ATOM3D: Tasks On Molecules in 3 Dimensions
Project description
ATOM3D: Tasks On Molecules in 3 Dimensions
ATOM3D enables machine learning on three-dimensional molecular structure.
Features
- Access to several datasets involving 3D molecular structure.
- LMDB data format for storing lots of molecules (and associated metadata).
- Utilities for splitting/filtering data based on many criteria.
For more detailed information, read the documentation.
Reference
We provide an overview on ATOM3D and details on the preparation of all datasets in our preprint:
R. J. L. Townshend, M. Vögele, P. Suriana, A. Derry, A. Powers, Y. Laloudakis, S. Balachandar, B. Anderson, S. Eismann, R. Kondor, R. B. Altman, R. O. Dror "ATOM3D: Tasks On Molecules in Three Dimensions", arXiv:2012.04035
Please cite this work if some of the ATOM3D code or datasets are helpful in your scientific endeavours. For specific datasets, please also cite the respective original source(s), given in the preprint.
Installation/Usage
Install with:
make requirements
To use rdkit functionality, please install within conda:
conda create -n atom3d python=3.6 pip rdkit
conda activate atom3d
make requirements
LMDB datasets
LMDB allows for compressed, fast, random access to your structures, all within a single database. Currently, we support creating LMDB datasets from PDB files, silent files, and xyz files.
Creating an LMDB dataset
From command line:
python -m atom3d.datasets PATH_TO_PDB_DIR PATH_TO_LMDB_OUTPUT --filetype {pdb,silent,xyz,xyz-gdb}
Loading an LMDB dataset
From python:
from atom3d.datasets import LMDBDataset
dataset = LMDBDataset(PATH_TO_LMDB)
print(len(dataset)) # Print length
print(dataset[0]) # Print 1st entry
From C++:
We provide example C++ code to load the LMDB datasets here.
For more usage, please see the documentation.
Contribute
- Issue Tracker: https://github.com/drorlab/atom3d/issues
- Source Code: https://github.com/drorlab/atom3d
Support
If you are having issues, please let us know. We have a mailing list located at: atom3d@googlegroups.com
License
The project is licensed under the MIT license.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.