name = "Cytochrome C"

conf = PDBConfiguration('2YCC.pdb')

# construct the peptide chains
chains = conf.createPeptideChains()

# construct the isolated heme group
heme = conf.createGroups({'HEM': 'bound_heme'})[0]

# convert cysteins to cystines
chains[0][18]._makeCystine()
chains[0][21]._makeCystine()

# attach the heme group
chains[0].addGroup(heme, [(heme.CAB, chains[0][18].sidechain.S_gamma),
                          (heme.CAC, chains[0][21].sidechain.S_gamma)])

# assign positions to undefined hydrogen atoms
chains[0].findHydrogenPositions()

del conf
