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;
}
public void setIsPDB() {
atomSetCollection.setGlobalBoolean(AtomSetCollection.GLOBAL_ISPDB);
atomSetCollection.setAtomSetAuxiliaryInfo("isPDB", Boolean.TRUE);
if (htParams.get("pdbNoHydrogens") != null)
atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
"pdbNoHydrogens", htParams.get("pdbNoHydrogens"));
}
@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());
}
protected void newAtomSet(String name) {
if (atomSetCollection.getCurrentAtomSetIndex() >= 0) {
atomSetCollection.newAtomSet();
atomSetCollection.setCollectionName(
"<collection of " + (atomSetCollection.getCurrentAtomSetIndex() + 1) + " models>");
} else {
atomSetCollection.setCollectionName(name);
}
atomSetCollection.setAtomSetAuxiliaryInfo(
"name", name, Math.max(0, atomSetCollection.getCurrentAtomSetIndex()));
}
protected void addSites(Map<String, Map<String, Object>> htSites) {
atomSetCollection.setAtomSetAuxiliaryInfo("pdbSites", htSites);
String sites = "";
for (Map.Entry<String, Map<String, Object>> entry : htSites.entrySet()) {
String name = entry.getKey();
Map<String, Object> htSite = entry.getValue();
char ch;
for (int i = name.length(); --i >= 0; )
if (!Character.isLetterOrDigit(ch = name.charAt(i)) && ch != '\'')
name = name.substring(0, i) + "_" + name.substring(i + 1);
// String seqNum = (String) htSite.get("seqNum");
String groups = (String) htSite.get("groups");
if (groups.length() == 0) continue;
addSiteScript("@site_" + name + " " + groups);
// addJmolScript("@" + seqNum + " " + groups);
addSiteScript("site_" + name + " = \"" + groups + "\".split(\",\")");
sites += (sites == "" ? "" : ",") + "site_" + name;
}
addSiteScript("site_list = \"" + sites + "\".split(\",\")");
}
