private void checkRange(Structure s, String range) {
GroupIterator iter = new GroupIterator(s);
Group g1 = iter.next();
Group g2 = null;
while (iter.hasNext()) {
g2 = iter.next();
}
assertNotNull(g1);
assertNotNull(g2);
String chainId = g1.getChain().getChainID();
String rangeTest =
chainId + ":" + g1.getResidueNumber().toString() + "-" + g2.getResidueNumber().toString();
assertEquals("The expected range and the detected range don;t match!", rangeTest, range);
}
/**
* Calculates ASA for all atoms and return them as a GroupAsa array (one element per residue in
* structure) containing ASAs per residue and per atom. The sorting of Groups in returned array is
* as specified by {@link org.biojava.bio.structure.ResidueNumber}
*
* @return
*/
public GroupAsa[] getGroupAsas() {
TreeMap<ResidueNumber, GroupAsa> asas = new TreeMap<ResidueNumber, GroupAsa>();
double[] asasPerAtom = calculateAsas();
for (int i = 0; i < atoms.length; i++) {
Group g = atoms[i].getGroup();
if (!asas.containsKey(g.getResidueNumber())) {
GroupAsa groupAsa = new GroupAsa(g);
groupAsa.addAtomAsaU(asasPerAtom[i]);
asas.put(g.getResidueNumber(), groupAsa);
} else {
GroupAsa groupAsa = asas.get(g.getResidueNumber());
groupAsa.addAtomAsaU(asasPerAtom[i]);
}
}
return (GroupAsa[]) asas.values().toArray(new GroupAsa[asas.size()]);
}
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();
}
}
