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 outside 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.

evaluate(reference: AtomArray, pose: AtomArray) → float

Calculate the percentage of bonds that are outside acceptable ranges.

Parameters:

referenceAtomArray

Not used in this metric as we compare against ideal bond lengths.

poseAtomArray

The structure to evaluate.

Returns:

float

Percentage of bonds outside acceptable ranges (0.0 to 1.0).

smaller_is_better() → bool

Whether as smaller value of this metric is considered a better prediction.

ABSTRACT: Must be overridden by subclasses.

Returns:

bool

If true, a smaller value of this metric is considered a better prediction. Otherwise, a larger value is considered a better prediction.