SecondaryStructureEnergy

Definition

The secondary structure energy is the fraction of selected residues whose assigned secondary structure does not match the target.

E_{\mathrm{SS}} = \frac{1}{N_G} \sum_{\alpha \in G} \mathbb{I}[\mathrm{SS}_\alpha \neq \mathrm{SS}_{\mathrm{target}}]

$\mathbb{I}$ is the indicator function (1 if the condition is true, 0 otherwise)
$\mathrm{SS}_\alpha$ is the secondary structure assignment for residue $\alpha$
$\mathrm{SS}_{\mathrm{target}}$ is the target secondary structure (alpha-helix, beta-sheet, or coil)
$N_G$ is the number of residues in the group $G$

Parameters

Oracle

required

The oracle to use for the energy term.

list[Residue]

required

Which residues to include in the calculation.

str

required

Which secondary structure type to drive towards. Options are ‘alpha-helix’, ‘beta-sheet’, or ‘coil’.

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.

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 groups of residues that should form beta-sheets
groups = [residues[(i * 50) + 5 : (i * 50) + 35] for i in range(4)]

secondary_structure = bg.energies.SecondaryStructureEnergy(
    oracle=esmfold,
    residues=groups,
    target_secondary_structure="beta-sheet",
    weight=1.0,
)

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

Overview

Core

Energies

Minimizers

Mutation

Oracles

Callbacks

Analysis

SecondaryStructureEnergy

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example