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Definition

The globular energy is the standard deviation of backbone atom distances from the group centroid, promoting spherical compactness. Eglob=std(∥xa−c∥)a∈GE_{\mathrm{glob}} = \mathrm{std}\left(\| \mathbf{x}_a - \mathbf{c} \|\right)_{a \in G}
  • xa\mathbf{x}_a are backbone atom positions
  • c\mathbf{c} is the centroid of the backbone atoms in the group
  • std\mathrm{std} is the standard deviation over all backbone atoms in the group GG

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Parameters

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oracle
Oracle
required
The oracle to use for the energy term.
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residues
list[Residue] | None
default:"None"
Which residues to include in the calculation. Considers all residues by default.
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inheritable
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.
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weight
float
default:"1.0"
The weight of the energy term.
​
name
str | None
default:"None"
Optional name to append to the energy term name.

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Methods

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compute

Parameters
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oracles_result
OraclesResultDict
required

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Example

import bagel as bg

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

# Drive the structure toward a compact, spherical shape
globular = bg.energies.GlobularEnergy(
    oracle=esmfold,
    residues=residues,
    weight=1.0,
)

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