Version Update

.github/workflows/install_test.yml

@@ -0,0 +1,37 @@
+# .github/workflows/test-install.yml
+name: Test PyProject Install
+
+on:
+  pull_request:
+    branches: [main]
+
+jobs:
+  test-install:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Upgrade pip and build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Install package via pip (pyproject.toml)
+        run: |
+          pip install uv
+          uv pip install . --system
+
+      - name: Verify package import
+        run: |
+          python -c "import provada"

.gitignore

@@ -0,0 +1,166 @@
+# Added
+.DS_Store
+**results
+**tmp_
+**logs
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.gitmodules

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+[submodule "ProteinMPNN"]
+	path = ProteinMPNN
+	url = https://github.com/dauparas/ProteinMPNN.git

README.md

@@ -29,52 +29,54 @@ The fitness score combines multiple objectives. A key component is a lightweight
 
 ## Installation
 
-### 1. Prerequisites
-
-Before installing, please ensure your system meets the following requirements:
-
-*   **Python 3.11+**: This package requires Python version 3.11 or newer. You can verify your version by running:
-    ```bash
-    python3 --version
-    ```
-    Make sure that the `python3` command used to create the virtual environment in the next step points to a compatible version.
-
-*   **ProteinMPNN**: This package relies on a local installation of ProteinMPNN for structure-based sequence design. Please follow the official [ProteinMPNN installation guide](https://github.com/dauparas/ProteinMPNN) to set it up first.
-
-    **Crucially**, after installing ProteinMPNN, you must **update the `MPNN_SCRIPT` path in `provada/paths.py`** to point to your local `protein_mpnn_run.py` script.
-
-### 2. Package Installation
-
-We strongly recommend installing ProVADA in a clean, dedicated virtual environment.
-
-The following commands will clone the repository, set up a virtual environment, and install the `provada` package with all its required Python libraries.
+Follow the instructions below to install ProVADA.
 
+### 1. Clone the repository
 ```bash
 # 1. Clone this repository from GitHub
 git clone https://github.com/SUwonglab/provada.git
 cd provada
+```
 
-# 2. Create and activate a virtual environment using a compatible Python version
-#    (The following commands create a 'venv' folder in your project directory)
+### 2. Create and activate a virtual environment
+```bash
+conda create -n provada-env python=3.11 -y
+conda activate provada-env
+pip install uv
+uv pip install .
+```
 
-# On macOS / Linux:
-python3 -m venv venv
-source venv/bin/activate
 
-# On Windows:
-# python -m venv venv
-# venv\Scripts\activate
+### 3. ProteinMPNN Set up
+ProVADA uses ProteinMPNN as a local dependency for structure-based sequence design.
+Run the command below to populate the ProteinMPNN submodule with the required source code.
 
-# 3. Install the provada package and its dependencies
-#    This command reads the pyproject.toml file and installs everything needed.
-pip install .
+```bash
+git submodule update --init --recursive
 ```
 
 
 
-
 ## Usage
 
+We provide an example script to run ProVADA on the example Renin protein described in the manuscript.
+
+```bash
+python run_provada.py \
+    --input_pdb_path 'inputs/renin/renin_af3.pdb' \
+    --input_sequence_path 'inputs/renin/example_seq_renin.txt' \
+    --classifier_weights 'inputs/renin/logreg_model_weights.pkl' \
+    --fixed_positions_files 'inputs/renin/interface_positions.txt' 'inputs/renin/conserved_positions.txt' \
+    --force_design_residues 'C' \
+    --output_dir './results/test_hard_fix' \
+    --trajectory_file 'test_fix_300iter_2.csv' \
+    --save_trajectory \
+    --greedy
+```
+
+### Example
+
+
 ### A Note on Using Your Own Proteins
 
 The ProVADA workflow relies on two key utility scripts to prepare PDB structures for ProteinMPNN: `provada/utils/pdb_to_mpnn_jsonl.py` and `provada/utils/define_design_constraints.py`.

inputs/README.md

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+# Example Inputs
+
+This directory contains example input files for the ProVADA pipeline.

inputs/renin/conserved_positions.txt

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+27
+29
+69
+129
+316
+319

inputs/renin/example_seq_renin.txt

@@ -0,0 +1 @@
+LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR