RingSymmetryEnergy

Definition

The ring symmetry energy is the standard deviation of pairwise centroid distances between groups, penalizing asymmetric spacing.

E_{\mathrm{sym}} = \mathrm{std}\left(d_{G_i, G_j}\right)

$d_{G_i, G_j}$ is the distance between the backbone centroids of groups $G_i$ and $G_j$
The standard deviation is taken over all unique group pairs (or only direct neighbours if direct_neighbours_only=True)

Parameters

FoldingOracle

required

The oracle to use for the energy term.

list[list[Residue]]

required

A list of at least length 2, with each element containing a list of residues corresponding to a symmetry group.

bool

default:"True"

If a new residue is added next to a residue included in this energy term, this dictates whether that new residue could then be added to this energy term.

bool

default:"False"

Whether to compare the spacing of each each group to its direct neighbour (compare group i to group i+1 only), or each group to all other groups. Defaults to the latter.

float

default:"1.0"

The weight of the energy term.

str | None

default:"None"

Optional name to append to the energy term name.

Methods

compute

Parameters

OraclesResultDict

required

Example

import numpy as np
import bagel as bg

# Create a 190-residue chain
sequence = np.random.choice(list(bg.constants.aa_dict.keys()), size=190)
residues = [bg.Residue(name=aa, chain_ID="A", index=i, mutable=True) for i, aa in enumerate(sequence)]

# Create the folding oracle
esmfold = bg.oracles.ESMFold()

# Define 4 symmetry groups of 40 residues each (with 10-residue gaps)
symmetry_groups = [residues[i * 50 : (i * 50) + 40] for i in range(4)]

ring_symmetry = bg.energies.RingSymmetryEnergy(
    oracle=esmfold,
    symmetry_groups=symmetry_groups,
    weight=1.0,
)

# Add to a state
state = bg.State(
    chains=[bg.Chain(residues)],
    energy_terms=[ring_symmetry],
    name="my_state",
)

Overview

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Analysis

RingSymmetryEnergy

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example