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Definition

The pLDDT energy is the negated mean pLDDT over the specified residue groups. EpLDDT=−1NG∑α∈GpLDDTαE_{\mathrm{pLDDT}} = -\frac{1}{N_G} \sum_{\alpha \in G} \mathrm{pLDDT}_\alpha
  • GG is the set of residues in the specified groups
  • NGN_G is the number of residues in GG
  • pLDDTα\mathrm{pLDDT}_\alpha is the predicted local distance difference test score for residue α\alpha

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Parameters

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oracle
FoldingOracle
required
The oracle to use for the energy term.
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residues
list[Residue] | None
required
Which residues to include in the calculation.
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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()

# 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",
)