private void addAtom(String line, Section actualSection) {
if (actualSection != null) {
List<String> split = reworkLine(line);
List<Atom> atoms = actualSection.getAtoms();
AtomImpl a = new AtomImpl();
int length = split.size();
if (length >= 7) {
a.setNr(Integer.parseInt(split.get(0)));
a.setType(split.get(1));
a.setResNr(Integer.parseInt(split.get(2)));
a.setResName(split.get(3));
a.setAtomName(split.get(4));
a.setChargeGroupNr(Integer.parseInt(split.get(5)));
a.setC1(new BigDecimal(split.get(6)));
}
if (length >= 8) {
a.setC2(new BigDecimal(split.get(7)));
}
if (length == 11) {
a.setTypeB(split.get(8));
a.setC3(new BigDecimal(split.get(9)));
a.setC4(new BigDecimal(split.get(10)));
}
if (length < 7 || length > 11) {
ch.printErrorln(String.format("some ATOMS values are lost! --> %s", line));
} else {
atoms.add(a);
}
}
}
private void removeUnnecessaryData() {
Set<AtomType> clear = Sets.newHashSet();
List<Atom> atoms = Lists.newArrayList();
List<AtomType> atomTypes = structure.getAtomTypes();
for (Section section : structure.getSections()) {
if (section.getSectionType().equals(SectionType.STRUCTUREDATA)) {
atoms.addAll(section.getAtoms());
}
}
for (AtomType atomType : atomTypes) {
AtomType delete = atomType;
for (Atom atom : atoms) {
if (atomType.getName().contains(atom.getType())) {
delete = null;
}
}
if (delete != null) {
clear.add(delete);
}
}
clear.forEach(atomTypes::remove);
}