PTMEnergy

Definition

The pTM energy is the negated predicted Template Modelling score, so that minimizing energy corresponds to maximizing structural confidence.

E_{\mathrm{pTM}} = -\mathrm{pTM}

$\mathrm{pTM}$ is the predicted Template Modelling score returned by the folding oracle (range 0 to 1)

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.

Methods

compute

Parameters

OraclesResultDict

required

Example

import bagel as bg

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

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

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

EnergyTerm

ChemicalPotentialEnergy

Overview

Core

Energies

Minimizers

Mutation

Oracles

Callbacks

Analysis

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example