+
+
+# Specficially ignore pdbfiles in proaffinity
+proaffinity-gnn/pdbfiles

README.md

@@ -6,123 +6,156 @@
 ![PyPI - Wheel](https://img.shields.io/pypi/wheel/ioNERDSS.svg)
 [![codecov](https://codecov.io/gh/JohnsonBiophysicsLab/ionerdss/graph/badge.svg?token=IUUUOZT0VJ)](https://codecov.io/gh/JohnsonBiophysicsLab/ionerdss)
 
-**ionerdss** is a Python library that provides user‐friendly tools for setting up and analyzing output from the [NERDSS](https://github.com/JohnsonBiophysicsLab/NERDSS) reaction‐diffusion simulator. Its goal is to streamline model building (from PDB files or from scratch), data analysis, and visualization for simulation workflows.
+**ionerdss** is a Python library that provides user‐friendly tools for setting up and analyzing output from the [NERDSS](https://github.com/JohnsonBiophysicsLab/NERDSS) reaction‐diffusion simulator.
 
 ---
 
 ## Installation
 
-1. From PyPI (recommended):
-   - **Python version:** 3.9 or later
+### 1. From PyPI (Recommended)
 
-Create a conda environment (optional but recommended):
-
-Download and install Anaconda or Miniconda, then create a new conda environment for `ionerdss`:
+Requires Python 3.9 or later.
 
 ```bash
-conda create -n ionerdss python=3.9
-conda activate ionerdss
+pip install ioNERDSS
+```
+To include optional features, you can specify them during installation:
+```bash
+# Example: Install with ODE solver and rendering tools
+pip install "ioNERDSS[ode,ovito_rendering]"
 ```
 
-Install the latest release directly from PyPI:
+### 2. For Development (from GitHub)
 
+**Quick Start (Clone and Test):**
 ```bash
-pip install ioNERDSS
+# Requires Python 3.9+
+git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
+cd ionerdss
+pip install -e ".[test,jupyter]"  # Essential dev dependencies
+pytest
 ```
 
-2. From GitHub (for the latest development version):
-   - If you want to use the latest features or contribute to the development, you can install directly from the GitHub repository:
+**Detailed Setup for Contributors:**
+
+If you want to contribute to development, work with examples, or need a specific environment setup:
+
+**Prerequisites:**
+*   [Git](https://git-scm.com/)
+*   Python 3.9+
+*   Your choice of environment manager: `conda`, `venv`, etc.
+*   Optionally, [uv](https://github.com/astral-sh/uv) for faster performance
+
+**Setup Instructions:**
+
+1.  **Clone the repository:**
+    ```bash
+    git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
+    cd ionerdss
+    ```
+
+2.  **Create and activate an environment:**
+
+    *   **Using `conda` (Recommended for full environment):**
+        ```bash
+        conda env create -f env/environment.yml
+        conda activate ionerdss-dev
+        ```
+    *   **Using `uv` and `venv` (Fastest):**
+        ```bash
+        python -m venv .venv
+        source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+        uv pip install -r env/requirements-dev.txt
+        ```
+    *   **Using `pip` and `venv`:**
+        ```bash
+        python -m venv .venv
+        source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+        pip install -r env/requirements-dev.txt
+        ```
+
+This installs `ionerdss` in editable mode with testing and Jupyter dependencies for typical development.
+
+**For comprehensive development** (including heavy rendering and documentation tools):
+```bash
+pip install -e ".[all]"
+```
 
-To install from source (e.g., if you’ve cloned this repo and want the most recent changes):
+---
 
+## Running Tests
+
+To run the unit tests locally, ensure you have installed the development environment (which includes `pytest` and `pytest-cov`).
+
+Then, from the project root folder, run:
 ```bash
-git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
-cd ionerdss
-pip install -r requirements.txt
-pip install -e .  # Editable mode: updates reflect immediately in the environment
+pytest
 ```
 
 ---
 
-## Quick Start
+## Usage
 
 ```python
 import ionerdss as ion
-ion.some_function()  # Replace with actual function calls to set up model and analyze results
+
+# Create a PDB model from structure
+model = ion.PDBModel(pdb_id="1abc")
+model.generate_model()
+
+# Run analysis on simulation data
+analysis = ion.Analysis("path/to/simulation/data")
+analysis.plot_time_evolution()
 ```
 
-For extended examples, see the [tutorials](https://ionerdss.readthedocs.io/en/latest/ionerdss_tutorials.html).
+## Examples
 
