private static SecStrucGroup[] initGroupArray(Structure s) {
List<SecStrucGroup> groupList = new ArrayList<SecStrucGroup>();
// GroupIterator iter = new GroupIterator(s);
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
// System.out.println(g);
// we can also calc secstruc if hetatom is a modified amino acid.
if (g.hasAminoAtoms()) {
SecStrucGroup sg = new SecStrucGroup();
sg.setPDBCode(g.getPDBCode());
sg.setPDBFlag(true);
try {
sg.setPDBName(g.getPDBName());
} catch (PDBParseException e) {
e.printStackTrace();
}
sg.setParent(g.getChain());
try {
sg.setN((Atom) g.getAtomByPDBname(" N ").clone());
sg.setCA((Atom) g.getAtomByPDBname(" CA ").clone());
sg.setC((Atom) g.getAtomByPDBname(" C ").clone());
sg.setO((Atom) g.getAtomByPDBname(" O ").clone());
sg.setOriginal(g);
// create H in calc_H
} catch (StructureException e) {
e.printStackTrace();
// one of these atoms is not found!
continue;
}
SecStrucState state = new SecStrucState();
Map m = sg.getProperties();
if (m == null) {
m = new HashMap();
sg.setProperties(m);
}
m.put("secstruc", state);
groupList.add(sg);
} else {
// System.out.println("not an amino group");
}
}
}
return (SecStrucGroup[]) groupList.toArray(new SecStrucGroup[groupList.size()]);
}
