"Merges" Residues in MDTraj Topology Object

fix_topology.py

def fix_topology(topology):
	
	new_top = topology.copy()

	residues = {}
	for chain in new_top.chains:
		#print chain
		for residue in chain.residues:
			resname = str(residue)
			if resname in residues.keys():
				residues[resname].append(residue)
			else:
				residues[resname] = [residue]

	for resname in residues.keys():
		fragments = residues[resname]
		if len(fragments) > 1:
			main_fragment = fragments[0]
			new_atom_list = []
			new_atom_list += main_fragment._atoms
			for i in range(1,len(fragments)):
				fragment = fragments[i]
				for atom in fragment.atoms:
					atom.residue = main_fragment
				new_atom_list += fragment._atoms
				fragment._atoms = []
				fragment.chain = main_fragment.chain
			main_fragment._atoms = new_atom_list

	return new_top