ChemicalPotentialEnergy

Definition

The chemical potential energy penalizes deviations from a target number of residues.

E_{\mathrm{chem}} = \mu \left| N_{\mathrm{total}} - N_{\mathrm{target}} \right|^{p}

$\mu$ is the chemical potential
$N_{\mathrm{total}}$ is the current total number of residues across all chains
$N_{\mathrm{target}}$ is the target residue count
$p$ is the exponent (default 1)

Parameters

Oracle

required

The oracle to use for the energy term.

float

default:"1.0"

The power to raise the number of residues to.

int

default:"0"

The target size of the system.

float

default:"1.0"

The chemical potential of the system.

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 any oracle (ChemicalPotentialEnergy only depends on residue count)
esmfold = bg.oracles.ESMFold()

# Penalize deviations from a target chain length of 50 residues
chem_potential = bg.energies.ChemicalPotentialEnergy(
    oracle=esmfold,
    target_size=50,
    chemical_potential=1.0,
    weight=1.0,
)

# Add to a state (typically combined with GrandCanonical mutation)
state = bg.State(
    chains=[chain],
    energy_terms=[chem_potential],
    name="my_state",
)

PTMEnergy

PLDDTEnergy

Overview

Core

Energies

Minimizers

Mutation

Oracles

Callbacks

Analysis

ChemicalPotentialEnergy

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example