text: #!/usr/bin/env python
  
  import sys
  
  from openeye import oechem
  
  
  class BumpCheck:
      def __init__(self, prot_mol, cutoff=2.0):
          self.near_nbr = oechem.OENearestNbrs(prot_mol, cutoff)
          self.cutoff = cutoff
  
      def count(self, lig_mol):
          bump_count = 0
          for nb in self.near_nbr.GetNbrs(lig_mol):
              if (not nb.GetBgn().IsHydrogen()) and (not nb.GetEnd().IsHydrogen()) and nb.GetDist() <= self.cutoff:
                  bump_count += 1
          return bump_count
  
  
  if __name__ == "__main__":
      PROT = sys.argv[1]
      LIG = sys.argv[2]
      prot = oechem.OEMol()
      oechem.OEReadPDBFile(oechem.oemolistream(PROT), prot)
  
      bump_check = BumpCheck(prot)
      for lig_mol in oechem.oemolistream(LIG).GetOEGraphMols():
          print(bump_check.count(lig_mol))
  