public static void main(String[] args) {
String file = "/Users/ap3/tmp/4hhb.ce";
try {
BufferedReader in = new BufferedReader(new FileReader(file));
StringBuffer xml = new StringBuffer();
String str;
while ((str = in.readLine()) != null) {
xml.append(str);
}
in.close();
AFPChain[] afps = AFPChainXMLParser.parseMultiXML(xml.toString());
AFPChain afpChain = afps[0];
UserConfiguration config = WebStartMain.getWebStartConfig();
AtomCache cache = new AtomCache(config.getPdbFilePath(), config.isSplit());
Atom[] ca1 = cache.getAtoms(afpChain.getName1());
Atom[] ca2 = cache.getAtoms(afpChain.getName2());
AFPChainXMLParser.rebuildAFPChain(afpChain, ca1, ca2);
// StructureAlignment algorithm =
// StructureAlignmentFactory.getAlgorithm(afpChain.getAlgorithmName());
StructureAlignmentJmol jmol = StructureAlignmentDisplay.display(afpChain, ca1, ca2);
DisplayAFP.showAlignmentImage(afpChain, ca1, ca2, jmol);
} catch (Exception e) {
e.printStackTrace();
}
}
public void loadStructureFromCache() {
String pdbId = "4hhb";
String chainName = "4hhb.A";
String entityName = "4hhb:0";
// we can set a flag if the file should be cached in memory
// this will enhance IO massively if the same files have to be accessed over and over again.
// since this is a soft cache, no danger of memory leak
// this is actually not necessary to provide, since the default is "true" if the AtomCache is
// being used.
System.setProperty(InputStreamProvider.CACHE_PROPERTY, "true");
AtomCache cache = new AtomCache();
try {
System.out.println("======================");
Structure s = cache.getStructure(pdbId);
System.out.println("Full Structure:" + s);
Atom[] ca = cache.getAtoms(chainName);
System.out.println("got " + ca.length + " CA atoms");
Structure firstEntity = cache.getStructure(entityName);
System.out.println("First entity: " + firstEntity);
} catch (Exception e) {
e.printStackTrace();
}
}