Definition
The pTM energy is the negated predicted Template Modelling score, so that minimizing energy corresponds to maximizing structural confidence.
EpTM=−pTM
- pTM is the predicted Template Modelling score returned by the folding oracle (range 0 to 1)
Parameters
The oracle to use for the energy term.
The weight of the energy term.
Optional name to append to the energy term name.
Methods
compute
Parameters
oracles_result
OraclesResultDict
required
Example
import bagel as bg
# Create the folding oracle
esmfold = bg.oracles.ESMFold()
# Create the energy term
ptm_energy = bg.energies.PTMEnergy(
oracle=esmfold,
weight=1.0,
)
# Add to a state
state = bg.State(
chains=[chain],
energy_terms=[ptm_energy],
name="my_state",
)
