/** @short Find a message body part through its slash-separated string path */
Imap::Mailbox::TreeItemPart *MsgPartNetAccessManager::pathToPart(const QModelIndex &message, const QString &path)
{
QStringList items = path.split('/', QString::SkipEmptyParts);
const Mailbox::Model *model = 0;
Imap::Mailbox::TreeItem *target = Mailbox::Model::realTreeItem(message, &model);
Q_ASSERT(model);
Q_ASSERT(target);
bool ok = ! items.isEmpty(); // if it's empty, it's a bogous URL
for (QStringList::const_iterator it = items.constBegin(); it != items.constEnd(); ++it) {
uint offset = it->toUInt(&ok);
if (!ok) {
// special case, we have to dive into that funny, irregular special parts now
if (*it == QLatin1String("HEADER"))
target = target->specialColumnPtr(0, Imap::Mailbox::TreeItem::OFFSET_HEADER);
else if (*it == QLatin1String("TEXT"))
target = target->specialColumnPtr(0, Imap::Mailbox::TreeItem::OFFSET_TEXT);
else if (*it == QLatin1String("MIME"))
target = target->specialColumnPtr(0, Imap::Mailbox::TreeItem::OFFSET_MIME);
else
return 0;
continue;
}
if (offset >= target->childrenCount(const_cast<Mailbox::Model *>(model))) {
return 0;
}
target = target->child(offset, const_cast<Mailbox::Model *>(model));
}
return dynamic_cast<Imap::Mailbox::TreeItemPart *>(target);
}
bool CEPasteDialog::isVaspFormat(const QString &text)
{
QStringList lines = text.split("\n");
// Title + scale + 3 vectors + composition + direct/cartesian + (no atoms)
if (lines.size() < 7) {
return false;
}
unsigned int lineIndex = 0;
const QString *line;
QStringList lineList;
bool ok;
unsigned int numAtoms = 0;
// First line is comment
line = &lines[lineIndex++];
// Next is a scale factor, single float
line = &lines[lineIndex++];
line->toDouble(&ok);
if (!ok) {
return false;
}
// Next three lines are cell vectors, three floats
for (int vecInd = 0; vecInd < 3; ++vecInd) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
for (int i = 0; i < 3; ++i) {
lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
}
}
// Next line is a list of unsigned integers (composition)
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
int numSpecies = lineList.size();
if (numSpecies == 0) {
return false;
}
// Check if the first field is an unsigned int (VASP 4.x) or a char (5.x)
bool vaspVersionLessThan5;
lineList.first().toUInt(&vaspVersionLessThan5);
// If vasp >= 5.x, skip the line containing the atomic symbols.
if (!vaspVersionLessThan5) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != numSpecies) {
return false;
}
}
// Read in the total number of atoms
for (QStringList::const_iterator
it = lineList.constBegin(),
it_end = lineList.constEnd();
it != it_end; ++it) {
numAtoms += it->toUInt(&ok);
if (!ok) {
return false;
}
}
// Next line is a string. First character is important:
line = &lines[lineIndex++];
if (line->size() && line->at(0).toLower() == QChar('s')){
// If first letter is s (selective dynamics), skip one more line
line = &lines[lineIndex++];
}
// Current line is a string, contents not important here
// Next [numAtoms] lines are vectors. So long as they're ok, we
// have a POSCAR or CONTCAR!
