TMol provides all-atom scoring, packing, minimization, and FastRelax in PyTorch. It batches proteins, nucleic acids, ligands, and complexes on CPU or CUDA, with gradients through coordinate scoring.
Documentation · Tutorials · API reference
Install
pip install tmol
TMol 0.1.59 uses AtomWorks 3 and includes ligand preparation with RDKit and OpenBabel in the standard install.
TMol first looks for a matching prebuilt wheel and otherwise builds locally. For binary installs, supported platforms, and troubleshooting, see the installation guide and GitHub Releases.
Verify the installation:
python -c "import tmol; print(tmol.__version__)"
Quick start
Score a structure on GPU when CUDA is available, otherwise on CPU:
import torch
import tmol
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
pose = tmol.pose_stack_from_pdb("input.pdb", device)
score_function = tmol.beta2016_score_function(device)
score = score_function.render_whole_pose_scoring_module(pose)
print(score(pose.coords))
See the quickstart for minimization and ligand preparation. The guides cover batching, packing, score analysis, and model inputs; the task index links individual operations to examples and APIs.
Development
git clone https://github.com/uw-ipd/tmol.git
cd tmol
TMOL_DISABLE_WHEEL_FETCH=1 pip install -e ".[dev]"
The development guide covers builds, tests, benchmarks, and releases. See the contributor guide for code and documentation conventions, or agent skills for reusable coding-agent instructions.
Citation
If you use TMol in your work, please cite:
Andrew Leaver-Fay, Jeff Flatten, Alex Ford, Joseph Kleinhenz, Henry Solberg, David Baker, Andrew M. Watkins, Brian Kuhlman, Frank DiMaio, tmol: a GPU-accelerated, PyTorch implementation of Rosetta's relax protocol (manuscript in preparation).
TMol is available under the terms in LICENSE.
1 maintainer
Metadata
1 maintainer
Release files for tmol 0.1.59
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| tmol-0.1.59.tar.gz | 66.5 MB | Details |
Release files / tmol-0.1.59.tar.gz
| Download URL | tmol-0.1.59.tar.gz |
|---|---|
| Size | 66.5 MB |
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