public void setCalculationValues() {
atom tempa;
int temp;
int atom1 = myAtoms[0].getMM3TypeNum();
int atom2 = myAtoms[1].getMM3TypeNum();
int atom3 = myAtoms[2].getMM3TypeNum();
int atom4 = myAtoms[3].getMM3TypeNum();
if (atom1 > atom2) {
temp = atom1;
atom1 = atom2;
atom2 = temp;
tempa = myAtoms[0];
myAtoms[0] = myAtoms[1];
myAtoms[1] = tempa;
}
if (atom3 > atom4) {
temp = atom3;
atom3 = atom4;
atom4 = temp;
tempa = myAtoms[2];
myAtoms[2] = myAtoms[3];
myAtoms[3] = tempa;
}
try {
AtomDataFile dataFile =
new AtomDataFile(newNanocad.txtDir + newNanocad.fileSeparator + "mm3estaticdata.txt");
// AtomDataFile dataFile= new AtomDataFile("mm3estaticdata.txt");
if (dataFile.findData(atom1, atom2, 0, 1)) {
firstCharge = dataFile.parseDouble(2);
firstDistribution = dataFile.parseDouble(3);
} else {
// System.out.println("No data for " + atom1 + " " + atom2 + " dipole.");
firstCharge = 0.0;
firstDistribution = 0.0;
}
if (dataFile.findData(atom3, atom4, 0, 1)) {
secondCharge = dataFile.parseDouble(2);
secondDistribution = dataFile.parseDouble(3);
} else {
// System.out.println("No data for " + atom3 + " " + atom4 + " dipole.");
secondCharge = 0.0;
secondDistribution = 0.0;
}
} catch (java.io.IOException e) {
System.err.println("Dipole data lookup error");
e.printStackTrace();
}
}
public void setCalculationValues() {
int atom1 = myAtoms[0].getMM3TypeNum();
int atom2 = myAtoms[1].getMM3TypeNum();
int atom3 = myAtoms[2].getMM3TypeNum();
if (atom1 < atom3 || atom1 < 1 || atom2 < 1 || atom3 < 1) {
kBondAngle = 0.0;
return;
}
try {
AtomDataFile dataFile =
new AtomDataFile(newNanocad.txtDir + newNanocad.fileSeparator + "mm3strbenddata.txt");
// AtomDataFile dataFile = new AtomDataFile("mm3strbenddata.txt");
if (dataFile.findData(atom1, 0)) kBondAngle = dataFile.parseDouble(1);
else {
kBondAngle = 0.0;
return;
}
dataFile = new AtomDataFile(newNanocad.txtDir + newNanocad.fileSeparator + "mm3adata.txt");
// dataFile = new AtomDataFile("mm3adata.txt");
if (dataFile.findData(atom2, atom1, atom3, 1, 0, 2))
idealAngle = convert * dataFile.parseDouble(4);
else {
idealAngle = 0.0;
return;
}
dataFile = new AtomDataFile(newNanocad.txtDir + newNanocad.fileSeparator + "mm3ldata.txt");
// dataFile = new AtomDataFile("mm3ldata.txt");
if (dataFile.findData(Math.min(atom1, atom2), Math.max(atom1, atom2), 0, 1))
idealLength1 = dataFile.parseDouble(3);
else {
idealLength1 = 0.0;
return;
}
if (dataFile.findData(Math.min(atom2, atom3), Math.max(atom2, atom3), 0, 1))
idealLength2 = dataFile.parseDouble(3);
else {
idealLength2 = 0.0;
return;
}
} catch (java.io.IOException e) {
System.err.println("Stretch-bend data lookup error");
e.printStackTrace();
}
}