Member denoptim.graph.DGraph.getBondingAPIndex (Vertex srcVert, int dapidx, Vertex dstVert): this depends on vertedID rather than reference
Member denoptim.utils.GraphConversionTool.getGraphFromString (String strGraph, boolean useMolInfo, FragmentSpace fragSpace): this method reads the old string representation, which cannot represent all possible states of a Template. Use JSON string instead.