Module salt_bridge

Find salt-bridge interactions.

Examples

Find all salt bridge interactions within a protein:

   st = StructureReader("protein.maegz").next()
   for (atom1, atom2) in SaltBridgeFinder.find(st):
       print "Salt bridge between atoms %i and %i" % (atom1, atom2)

Find all salt bridges within a single protein chain:

   st = StructureReader("protein.maegz").next()
   atoms = st.chain["C"].getAtomList()
   for (atom1, atom2) in SaltBridgeFinder.find(st, atoms):
       print "Salt bridge between atoms %i and %i" % (atom1, atom2)

Find all salt bridges between a protein and a ligand:

   reader = StructureReader("protein_and_ligand.maegz")
   prot = reader.next()
   lig = reader.next()
   for (atom1, atom2) in SaltBridgeFinder.find(prot, struc2=lig):
       print "Salt bridge between atoms %i and %i" % (atom1, atom2)