/**
* Creates an instance of an AtomCache that is pointed to the a particular path in the file
* system.
*
* @param pdbFilePath a directory in the file system to use as a location to cache files.
* @param cachePath
*/
public AtomCache(String pdbFilePath, String cachePath) {
logger.debug(
"Initialising AtomCache with pdbFilePath={}, cachePath={}", pdbFilePath, cachePath);
if (!pdbFilePath.endsWith(FILE_SEPARATOR)) {
pdbFilePath += FILE_SEPARATOR;
}
// we are caching the binary files that contain the PDBs gzipped
// that is the most memory efficient way of caching...
// set the input stream provider to caching mode
System.setProperty(InputStreamProvider.CACHE_PROPERTY, "true");
setPath(pdbFilePath);
this.cachePath = cachePath;
fetchBehavior = FetchBehavior.DEFAULT;
obsoleteBehavior = ObsoleteBehavior.DEFAULT;
currentlyLoading.clear();
params = new FileParsingParameters();
setUseMmCif(true);
}
public static void main(String[] args) throws IOException {
String timeStamp =
new SimpleDateFormat("yyyyMMdd_HHmmss").format(Calendar.getInstance().getTime());
String uri = args[0] + "_" + timeStamp + ".seq";
Set<String> pdbIds = getAll();
StructureIO.setAtomCache(cache);
cache.setPath("/Users/Chris/Documents/RCSB/Data/Protein_chains/cache/");
long start = System.nanoTime();
toSequenceFile(uri, pdbIds, true);
long end = System.nanoTime();
System.out.println("Time: " + (end - start) / 1E9 + " sec.");
}