OverallPLDDTEnergy

Definition

The overall pLDDT energy is the negated mean pLDDT over all residues in the structure.

E_{\mathrm{pLDDT}} = -\frac{1}{N} \sum_{\alpha} \mathrm{pLDDT}_\alpha

$N$ is the total number of residues in the structure
$\mathrm{pLDDT}_\alpha$ is the predicted local distance difference test score for residue $\alpha$

Parameters

FoldingOracle

required

The oracle to use for the 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.

Example

import bagel as bg

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

# Create the energy term
overall_plddt = bg.energies.OverallPLDDTEnergy(
    oracle=esmfold,
    weight=1.0,
)

# Add to a state
state = bg.State(
    chains=[chain],
    energy_terms=[overall_plddt],
    name="my_state",
)

PLDDTEnergy

SurfaceAreaEnergy

Overview

Core

Energies

Minimizers

Mutation

Oracles

Callbacks

Analysis

OverallPLDDTEnergy

Definition

Parameters

Example

​Definition

​Parameters

​Example

Definition

Parameters

Example