Prism Pruner

PRISM (Pruning Interface for Similar Molecules) is the modular similarity pruning code originally from FIRECODE, in a polished standalone package. It filters out duplicate structures from conformational ensembles, leaving behind non-redundant states.

The code implements a cached, iterative, divide-and-conquer approach on increasingly large subsets of the ensemble and removes duplicates as assessed by one of three metrics:

• Relative deviation of the moments of inertia on the principal axes
• Heavy-atom RMSD and maximum deviation
• Rotamer-corrected heavy-atom RMSD and maximum deviation

Installation

The package is distributed through PyPI. Installation through uv is recommended.

uv pip install prism_pruner

Usage

The main pruning functions are in prism_pruner.pruning, and a wrapper that chains up to all three is also available. The functions return the pruned ensemble structures and the relative boolean mask.

from prism_pruner.conformer_ensemble import ConformerEnsemble
from prism_pruner.pruner import prune

ensemble = ConformerEnsemble.from_xyz("ensemble.xyz")

ensemble.coords.shape # (1086, 136, 3)

pruned, mask = prune(
    ensemble.coords,
    ensemble.atoms,

    # the third pruning routine can be
    # slow and is often not necessary,
    # so it's off by default
    rot_corr_rmsd_pruning=False,

    debugfunction=print,
)

pruned.shape # (387, 136, 3)
mask.shape # (1086,)
# where pruned is ensemble.coords[mask]

For additional performance, it is also possible to read/provide energies to only evaluate the similarity of structures that are energetically close.

For additional usage, see the examples folder.

CLI usage

A simple CLI is also provided:

usage: prism_pruner [-h] [-e] [-t TIMEOUT] inputfile

Will write the pruned ensemble to inputfile_pruned.xyz.

Credits

This package was created with Cookiecutter and the jevandezande/pixi-cookiecutter project template.