The unified generative‑AI framework that streamline training the 3D molecular diffusion models to their deployment in data-driven computational chemistry pipelines
- End-to-End 3D Molecular Generation Workflow: Support training diffusion model, and preditive models, and utilize them for various molecular generation tasks, all within a unified framework.
- Curriculum learning: Efficient way for training and fine-tuning 3D molecular diffusion models
- Guidance Tools: Generate molecules with specific characteristics:
- Property-Targeted Generation: Generate molecules with a target physicochemical or electronic properties (e.g., excitation energy, dipole moment)
- Inpainting: Systematically explore structural variants around reference molecules
- Outpainting: Extend a molecule by generating new parts.
- Command-Line Interface: A user-friendly CLI for training, generation, and prediction.
For a more detailed installation, including setting up a conda environment and installing necessary packages, follow these steps:
# create new python environment
conda create -n moleculardiffusion python=3.11 -c defaults
conda activate moleculardiffusion
# install pytorch according to instructions (use CUDA version for your system)
# https://pytorch.org/get-started/
pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu124
# install pytorch geometric (use CUDA version for your system)
# https://pytorch-geometric.readthedocs.io/
pip install torch_geometric
# Optional dependencies:
pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.4.0+cu124.html
conda install conda-forge::openbabel
conda install xtb==6.7.1
# install other libraries
pip install fire seaborn decorator numpy scipy rdkit-pypi posebusters==0.5.1 networkx matplotlib pandas scikit-learn tqdm pyyaml omegaconf ase morfeus-ml morfeus-ml wandb rmsd
pip install hydra-core==1.* hydra-colorlog rootutils
# install cell2mol
git clone https://github.com/lcmd-epfl/cell2mol
cd cell2mol
python setup.py install
cd ..
rm -rf cell2mol
# Install the package. Use editable mode (-e) to make the MolCraftDiff CLI tool available.
pip install -e .
# optional for some featurizer/metrics
# this require numpy==1.24.*
pip install cosymlib
Pre-trained diffusion models are available at Hugging Face or in the models/edm_pretrained/ directory. We suggest to start from this model for downstream application.
There are two ways to run experiments: using the MolCraftDiff command-line tool (recommended) or by executing the Python scripts directly.
Make sure you have installed the package in editable mode as described above, and that you run the commands from the root of the project directory.
Commands:
train: Run a training job.generate: Run a molecule generation job.predict: Run prediction with a trained model.eval_predict: Evaluate predictions.analyze: Perform analysis and post-processing on generated molecules.
Command Syntax:
MolCraftDiff [COMMAND] [CONFIG_NAME/ARGUMENTS]
[COMMAND]: One oftrain,generate,predict,eval_predict, oranalyze.[CONFIG_NAME]: The name of the configuration file from theconfigs/directory (e.g.,train,example_diffusion_config).[ARGUMENTS]: Additional command-line arguments to override configuration settings.
Examples:
# Train a model using the 'example_diffusion_config.yaml' configuration
MolCraftDiff train example_diffusion_config
# Generate molecules using the 'my_generation_config.yaml' configuration
MolCraftDiff generate my_generation_config
# Predict properties using a trained model
MolCraftDiff predict my_prediction_config
Getting Help:
To see the main help message and a list of all commands:
MolCraftDiff --help
To get help for a specific command:
MolCraftDiff train --help
You can also execute the scripts in the scripts/ directory directly.
Training:
python scripts/train.py tasks=[TASK]
where TASK is one of the following: diffusion, guidance, regression.
Generation:
python scripts/generate.py interference=[INTERFERENCE]
where INTERFERENCE is one of the following: gen_cfg, gen_cfggg, gen_conditional, gen.
Prediction:
python scripts/predict.py
The analyze command provides a suite of tools for processing and evaluating generated molecules.
Subcommands:
optimize: Optimize molecular geometries using GFN-xTB.metrics: Compute validity and connectivity metrics.compare: Calculate RMSD, energy differences, and geometric properties (bonds/angles) between generated and reference structures.xyz2mol: Convert XYZ files to SMILES and extract fingerprints/scaffolds.
Examples:
# Optimize geometries in a directory
MolCraftDiff analyze optimize -i generated_molecules/
# Compute validity metrics
MolCraftDiff analyze metrics -i generated_molecules/
# Compare generated structures with ground truth (requires optimized counterparts)
MolCraftDiff analyze compare generated_molecules/ --bonds
# Convert XYZ to SMILES
MolCraftDiff analyze xyz2mol -x generated_molecules/
Generated 3D molecules and their properties can be visualized using the 3DMolViewer package.
We also recommend our in-house and lightweight X11 molecular viewer V package.
A comprehensive set of tutorials is available in the tutorials/ directory, covering topics from basic model training to advanced generation techniques.
├── .project-root
├── justfile
├── pyproject.toml
├── README.md
├── setup.py
└── src
└── MolecularDiffusion
├── __init__.py
├── _version.py
├── molcraftdiff.py
├── callbacks
│ ├── __init__.py
│ └── train_helper.py
├── cli
│ ├── __init__.py
│ ├── analyze.py
│ ├── eval_predict.py
│ ├── generate.py
│ ├── main.py
│ ├── predict.py
│ └── train.py
├── configs
│ ├── data
│ ├── hydra
│ ├── interference
│ ├── logger
│ ├── tasks
│ └── trainer
├── core
│ ├── __init__.py
│ ├── core.py
│ ├── engine.py
│ ├── logger.py
│ └── meter.py
├── data
│ ├── __init__.py
│ ├── dataloader.py
│ ├── dataset.py
│ └── component
├── modules
│ ├── __init__.py
│ ├── layers
│ ├── models
│ └── tasks
├── runmodes
│ ├── __init__.py
│ ├── analyze
│ │ ├── __init__.py
│ │ ├── compute_energy_rmsd.py
│ │ ├── compute_metrics.py
│ │ ├── compute_pair_geometry.py
│ │ ├── xtb_optimization.py
│ │ └── xyz2mol.py
│ ├── generate
│ └── train
└── utils
├── __init__.py
├── comm.py
├── diffusion_utils.py
├── file.py
├── geom_analyzer.py
├── geom_constant.py
├── geom_constraint.py
├── geom_metrics.py
├── geom_utils.py
├── io.py
├── molgraph_utils.py
├── plot_function.py
├── pretty.py
├── sascore.py
├── smilify.py
└── torch.py
This project is licensed under the MIT License.
If you use MolecularDiffusion in your research, please cite the following:
ChemRxiv: MolecularDiffusion: A Unified Generative-AI Framework for 3D Molecular Design