for (unsigned int i = 0; i < numAtoms; ++i) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
for (int i = 0; i < 3; ++i) {
lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
}
}
return true;
}
bool CEPasteDialog::acceptVaspFormat()
{
// Validate identities field
QStringList idents = ui.edit_identities->text().simplified()
.split(QRegExp("\\s+|,|;"));
if (static_cast<unsigned int>(idents.size()) != m_numAtomTypes) {
QMessageBox::critical
(this,
tr("Bad Compostion"),
tr("The identities field must contain the same number of "
"space delimited entries as line 6 of the POSCAR."));
return false;
}
bool ok;
QList<unsigned int> compAtomicNums;
QList<unsigned int> compCounts;
for (QStringList::const_iterator
it = idents.constBegin(),
it_end = idents.constEnd();
it != it_end; ++it) {
// Attempt to use the string as a uint
unsigned int atomicNum = it->toUInt(&ok);
// If this doesn't work, try passing the string to OB's translator
if (!ok) {
atomicNum = OpenBabel::etab.GetAtomicNum(it->toStdString().c_str());
}
compAtomicNums.append(atomicNum);
}
QStringList lines = m_text.split("\n");
unsigned int lineIndex = 0;
const QString *line;
QStringList lineList;
unsigned int numAtoms = 0;
QList<Eigen::Vector3d> positions;
QList<unsigned int> atomicNums;
Eigen::Matrix3d cellMatrix;
// First line is comment
line = &lines[lineIndex++];
// Next is a scale factor, single float
line = &lines[lineIndex++];
double scale = line->toDouble(&ok);
if (!ok) {
return false;
}
// Next three lines are cell vectors, three floats
for (int vecInd = 0; vecInd < 3; ++vecInd) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
for (int i = 0; i < 3; ++i) {
double v = lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
cellMatrix(vecInd, i) = v * scale;
}
}
// Next line is a list of unsigned integers (composition)
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
// If vasp >= 5.x, this may be a list of atomic symbols. Skip it if so,
// since the user should have already specified/verified the composition
// in the GUI by this point.
if (lineList.isEmpty()) {
return false;
}
bool vaspVersionLessThan5;
lineList.first().toUInt(&vaspVersionLessThan5);
if (!vaspVersionLessThan5) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
}
for (QStringList::const_iterator it = lineList.constBegin(),
it_end = lineList.constEnd(); it != it_end; ++it) {
unsigned int v = it->toUInt(&ok);
if (!ok) {
return false;
}
numAtoms += v;
compCounts.append(v);
}
// Next line is a string. First character is important:
line = &lines[lineIndex++];
if (line->size() && line->at(0).toLower() == QChar('s')){
// If first letter is s (selective dynamics), skip one more line
line = &lines[lineIndex++];
}
// Current line is a string. If it starts with K, k, C, or c,
// positions are in cartesian units. Otherwise, reciprocal units.
bool isCartesian = false;
if (line->size() &&
(line->at(0).toLower() == QChar('k') ||
line->at(0).toLower() == QChar('c') ) ) {
isCartesian = true;
}
// Next [numAtoms] lines are vectors. So long as they're ok, we
// have a POSCAR or CONTCAR!
for (unsigned int i = 0; i < numAtoms; ++i) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
Eigen::Vector3d vec;
for (int i = 0; i < 3; ++i) {
double v = lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
vec(i) = v;
}
positions.append(vec);
}
// Build list of atomic numbers
Q_ASSERT(compAtomicNums.size() == compCounts.size());
for (int i = 0; i < compCounts.size(); ++i) {
for (unsigned int j = 0; j < compCounts.at(i); ++j) {
atomicNums.append(compAtomicNums.at(i));
}
}
Q_ASSERT(atomicNums.size() == positions.size());
// Set unit cell
QWriteLocker locker (m_molecule->lock());
OpenBabel::OBUnitCell *cell = m_molecule->OBUnitCell();
cell->SetData(Eigen2OB(cellMatrix));
// Convert to cartesian coords if necessary:
if (!isCartesian) {
for (QList<Eigen::Vector3d>::iterator
it = positions.begin(),
it_end = positions.end();
it != it_end; ++it) {
*it = OB2Eigen(cell->FractionalToCartesian
(Eigen2OB(*it)));
}
}
// Remove old atoms
QList<Avogadro::Atom*> oldAtoms = m_molecule->atoms();
for (QList<Avogadro::Atom*>::iterator
it = oldAtoms.begin(),
it_end = oldAtoms.end();
it != it_end;
++it) {
m_molecule->removeAtom(*it);
}
// Add new atoms
for (int i = 0; i < positions.size(); ++i) {
Atom *atom = m_molecule->addAtom();
atom->setAtomicNumber(atomicNums.at(i));
atom->setPos(positions.at(i));
}
return true;
}