peppr.BondLengthViolations

class peppr.BondLengthViolations(tolerance: float = 0.1, reference_bonds: Dict[Tuple[str, str], ndarray] | None = None)

Check for unusual bond lengths in the structure by comparing against reference values. Returns the percentage of bonds that are within acceptable ranges.

Parameters:

tolerancefloat, optional

The tolerance in Angstroms for acceptable deviation from ideal bond lengths. Default is 0.1 Angstroms.

reference_bondsdict, optional

Dictionary mapping atom type pairs to ideal bond lengths. If not provided, uses a default set of common bond lengths.

__init__(tolerance: float = 0.1, reference_bonds: Dict[Tuple[str, str], ndarray] | None = None) → None

Methods

__init__([tolerance, reference_bonds])
evaluate(reference, pose)	Calculate the percentage of bonds that are outside acceptable ranges.
smaller_is_better()	Whether as smaller value of this metric is considered a better prediction.

Attributes

name
thresholds