Structure Ensemble RMSD

Generate a conformational ensemble and compute RMSD against a target structure via PyMOL.

License: This constraint can use multiple tools, each under its own license. See the Tools Used tab and each tool’s page for license details.

This constraint is open source. Any third-party models, product names, or trademarks referenced are the property of their respective owners, and Proto is not affiliated with them.

---

Tools Used Tools Used Source Source

proto-bio/proto-language/proto_language/constraint/protein_structure/structure_ensemble_similarity_constraint.py

View source

Generate conformational ensembles and compute RMSD against an experimental.

target structure.

This constraint:

1. Prepares the target structure (extracting chain/residue range if specified).
2. For each proposal sequence, generate a conformational ensemble.
3. Computes PyMOL-aligned RMSD between each ensemble frame and the target.
4. Summarizes the RMSDs using the specified aggregation method.
5. Converts the summarized RMSD to a 0-1 score using a sigmoid function.

API Reference

ConfigStructureEnsembleSimilarityConfig Source

Configuration for structure ensemble similarity constraints.

This constraint generates a conformational ensemble for a proposal protein sequence and computes the RMSD between ensemble members and an experimental target structure using PyMOL alignment.

target_structure · Structure | string · required

Target structure: a Structure object, file path (.pdb/.cif), or raw PDB/CIF content string.

target_chain_id · string

Chain ID to extract from the target structure (e.g., ‘A’).

target_residue_range · array

Residue range (start, end) to extract from target (1-indexed, inclusive).

proposal_residue_range · array

Residue range (start, end) of the proposal sequence to use.

bioemu_config · BioEmuConfig

Dictionary of configuration parameters passed to the ensemble prediction tool.

rmsd_aggregation · enum · default: "min"

How to summarize ensemble RMSD values: min (best match), p10, mean, or median.

Options: min, p10, mean, median

pymol_alignment_method · enum · default: "align"

PyMOL alignment routine for ensemble RMSD calculation.

Options: cealign, align

inflection_point_angstroms · number · default: "3.0"

RMSD in Ångströms where the sigmoid score equals 0.5; values below 3 Å are generally a good match.

sigmoid_slope · number · default: "3.0"

Steepness of the penalty curve.

verbose · boolean · default: "False"

Whether to print progress messages.

ReturnsConstraintOutput

Per-proposal score in [0, 1] (0 is a perfect match) with ensemble RMSD summary/distribution metadata.

Usage

python

from proto_language.core import Constraint
from proto_language.constraint import structure_ensemble_rmsd_constraint, StructureEnsembleSimilarityConfig

constraint = Constraint(
    inputs=[segment],
    function=structure_ensemble_rmsd_constraint,
    function_config=StructureEnsembleSimilarityConfig(
        # Configure parameters here
    ),
)

scores = constraint.evaluate()

Metadata

Property	Value
Key	structure-ensemble-rmsd
Function	structure_ensemble_rmsd_constraint
Category	protein_structure
Mode	discrete
Uses GPU	True
Supported Types	protein