compute_clashes

static StructureSimilarity.compute_clashes(pdb, chain1='A', chain2='B')[source]

Compute number of atomic clashes.

Note

Clashes were defined as contacts between nonhydrogen atoms separated by <3.0Å. Structural models where number of clashes was 2 SD away from the average are excluded for assessment in CAPRI. see ref: https://doi.org/10.1002/prot.10393

Parameters:

  • pdb (file) – pdb file or data

  • chain1 (str) – first chain ID. Defaults to ‘A’.

  • chain2 (str) – second chain ID. Defaults to ‘B’.

Returns:

int – number of atomic clashes.