private void addAtomType(String line) {
List<String> split = reworkLine(line);
// TODO replace when atom atom translation dictionary exists --> special handling of oplsaa FF
// produces errors if oplsaa is used
if (split.size() == 8) {
String s = split.get(0);
String s1 = split.get(1);
split.remove(0);
split.remove(0);
split.add(0, s + " " + s1);
}
if (split.size() == 7) {
List<AtomType> atomTypes = structure.getAtomTypes();
AtomTypeImpl at = new AtomTypeImpl();
at.setName(split.get(0));
at.setNum(split.get(1));
at.setC1(new BigDecimal(split.get(2)));
at.setC2(new BigDecimal(split.get(3)));
at.setParticleType(split.get(4));
at.setC3(new BigDecimal(split.get(5)));
at.setC4(new BigDecimal(split.get(6)));
atomTypes.add(at);
} else {
ch.printErrorln(String.format("some ATOMTYPES values are lost! --> %s", line));
}
}
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);
}
