private void loadVdParams(List<String> atoms) {
vdParams = new HashMap<String, List<Double>>();
for (String s : atoms) {
String[] t = s.split(" +");
if (t.length > 6 && !t[0].contains(";")) {
String key = t[0];
// System.out.println(key);
List<Double> value = new ArrayList<Double>();
value.add(Double.parseDouble(t[5]));
value.add(Double.parseDouble(t[6]));
// System.out.println(value);
vdParams.put(key, value);
}
}
}
private void loadBondParams(List<String> bonds) {
bondParams = new HashMap<List<String>, List<Double>>();
for (String s : bonds) {
String[] t = s.split(" +");
if (t.length > 5 && !t[0].contains(";")) {
List<String> key = new ArrayList<String>();
key.add(t[1]);
key.add(t[2]);
// System.out.println(key);
List<Double> value = new ArrayList<Double>();
value.add(Double.parseDouble(t[4]));
value.add(Double.parseDouble(t[5]));
// System.out.println(value);
bondParams.put(key, value);
}
}
}
private void loadImproperDihedralParams(List<String> dihedrals) {
improperDihedralParams = new HashMap<List<String>, List<Double>>();
for (String s : dihedrals) {
String[] t = s.split(" +");
if (t.length > 6 && !t[0].contains(";")) {
List<String> key = new ArrayList<String>();
key.add(t[0]);
key.add(t[1]);
key.add(t[2]);
key.add(t[3]);
// System.out.println(key);
List<Double> value = new ArrayList<Double>();
value.add(Double.parseDouble(t[5]));
value.add(Double.parseDouble(t[6]));
// System.out.println(value);
improperDihedralParams.put(key, value);
}
}
}
public List<Double> getProperDihedralParams(List<String> atoms) {
List<String> key = new ArrayList<String>(atoms);
List<String> key2 = new ArrayList<String>(atoms);
Collections.reverse(key2);
List<Double> value = properDihedralParams.get(key);
if (value == null) {
value = properDihedralParams.get(key2);
}
if (value == null) {
key.set(0, "X");
key.set(3, "X");
value = properDihedralParams.get(key);
}
if (value == null) {
key2.set(0, "X");
key2.set(3, "X");
value = properDihedralParams.get(key2);
}
return value;
}
private void loadNonBondedParams() {
String fileName = "res/amber03/ffnonbonded.itp";
List<String> fileAsList = FileReader.readFile(fileName);
int atomtypes = fileAsList.indexOf("[ atomtypes ]");
loadVdParams(fileAsList.subList(atomtypes + 1, fileAsList.size()));
}
private void loadBondedParams() {
String fileName = "res/amber03/ffbonded.itp";
List<String> fileAsList = FileReader.readFile(fileName);
int bondtypes = fileAsList.indexOf("[ bondtypes ]");
int constrainttypes = fileAsList.indexOf("[ constrainttypes ]");
int angletypes = fileAsList.indexOf("[ angletypes ]");
int improperDihedral = fileAsList.indexOf("[ dihedraltypes ]");
int properDihedral = fileAsList.lastIndexOf("[ dihedraltypes ]");
// System.out.println(bondtypes);
// System.out.println(constrainttypes);
// System.out.println(angletypes);
// System.out.println(improperDihedral);
// System.out.println(properDihedral);
loadBondParams(fileAsList.subList(bondtypes + 1, constrainttypes));
loadAngleParams(fileAsList.subList(angletypes + 1, improperDihedral));
loadImproperDihedralParams(fileAsList.subList(improperDihedral + 1, properDihedral));
loadProperDihedralParams(fileAsList.subList(properDihedral + 1, fileAsList.size()));
}