private Object finish() {
String s = (String) htParams.get("loadState");
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("loadState", s == null ? "" : s);
s = (String) htParams.get("smilesString");
if (s != null) atomSetCollection.setAtomSetCollectionAuxiliaryInfo("smilesString", s);
if (!htParams.containsKey("templateAtomCount"))
htParams.put("templateAtomCount", Integer.valueOf(atomSetCollection.getAtomCount()));
if (htParams.containsKey("bsFilter"))
htParams.put(
"filteredAtomCount",
Integer.valueOf(BitSetUtil.cardinalityOf((BitSet) htParams.get("bsFilter"))));
if (!calculationType.equals("?"))
atomSetCollection.setAtomSetCollectionAuxiliaryInfo("calculationType", calculationType);
String name = atomSetCollection.getFileTypeName();
String fileType = name;
if (fileType.indexOf("(") >= 0) fileType = fileType.substring(0, fileType.indexOf("("));
for (int i = atomSetCollection.getAtomSetCount(); --i >= 0; ) {
atomSetCollection.setAtomSetAuxiliaryInfo("fileName", filePath, i);
atomSetCollection.setAtomSetAuxiliaryInfo("fileType", fileType, i);
}
atomSetCollection.freeze(reverseModels);
if (atomSetCollection.errorMessage != null)
return atomSetCollection.errorMessage + "\nfor file " + filePath + "\ntype " + name;
if ((atomSetCollection.bsAtoms == null
? atomSetCollection.getAtomCount()
: atomSetCollection.bsAtoms.cardinality())
== 0
&& fileType.indexOf("DataOnly") < 0)
return "No atoms found\nfor file " + filePath + "\ntype " + name;
return atomSetCollection;
}
@SuppressWarnings("unchecked")
public void setMOData(Map<String, Object> moData) {
atomSetCollection.setAtomSetAuxiliaryInfo("moData", moData);
if (moData == null) return;
List<Map<String, Object>> orbitals = (List<Map<String, Object>>) moData.get("mos");
if (orbitals != null)
Logger.info(
orbitals.size()
+ " molecular orbitals read in model "
+ atomSetCollection.getAtomSetCount());
}
