qreal PosteRazorCore::convertCmToDistance(qreal cm) const
{
return Types::convertBetweenUnitsOfLength(cm, Types::UnitOfLengthCentimeter, unitOfLength());
}
bool File::Mol::generate()
{
int atomTypes = 0;
float x, y, z;
clear();
addString(basisType_);
addString(basisSet_);
addString(comment_);
QList<Chemistry::Atom*> atomsList;
for (quint16 i = 0; i < molecule().atomsCount(); ++i)
{
atomsList << &molecule().atom(i);
}
while (atomsList.count() > 0)
{
QList<Chemistry::Atom*> atomsOfTheSameTypeList;
atomsOfTheSameTypeList << atomsList.takeFirst();
quint8 charge = atomsOfTheSameTypeList[0]->atomicNumber();
int n = atomsList.count();
int i = 0;
while (i < n)
{
if (atomsList[i]->atomicNumber() == charge)
{
atomsOfTheSameTypeList << atomsList.takeAt(i);
n--;
}
else
{
i++;
}
}
QString atomsOfTheSameTypeHeader = QString("Charge=%1 Atoms=%2").arg(
charge).arg(atomsOfTheSameTypeList.count());
if (basisType_ == "ATOMBASIS")
atomsOfTheSameTypeHeader += QString(" Basis=%1").arg(
hashBasisSets_[charge]);
addString(atomsOfTheSameTypeHeader);
for (quint16 i = 0; i < atomsOfTheSameTypeList.count(); ++i)
{
x = atomsOfTheSameTypeList[i]->centre().x();
y = atomsOfTheSameTypeList[i]->centre().y();
z = atomsOfTheSameTypeList[i]->centre().z();
if (unitOfLength() == UnitOfLengthBohr)
{
x = x / bohrsToAngstroms;
y = y / bohrsToAngstroms;
z = z / bohrsToAngstroms;
}
QString temp = QString("%1%2\t%3%4%5").arg(
atomsOfTheSameTypeList[i]->symbol()).arg(
i + 1).arg(
x, 12, 'f', 6).arg(
y, 12, 'f', 6).arg(
z, 12, 'f', 6);
if (atomsOfTheSameTypeList[i]->isotope() != 0)
temp += QString("\tIsotope=%1").arg(atomsOfTheSameTypeList[i]->isotope());
addString(temp);
}
atomTypes++;
}
setAtomTypes(atomTypes);
QString generalString(QString("Atomtypes=%1").arg(atomTypes));
if (unitOfLength() == UnitOfLengthAngstrom)
generalString.append(" Angstrom");
if (molecule().charge() != 0)
generalString.append(QString(" Charge=%1").arg(molecule().charge()));
if (gaussiansType() == GaussiansTypeCartesian)
generalString.append(" Cartesian");
insertString(generalStringIndex_ - 1, generalString);
return true;
}
qreal PosteRazorCore::convertDistanceToCm(qreal distance) const
{
return Types::convertBetweenUnitsOfLength(distance, unitOfLength(), Types::UnitOfLengthCentimeter);
}
void File::Mol::parseAtoms()
{
bool ok;
int i = generalStringIndex_;
QRegExp regExp;
regExp.setPattern("Charge=((\\d)(\\.\\d+)?)\\s+Atoms=(\\d+)(\\s+Basis=(.+)$)?");
for (int a = 0; a < atomTypes(); a++)
{
i++;
if (regExp.indexIn(string(i)) != -1)
{
int protons = regExp.cap(2).toInt(&ok);
int count = regExp.cap(4).toInt(&ok);
if (regExp.cap(5) != "")
{
hashBasisSets_[protons] = regExp.cap(6);
}
QRegExp regExpAtom("(\\w{1,4})\\s+(-?\\d?\\.\\d+)\\s+(-?\\d?\\.\\d+)\\s+(-?\\d?\\.\\d+)(\\s+Isotope=(\\d+))?");
for (int j = 0; j < count; j++)
{
i++;
quint8 isotope = 0;
float x, y, z;
if (regExpAtom.indexIn(string(i)) != -1)
{
x = regExpAtom.cap(2).toFloat(&ok);
if (!ok)
addParseError(File::ParseError(i, "Wrong x coordinate."));
y = regExpAtom.cap(3).toFloat(&ok);
if (!ok)
addParseError(File::ParseError(i, "Wrong y coordinate."));
z = regExpAtom.cap(4).toFloat(&ok);
if (!ok)
addParseError(File::ParseError(i, "Wrong z coordinate."));
if (unitOfLength() == UnitOfLengthBohr)
{
x = x * bohrsToAngstroms;
y = y * bohrsToAngstroms;
z = z * bohrsToAngstroms;
}
if (regExpAtom.cap(5) != "")
{
isotope = regExpAtom.cap(6).toInt(&ok);
if (!ok)
addParseError(File::ParseError(i, "Wrong isotope."));
}
molecule().newAtom(protons, isotope, Eigen::Vector3f(x, y, z));
}
}
}
}
}
