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();
}
}
private static void demoAtomCache() {
AtomCache cache = new AtomCache();
FileParsingParameters params = cache.getFileParsingParams();
params.setLoadChemCompInfo(false);
params.setAlignSeqRes(true);
params.setHeaderOnly(false);
params.setParseCAOnly(false);
params.setParseSecStruc(false);
String[] pdbIDs = new String[] {"4hhb", "1cdg", "5pti", "1gav", "WRONGID"};
for (String pdbID : pdbIDs) {
try {
Structure s = cache.getStructure(pdbID);
if (s == null) {
System.out.println("could not find structure " + pdbID);
continue;
}
// do something with the structure
System.out.println(s);
} catch (Exception e) {
// something crazy happened...
System.err.println("Can't load structure " + pdbID + " reason: " + e.getMessage());
e.printStackTrace();
}
}
}
public void testFetchObsolete() throws IOException, StructureException {
cache.setUseMmCif(false); // TODO Remove after implementing obsolete mmcif fetching
cache.setAutoFetch(true);
cache.setFetchCurrent(false);
cache.setFetchFileEvenIfObsolete(true);
Structure s;
// OBSOLETE PDB; should throw an exception
s = cache.getStructure("1CMW");
assertEquals("Failed to get OBSOLETE file 1CMW.", "1CMW", s.getPDBCode());
s = cache.getStructure("1HHB");
assertEquals("Failed to get OBSOLETE file 1HHB.", "1HHB", s.getPDBCode());
System.err.println(
"Please ignore the previous four errors. They are expected for this ancient PDB.");
}
public void testFetchCurrent() throws IOException, StructureException {
cache.setUseMmCif(false); // TODO Remove after implementing obsolete mmcif fetching
cache.setAutoFetch(true);
cache.setFetchCurrent(true);
cache.setFetchFileEvenIfObsolete(false);
Structure s;
try {
// OBSOLETE PDB; should throw an exception
s = cache.getStructure("1CMW");
fail("1CMW has no current structure. Should have thrown an error");
} catch (IOException e) {
// expected
System.err.println("Please ignore previous exceptions. They are expected.");
} catch (StructureException e) {
// expected
System.err.println("Please ignore previous exceptions. They are expected.");
}
s = cache.getStructure("1HHB");
assertEquals("Failed to get the current ID for 1HHB.", "4HHB", s.getPDBCode());
}
public static void main(String[] args) {
try {
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);
AtomCache cache = new AtomCache();
cache.setFileParsingParams(params);
Structure s = cache.getStructure("4hhb");
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
if (g instanceof AminoAcid) {
AminoAcid aa = (AminoAcid) g;
Map<String, String> sec = aa.getSecStruc();
System.out.println(
c.getChainID()
+ " "
+ g.getResidueNumber()
+ " "
+ g.getPDBName()
+ " "
+ " "
+ sec);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
public void testAtomCacheNameParsing() throws IOException, StructureException {
String name1 = "4hhb";
Structure s = cache.getStructure(name1);
assertNotNull(s);
assertTrue(s.getChains().size() == 4);
String name2 = "4hhb.C";
String chainId2 = "C";
s = cache.getStructure(name2);
assertTrue(s.getChains().size() == 1);
Chain c = s.getChainByPDB(chainId2);
assertEquals(c.getChainID(), chainId2);
String name3 = "4hhb:1";
String chainId3 = "B";
s = cache.getStructure(name3);
assertNotNull(s);
assertTrue(s.getChains().size() == 1);
c = s.getChainByPDB(chainId3);
assertEquals(c.getChainID(), chainId3);
String name4 = "4hhb:A:10-20,B:10-20,C:10-20";
s = cache.getStructure(name4);
assertNotNull(s);
assertEquals(s.getChains().size(), 3);
c = s.getChainByPDB("B");
assertEquals(c.getAtomLength(), 11);
String name5 = "4hhb:(A:10-20,A:30-40)";
s = cache.getStructure(name5);
assertNotNull(s);
assertEquals(s.getChains().size(), 1);
c = s.getChainByPDB("A");
assertEquals(c.getAtomLength(), 22);
// This syntax also works, since the first paren is treated as a separator
String name6 = "4hhb(A:10-20,A:30-40)";
s = cache.getStructure(name6);
assertNotNull(s);
assertEquals(s.getChains().size(), 1);
c = s.getChainByPDB("A");
assertEquals(c.getAtomLength(), 22);
// Doesn't work, since no ':' in name
// This behavior is questionable; perhaps it should return 4hhb.C?
// It's not a very likely/important case, I'm just documenting behavior here.
String name7 = "4hhb(C)";
s = cache.getStructure(name7);
assertNull("Invalid substructure style: " + name7, s);
// Works since we detect a ':'
String name8 = "4hhb:(C)";
s = cache.getStructure(name8);
assertTrue(s.getChains().size() == 1);
c = s.getChainByPDB(chainId2);
assertEquals(c.getChainID(), chainId2);
}