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Definition

The ring symmetry energy is the standard deviation of pairwise centroid distances between groups, penalizing asymmetric spacing. Esym=std(dGi,Gj)E_{\mathrm{sym}} = \mathrm{std}\left(d_{G_i, G_j}\right)
  • dGi,Gjd_{G_i, G_j} is the distance between the backbone centroids of groups GiG_i and GjG_j
  • The standard deviation is taken over all unique group pairs (or only direct neighbours if direct_neighbours_only=True)

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Parameters

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oracle
FoldingOracle
required
The oracle to use for the energy term.
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symmetry_groups
list[list[Residue]]
required
A list of at least length 2, with each element containing a list of residues corresponding to a symmetry group.
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inheritable
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.
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direct_neighbours_only
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.
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weight
float
default:"1.0"
The weight of the energy term.
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name
str | None
default:"None"
Optional name to append to the energy term name.

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Methods

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compute

Parameters
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oracles_result
OraclesResultDict
required

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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",
)