- String atomSpecAlphaOnly = getAtomSpec(spec, true);
- String refSpecAlphaOnly = getAtomSpec(ref, true);
- cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
+ String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
+ String refSpecAlphaOnly = getAtomSpec(ref, backbone);
+ cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+ .append(refSpecAlphaOnly);