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Merge branch 'improve-nmr-spectra' into uv-cd-spectra
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Signed-off-by: Geoff Hutchison <[email protected]>
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@ghutchis
ghutchis committed Dec 19, 2024
2 parents 8e4ea5a + 6aa5d04 commit 554aef9
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Showing 3 changed files with 247 additions and 65 deletions.
150 changes: 148 additions & 2 deletions avogadro/qtplugins/spectra/spectradialog.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,14 @@ SpectraDialog::SpectraDialog(QWidget* parent)
: QDialog(parent), m_ui(new Ui::SpectraDialog)
{
m_ui->setupUi(this);

// hide the units for now
m_ui->unitsLabel->hide();
m_ui->unitsCombo->hide();

// only for NMR
m_ui->elementCombo->hide();

m_ui->dataTable->horizontalHeader()->setSectionResizeMode(
QHeaderView::Stretch);

Expand Down Expand Up @@ -121,6 +129,65 @@ void SpectraDialog::disconnectOptions()
SLOT(updatePlot()));
}

void SpectraDialog::updateElementCombo()
{
// update the element combo box
disconnect(m_ui->elementCombo, SIGNAL(currentIndexChanged(int)), this,
SLOT(changeSpectra()));
m_ui->elementCombo->clear();

// add the unique elements, with the element number as the data
for (auto& element : m_elements) {
// check to see if it's already in the combo box
bool found = false;
for (int i = 0; i < m_ui->elementCombo->count(); ++i) {
if (m_ui->elementCombo->itemData(i).toInt() == element) {
found = true;
break;
}
}
if (found)
continue;

switch (element) {
case 1:
m_ui->elementCombo->addItem("¹H", element);
break;
case 3:
m_ui->elementCombo->addItem("⁷Li", element);
break;
case 5:
m_ui->elementCombo->addItem("¹¹B", element);
break;
case 6:
m_ui->elementCombo->addItem("¹³C", element);
break;
case 7:
m_ui->elementCombo->addItem("¹⁵N", element);
break;
case 8:
m_ui->elementCombo->addItem("¹⁷O", element);
break;
case 9:
m_ui->elementCombo->addItem("¹⁹F", element);
break;
case 14:
m_ui->elementCombo->addItem("²⁹Si", element);
break;
case 15:
m_ui->elementCombo->addItem("³¹P", element);
break;
default:
m_ui->elementCombo->addItem(QString::number(element), element);
break;
}
}

// connect the element combo box
connect(m_ui->elementCombo, SIGNAL(currentIndexChanged(int)), this,
SLOT(changeSpectra()));
}

void SpectraDialog::changeSpectra()
{
// TODO: change the scale and offset based on defaults and settings
Expand All @@ -132,6 +199,8 @@ void SpectraDialog::changeSpectra()
SpectraType type =
static_cast<SpectraType>(m_ui->combo_spectra->currentData().toInt());

m_ui->elementCombo->hide();

switch (type) {
case SpectraType::Infrared:
m_ui->scaleSpinBox->setValue(1.0);
Expand All @@ -151,9 +220,8 @@ void SpectraDialog::changeSpectra()
m_ui->scaleSpinBox->setValue(1.0);
m_ui->offsetSpinBox->setValue(0.0);
// todo: these should be per element
m_ui->xAxisMinimum->setValue(0.0);
m_ui->xAxisMaximum->setValue(200.0);
m_ui->peakWidth->setValue(0.1);
m_ui->elementCombo->show();
break;
case SpectraType::Electronic:
m_ui->scaleSpinBox->setValue(1.0);
Expand All @@ -166,6 +234,7 @@ void SpectraDialog::changeSpectra()
case SpectraType::CircularDichroism:
m_ui->scaleSpinBox->setValue(1.0);
m_ui->offsetSpinBox->setValue(0.0);
// default to eV
m_ui->xAxisMinimum->setValue(5.0);
m_ui->xAxisMaximum->setValue(1.0);
m_ui->peakWidth->setValue(0.1);
Expand All @@ -179,6 +248,83 @@ void SpectraDialog::changeSpectra()
break;
}

// a bunch of special work depending on the NMR element
if (type == SpectraType::NMR) {
// get the element
int element = m_ui->elementCombo->currentData().toInt();

qDebug() << " NMR element: " << element;

// tweak the default axis range
// based on https://imserc.northwestern.edu/guide/eNMR/chem/NMRnuclei.html
switch (element) {
case 1: // 1H
m_ui->xAxisMinimum->setValue(12.0);
m_ui->xAxisMaximum->setValue(0.0);
break;
case 3: // 7Li
m_ui->xAxisMinimum->setValue(-16.0);
m_ui->xAxisMaximum->setValue(11.0);
break;
case 5: // 11B
m_ui->xAxisMinimum->setValue(100.0);
m_ui->xAxisMaximum->setValue(-120.0);
break;
case 6: // 13C
m_ui->xAxisMinimum->setValue(200.0);
m_ui->xAxisMaximum->setValue(0.0);
break;
case 7: // 15N
m_ui->xAxisMinimum->setValue(800.0);
m_ui->xAxisMaximum->setValue(0.0);
break;
case 8: // 17O
m_ui->xAxisMinimum->setValue(1600.0);
m_ui->xAxisMaximum->setValue(-50.0);
break;
case 9: // 19F
m_ui->xAxisMinimum->setValue(60.0);
m_ui->xAxisMaximum->setValue(-300.0);
break;
case 14: // 29Si
m_ui->xAxisMinimum->setValue(50.0);
m_ui->xAxisMaximum->setValue(-200.0);
break;
case 15: // 31P
m_ui->xAxisMinimum->setValue(250.0);
m_ui->xAxisMaximum->setValue(-250.0);
break;
default:
m_ui->xAxisMinimum->setValue(100.0);
m_ui->xAxisMaximum->setValue(-100.0);
break;
}

// the default NMR data has all the atoms in it,
// so we need to loop through m_elements to filter
MatrixX nmr = m_spectra["NMR"];

qDebug() << " NMR size: " << nmr.rows() << "x" << nmr.cols();
qDebug() << " m_elements size: " << m_elements.size();

std::vector<double> nmrPeaks;
for (int i = 0; i < m_elements.size(); ++i) {
if (m_elements[i] == element) {
nmrPeaks[i] = nmr(i, 0);
}
}
MatrixX newNMR(nmrPeaks.size(), 2);
for (int i = 0; i < nmrPeaks.size(); ++i) {
newNMR(i, 0) = nmrPeaks[i];
newNMR(i, 1) = 1.0;
}

m_currentSpectra = newNMR;
} else {
m_currentSpectra =
m_spectra[m_ui->combo_spectra->currentText().toStdString()];
}

updatePlot();
connectOptions();
}
Expand Down
10 changes: 9 additions & 1 deletion avogadro/qtplugins/spectra/spectradialog.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,11 @@ class SpectraDialog : public QDialog
void readSettings();

void setSpectra(const std::map<std::string, MatrixX>& spectra);
void setElements(const std::vector<unsigned char>& elements)
{
m_elements = elements;
updateElementCombo();
}

VTK::ChartWidget* chartWidget();

Expand All @@ -60,14 +65,17 @@ private slots:
void changeLineWidth();
void changeSpectra();

void updateElementCombo();
void updatePlot();

void toggleOptions();

private:
std::map<std::string, MatrixX> m_spectra;
std::vector<unsigned char> m_elements; // for NMR
MatrixX m_currentSpectra;

QString m_currentSpectra;
QString m_currentSpectraType;
Ui::SpectraDialog* m_ui;
};

Expand Down
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