-### Run a quick trial with our server
+The `examples/` directory contains hands-on Jupyter notebooks demonstrating real molecular systems:
+
+- **`Homo-3mer-5VA4.ipynb`** - 3-component homogeneous assembly
+- **`Hetero-30mer-4YD9.ipynb`** - 30-component heterogeneous system  
+- **`Homo-720mer-6MX4.ipynb`** - Large 720-component viral capsid
+- **`book_chapter_example_system_1.ipynb`** - Comprehensive tutorial example
+
+To run the examples locally:
+```bash
+git clone https://github.com/JohnsonBiophysicsLab/ionerdss.git
+cd ionerdss
+pip install -e ".[jupyter]"  # Install with Jupyter support
+jupyter lab examples/
+```
+
+For additional tutorials, see the [online documentation](https://ionerdss.readthedocs.io/en/latest/ionerdss_tutorials.html).
 
+### Run a quick trial with our server
 Go to the [NERDSS server](http://52.15.142.249:5000/).
 
 ---
 
 ## Documentation
 - **User Guide:** [ionerdss user guide](https://ionerdss.readthedocs.io/en/latest/ionerdss_documentation_v1_1.html).
+- **API Reference:** [API](https://ionerdss.readthedocs.io/en/latest/ionerdss.html).
 
-- **API Reference:** [API](https://ionerdss.readthedocs.io/en/latest/ionerdss.html). You can also build the docs locally using Sphinx:
+You can also build the docs locally using Sphinx:
 ```bash
-sphinx-apidoc -o docs/source ionerdss
-cd docs
+# Ensure you are in your activated environment
+pip install -e ".[docs]"  # Install documentation dependencies
+sphinx-apidoc -o website/source ionerdss
+cd website
 make html
 ```
-Then open docs/build/html/index.html in your browser.
+Then open `website/build/html/index.html` in your browser.
 
 ---
 
-## Repository Structure
-```
-ionerdss/
-├── .github/workflows/     # Continuous Integration workflows
-├── docs/                  # Documentation
-│   ├── source/            # Sphinx source files
-│   ├── make.bat           # Windows build script
-│   └── Makefile           # Unix build script
-├── ionerdss/              # Main Python package
-│   ├── nerdss_model/      # Model building tools (v1.2.0)
-│   ├── nerdss_simulation/ # Simulation tools (v1.2.0)
-│   ├── nerdss_analysis/   # Data analysis tools (v1.2.0)
-│   └── __init__.py 
-├── tests/                 # Unit tests
-├── data/                  # Test and tutorial data
-└── setup.py               # Installation & packaging
-```
-
----
+## Docker Development Environment
 
-## Develop using docker container:  
+For isolated development with Jupyter Lab:
 ```bash
 docker build --no-cache -t ionerdss_dev . 
 docker run -it --rm -v $(pwd):/app -p 8888:8888 ionerdss_dev
 ```
-
----
-
-## Best Practices
-
-1. **Docstrings & Sphinx**  
-   - Write clear docstrings in Google‐style to help auto‐generate documentation.
-
-2. **Code Organization**  
-   - Keep related functionality grouped in submodules.
-
-3. **Tests**  
-   - Add or update unit tests in `tests/` for any new function. We use [unittest](https://docs.python.org/3/library/unittest.html).
-
-   - To run the tests locally, in the project root folder, use the following command:
-     ```bash
-     pip install -r requirements.txt
-     export PYTHONPATH=$(pwd)
-     pytest
-     ```
-
-4. **Versioning & Releases**  
-   - Update `setup.py` with a new version number. A GitHub release will auto‐update the PyPI package.
-
-5. **Contributions**  
-   - Fork the repo, create a feature branch, and open a pull request.
+This creates a containerized environment with Jupyter Lab accessible at `http://localhost:8888`.
 
 ---
 

data/7uhy.cif

@@ -3645,7 +3645,7 @@ _entity.details
 2 polymer     man "GATOR complex protein WDR24"   88326.953  2  ? ? ? ? 
 3 polymer     man "GATOR complex protein WDR59"   109938.391 2  ? ? ? ? 
 4 polymer     man "Isoform B of Nucleoporin SEH1" 46636.289  6  ? ? ? ? 
-5 polymer     man "Protein SEC13 homolog"         35578.438  2  ? ? ? ? 
+5 polymer     man "Protein SEC13 repeated_chain"         35578.438  2  ? ? ? ? 
 6 polymer     man Unknown                         1294.587   2  ? ? ? ? 
 7 polymer     man Unknown                         698.854    2  ? ? ? ? 
 8 non-polymer syn "ZINC ION"                      65.409     32 ? ? ? ?