Installation

From PyPI

pip install molscope

The package is published on PyPI at pypi.org/project/molscope.

From a local checkout

git clone https://github.com/roshan2004/molscope
cd molscope
uv sync
uv run pytest

Optional dependencies

pip install "molscope[fast]"   # scipy KD-tree bond search
pip install "molscope[viz]"    # py3Dmol notebook viewer
pip install "molscope[graph]"  # NetworkX exporter
pip install "molscope[chem]"   # RDKit chemical perception
pip install "molscope[cif]"    # Gemmi CIF/mmCIF parser and validation helpers
pip install "molscope[gpu]"    # PyTorch dense distance/contact-map backend
pip install "molscope[pyg]"    # PyTorch + PyTorch Geometric exporter
pip install "molscope[dgl]"    # PyTorch + DGL exporter
pip install "molscope[gnn]"    # NetworkX + PyG + DGL exporters

The gpu, pyg, dgl, and gnn extras use the default PyPI PyTorch/DGL/PyG packages. If you need a specific CUDA, ROCm, Apple Silicon, or cluster build, install the matching PyTorch stack first from the backend project's instructions, then install MolScope normally:

pip install torch torch_geometric
pip install dgl
pip install molscope

Documentation site

Build the docs locally with:

uv sync --group docs
uv run mkdocs serve