PLDDTEnergy

Definition

The pLDDT energy is the negated mean pLDDT over the specified residue groups.

E_{\mathrm{pLDDT}} = -\frac{1}{N_G} \sum_{\alpha \in G} \mathrm{pLDDT}_\alpha

$G$ is the set of residues in the specified groups
$N_G$ is the number of residues in $G$
$\mathrm{pLDDT}_\alpha$ is the predicted local distance difference test score for residue $\alpha$

Parameters

FoldingOracle

required

The oracle to use for the energy term.

list[Residue] | None

required

Which residues to include in the calculation.

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 bagel as bg

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

# Maximize pLDDT confidence for a specific group of residues (e.g. a binder)
plddt_energy = bg.energies.PLDDTEnergy(
    oracle=esmfold,
    residues=residues_binder,
    weight=5.0,
)

# Add to a state alongside other energy terms
state = bg.State(
    chains=[binder_chain, target_chain],
    energy_terms=[plddt_energy],
    name="my_state",
)

ChemicalPotentialEnergy

OverallPLDDTEnergy

Overview

Core

Energies

Minimizers

Mutation

Oracles

Callbacks

Analysis

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example