SurfaceAreaEnergy

Definition

The SASA energy is the mean solvent-accessible surface area of atoms in the group, normalized by a maximum SASA value.

E_{\mathrm{SASA}} = \frac{1}{N_{\mathrm{atoms},G}} \sum_{a \in G} \frac{\mathrm{SASA}_a}{\mathrm{SASA}_{\max}}

$\mathrm{SASA}_a$ is the solvent-accessible surface area of atom $a$
$\mathrm{SASA}_{\max}$ is a normalization constant (by default, the full surface area of a sulfur atom)
$N_{\mathrm{atoms},G}$ is the number of atoms in the group $G$

Parameters

FoldingOracle

required

The oracle to use for the energy term.

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.

list[Residue] | None

default:"None"

Which residues to include in the calculation. Considers all residues by default.

float | None

default:"None"

The VdW-radius of the solvent molecules used in the SASA calculation. Default is the water VdW-radius.

float | None

default:"None"

The maximum SASA value used if normalization is enabled. Default is the full surface area of a Sulfur atom.

float

default:"1.0"

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()

# Minimize exposed surface area for a specific group of residues
surface_energy = bg.energies.SurfaceAreaEnergy(
    oracle=esmfold,
    residues=residues,
    weight=1.0,
)

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

Overview

Core

Energies

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Mutation

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Callbacks

Analysis

SurfaceAreaEnergy

Definition

Parameters

Methods

compute

Example

​Definition

​Parameters

​Methods

​compute

​Example

Definition

Parameters

Methods

compute

Example