MAHLER

MAHLER (Metadynamics-Anchored Hybrid Learning for Engineering off-Rates) provides a command-line interface for our method of reweighting IfMetaD trajectories for predicting antibody off-rates.

Installation

pip install .

Usage

After installation the mahler CLI becomes available on your $PATH.

mahler --help

The package ships with the following example commands:

• mahler info [--json] prints diagnostic information about the CLI runtime.
• mahler fold will eventually run AlphaFold to acquire representative structures.
• mahler mdprep will cluster folded stuctures and create MD setups.
• mahler mdrun will run short MD for representation learning with RAVE.
• mahler rave will run the RAVE protocol and acquire a latent space.
• mahler reweight will reweight collected trajectories.