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Definition

The overall pLDDT energy is the negated mean pLDDT over all residues in the structure. EpLDDT=−1N∑αpLDDTαE_{\mathrm{pLDDT}} = -\frac{1}{N} \sum_{\alpha} \mathrm{pLDDT}_\alpha
  • NN is the total number of residues in the structure
  • 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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weight
float
default:"1.0"
The weight of the energy term.
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name
str | None
default:"None"
Optional name to append to the energy term name.

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Example

import bagel as bg

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

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

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