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Improve the spinner in Parametrize dialog #19

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fff1770
Improve the spinner in Parametrize dialog
panxl Mar 6, 2024
ee10b76
Merge remote-tracking branch 'upstream/gromacs' into gromacs
panxl Mar 14, 2024
df5b6c7
Merge remote-tracking branch 'upstream/gromacs' into gromacs
panxl Mar 21, 2024
b082fbe
Merge remote-tracking branch 'upstream/gromacs' into gromacs
panxl Mar 21, 2024
3886166
Update Parametrize Molecule dialog
panxl Mar 28, 2024
577adf5
Merge remote-tracking branch 'upstream/gromacs' into gromacs
panxl Mar 28, 2024
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54 changes: 33 additions & 21 deletions src/Amber/ParametrizeMoleculeDialog.C
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Original file line number Diff line number Diff line change
Expand Up @@ -45,11 +45,11 @@ ParametrizeMoleculeDialog::ParametrizeMoleculeDialog(QWidget* parent,
setWindowTitle(tr("Parametrize ") + name);

// set up the run button
QPushButton* runButton = m_dialog.buttonBox->button(QDialogButtonBox::Apply);
runButton->setText(tr("Run"));
QPushButton* stopButton = m_dialog.buttonBox->addButton("Stop", QDialogButtonBox::ActionRole);
QPushButton* runButton = m_dialog.runButton;
QPushButton* stopButton = m_dialog.stopButton;
stopButton->setEnabled(false);

// add a spinner
WaitingSpinner* spinner = new WaitingSpinner(this, false, false);
spinner->setRoundness(70.0);
spinner->setMinimumTrailOpacity(15.0);
Expand All @@ -59,8 +59,7 @@ ParametrizeMoleculeDialog::ParametrizeMoleculeDialog(QWidget* parent,
spinner->setLineWidth(2);
spinner->setInnerRadius(3);
spinner->setRevolutionsPerSecond(1);
m_dialog.horizontalLayout->addWidget(spinner);
m_dialog.horizontalLayout->setAlignment(spinner, Qt::AlignLeft);
m_dialog.horizontalLayout->insertWidget(2, spinner);

connect(runButton, &QPushButton::clicked, this, &ParametrizeMoleculeDialog::run);
connect(runButton, &QPushButton::clicked, runButton, [runButton]() { runButton->setEnabled(false); });
Expand Down Expand Up @@ -129,16 +128,21 @@ void ParametrizeMoleculeDialog::runAntechamber()
QString program = QDir(AmberDirectory).filePath("bin/antechamber");
qDebug () << "Antechamber executable location: " << program;

// Set working directory
Layer::System* system(m_molecule->findLayers<Layer::System>(Layer::Parents).first());
antechamber->setWorkingDirectory(system->getFile().absolutePath());
qDebug() << "Antechamber working directory: " << system->getFile().absolutePath();

// Prepare arguments and write the input mol2 file
QString name(m_molecule->text().split(' ').first());
m_molecule->writeToFile(QDir(system->getFile().absolutePath()).filePath(name + "_iqmol" + ".mol2"));
Layer::System* system(m_molecule->findLayers<Layer::System>(Layer::Parents).first());
QString cwd(system->getFile().absolutePath() + QDir::separator() + name);

if (!QDir(cwd).exists()) {
QDir().mkpath(cwd);
}
m_molecule->writeToFile(QDir(cwd).filePath(name + "_iqmol" + ".mol2"));
qDebug() << "charge" << m_molecule->totalCharge() << "multiplicity" << m_molecule->multiplicity() << forceField << name;

// Set working directory
antechamber->setWorkingDirectory(cwd);
qDebug() << "Antechamber working directory: " << cwd;

// Build arguments
QStringList arguments;
arguments << "-i" << name + "_iqmol" + ".mol2"
Expand All @@ -148,8 +152,6 @@ void ParametrizeMoleculeDialog::runAntechamber()
<< "-nc" << QString::number(m_molecule->totalCharge())
<< "-m" << QString::number(m_molecule->multiplicity())
<< "-s" << "2"
<< "-pf" << "yes"
<< "-dr" << "no"
<< "-rn" << name
<< "-at" << forceField
<< "-c" << "bcc";
Expand All @@ -167,7 +169,8 @@ void ParametrizeMoleculeDialog::antechamberFinished(int exitCode, QProcess::Exit
if (exitStatus == QProcess::NormalExit && exitCode == 0) {
qDebug() << "Antechamber finished";
m_dialog.logTextBrowser->append("Antechamber finished normally.\n");
emit m_molecule->parameterFileAvailable(m_molecule->text().split(' ').first() + ".mol2");
QString name(m_molecule->text().split(' ').first());
emit m_molecule->parameterFileAvailable(name + QDir::separator() + name + ".mol2");
runParmchk2();
} else {
qDebug() << "Antechamber crashed";
Expand Down Expand Up @@ -197,19 +200,27 @@ void ParametrizeMoleculeDialog::runParmchk2()
qDebug() << "Parmchk2 executable location: " << program;

