public void basicLoad() {
try {
PDBFileReader reader = new PDBFileReader();
// the path to the local PDB installation
reader.setPath("/tmp");
// are all files in one directory, or are the files split,
// as on the PDB ftp servers?
reader.setPdbDirectorySplit(true);
// should a missing PDB id be fetched automatically from the FTP servers?
reader.setAutoFetch(true);
// configure the parameters of file parsing
FileParsingParameters params = new FileParsingParameters();
// should the ATOM and SEQRES residues be aligned when creating the internal data model?
params.setAlignSeqRes(true);
// should secondary structure get parsed from the file
params.setParseSecStruc(false);
reader.setFileParsingParameters(params);
Structure structure = reader.getStructureById("4hhb");
System.out.println(structure);
Chain c = structure.getChainByPDB("C");
System.out.print(c);
System.out.println(c.getHeader());
} catch (Exception e) {
e.printStackTrace();
}
}
private void runSCOPTests() {
ScopDatabase scop = ScopFactory.getSCOP();
List<ScopDomain> domains = scop.getDomainsForPDB("4HHB");
assertTrue(domains.size() == 4);
// test case sensitivity;
List<ScopDomain> domains2 = scop.getDomainsForPDB("4hhb");
assertTrue(domains2.size() == domains.size());
// System.out.println(domains);
String scop1m02 =
"d1m02a_ 1m02 A: k.36.1.1 74353 cl=58788,cf=75796,sf=75797,fa=75798,dm=75799,sp=75800,px=74353";
List<ScopDomain> domains1m02 = scop.getDomainsForPDB("1m02");
assertTrue(domains1m02.size() == 1);
ScopDomain d1 = domains1m02.get(0);
assertNotNull(d1);
assertEquals(
"The toString() methods for ScopDomains don't match the scop display",
d1.toString(),
scop1m02);
List<ScopDomain> domains1cdg = scop.getDomainsForPDB("1CDG");
assertTrue(domains1cdg.size() == 4);
ScopDomain d2 = domains1cdg.get(0);
AtomCache cache = new AtomCache();
try {
Structure s = cache.getStructureForDomain(d2);
// checkRange(s,"A:496-581");
// now with ligands!
checkRange(s, "A:496-692");
} catch (Exception e) {
e.printStackTrace();
fail(e.getMessage());
}
// check a domain with multiple ranges
List<ScopDomain> domains1xzp = scop.getDomainsForPDB("1xzp");
assertTrue(domains1xzp.size() == 4);
try {
Structure s = cache.getStructureForDomain(domains1xzp.get(0));
Chain a = s.getChainByPDB("A");
// now with ligands...
assertEquals(a.getAtomGroups().size(), 176);
} catch (Exception e) {
e.printStackTrace();
fail(e.getMessage());
}
// check insertion codes
List<ScopDomain> domains2bq6 = scop.getDomainsForPDB("2bq6");
assertTrue(domains2bq6.size() == 2);
ScopDomain target = scop.getDomainByScopID("d2bq6a1");
assertNotNull(target);
try {
Structure s = cache.getStructureForDomain(target);
Chain a = s.getChainByPDB("A");
assertEquals(a.getAtomGroups().size(), 52);
checkRange(s, "A:1A-49");
} catch (Exception e) {
e.printStackTrace();
fail(e.getMessage());
}
}