- // TODO: consider bailing if nmatched less than 4 because superposition not
- // well defined.
- // TODO: refactor superposable position search (above) from jmol selection
- // construction (below)
- for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
- {
- if (pdbfnum == refStructure)
- {
- continue;
- }
- command.append("echo ");
- command.append("\"Superposing (");
- command.append(chainNames[pdbfnum]);
- command.append(") against reference (");
- command.append(chainNames[refStructure]);
- command.append(")\";\ncompare ");
- command.append("{");
- command.append(1 + pdbfnum);
- command.append(".1} {");
- command.append(1 + refStructure);
- command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
-
- // form the matched pair strings
- String sep = "";
- for (int s = 0; s < 2; s++)
+ if (selectioncom.length() > 0)
+ {// finally, mark all regions that were superposed.
+ if (selectioncom.substring(selectioncom.length() - 1).equals("|"))