peppr.find_clashes#
- peppr.find_clashes(atoms: AtomArray, vdw_scaling: float = 0.65) ndarray[tuple[int, ...], dtype[int64]][source]#
Find atom clashes in the given structure.
A clash is defined as a pair of non-bonded atoms whose distance is smaller than the sum of their Van-der-Waals radii (multiplied by a scaling factor).
- Parameters:
- atomsAtomArray
The structure to find the clashes in.
- vdw_scalingfloat, optional
The scaling factor for the Van-der-Waals radii.
- Returns:
- ndarray, shape=(n,2), dtype=int
The array of clashes. Each element represents a pair of atom indices that are in clash.