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 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 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();
}
}