// Set working directory
Layer::System* system(m_molecule->findLayers<Layer::System>(Layer::Parents).first());
parmchk2->setWorkingDirectory(system->getFile().absolutePath());
qDebug() << "Parmchk2 working directory: " << system->getFile().absolutePath();

// Prepare arguments
QString name(m_molecule->text().split(' ').first());
Layer::System* system(m_molecule->findLayers<Layer::System>(Layer::Parents).first());
QString cwd(system->getFile().absolutePath() + QDir::separator() + name);
parmchk2->setWorkingDirectory(cwd);
qDebug() << "Parmchk2 working directory: " << cwd;

QString forceFieldOption;
if (forceField == "gaff") {
forceFieldOption = "1";
} else if (forceField == "gaff2") {
forceFieldOption = "2";
} else {
forceFieldOption = "3";
}

// Build arguments
QStringList arguments;
arguments << "-i" << name + ".mol2"
<< "-f" << "mol2"
<< "-o" << name + ".frcmod"
<< "-s" << "2"
<< "-s" << forceFieldOption
<< "-a" << "N"
<< "-w" << "Y";
qDebug() << "Arguments: " << arguments;
Expand All @@ -226,7 +237,8 @@ void ParametrizeMoleculeDialog::parmchk2Finished(int exitCode, QProcess::ExitSta
if (exitStatus == QProcess::NormalExit && exitCode == 0) {
qDebug() << "Parmchk2 finished";
m_dialog.logTextBrowser->append("Parmchk2 finished normally.\n");
emit m_molecule->parameterFileAvailable(m_molecule->text().split(' ').first() + ".frcmod");
QString name(m_molecule->text().split(' ').first());
emit m_molecule->parameterFileAvailable(name + QDir::separator() + name + ".frcmod");
} else {
qDebug() << "Parmchk2 crashed";
m_dialog.logTextBrowser->append("Parmchk2 crashed.\n");
Expand Down
110 changes: 62 additions & 48 deletions src/Amber/ParametrizeMoleculeDialog.ui
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>245</width>
<height>420</height>
<height>461</height>
</rect>
</property>
<property name="windowTitle">
Expand Down Expand Up @@ -96,32 +96,53 @@
<string notr="true">amber</string>
</property>
</item>
<item>
<property name="text">
<string notr="true">bcc</string>
</property>
</item>
<item>
<property name="text">
<string notr="true">sybyl</string>
</property>
</item>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QDialogButtonBox" name="buttonBox">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="standardButtons">
<set>QDialogButtonBox::Apply|QDialogButtonBox::Close</set>
</property>
<property name="centerButtons">
<bool>false</bool>
</property>
</widget>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QPushButton" name="runButton">
<property name="text">
<string>Run</string>
</property>
</widget>
</item>
<item>
<spacer name="horizontalSpacer_2">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item>
<spacer name="horizontalSpacer_3">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item>
<widget class="QPushButton" name="stopButton">
<property name="text">
<string>Stop</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="Line" name="line">
Expand All @@ -131,39 +152,32 @@
</widget>
</item>
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<item>
<widget class="QLabel" name="label_4">
<property name="text">
<string>Output:</string>
</property>
</widget>
</item>
</layout>
<widget class="QLabel" name="label_4">
<property name="text">
<string>Output:</string>
</property>
</widget>
</item>
<item>
<widget class="QTextBrowser" name="logTextBrowser"/>
</item>
<item>
<widget class="QDialogButtonBox" name="buttonBox">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="standardButtons">
<set>QDialogButtonBox::Close</set>
</property>
<property name="centerButtons">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
<resources/>
<connections>
<connection>
<sender>buttonBox</sender>
<signal>accepted()</signal>
<receiver>ParametrizeMoleculeDialog</receiver>
<slot>accept()</slot>
<hints>
<hint type="sourcelabel">
<x>122</x>
<y>210</y>
</hint>
<hint type="destinationlabel">
<x>122</x>
<y>115</y>
</hint>
</hints>
</connection>
<connection>
<sender>buttonBox</sender>
<signal>rejected()</signal>
Expand All @@ -172,7 +186,7 @@
<hints>
<hint type="sourcelabel">
<x>122</x>
<y>210</y>
<y>440</y>
</hint>
<hint type="destinationlabel">
<x>122</x>
Expand Down
4 changes: 2 additions & 2 deletions src/Amber/SystemBuilderDialog.C
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Original file line number Diff line number Diff line change
Expand Up @@ -259,8 +259,8 @@ void SystemBuilderDialog::resetTleapInput()
if (atoms.size() > 1) {
QString name((*it)->text().split(' ').first());
addMolecule(*it);
findParameterFile(name + ".mol2");
findParameterFile(name + ".frcmod");
findParameterFile(name + QDir::separator() + name + ".mol2");
findParameterFile(name + QDir::separator() + name + ".frcmod");
}
}

Expand Down