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Initial port of align tool from Avogadro 1.x code
Signed-off-by: Geoff Hutchison <[email protected]>
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set(aligntool_srcs | ||
aligntool.cpp | ||
) | ||
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set(aligntool_uis | ||
) | ||
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set(aligntool_rcs | ||
aligntool.qrc | ||
) | ||
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avogadro_plugin(AlignTool | ||
"AlignTool" | ||
ToolPlugin | ||
aligntool.h | ||
AlignTool | ||
"${aligntool_srcs}" | ||
"${aligntool_uis}" | ||
"${aligntool_rcs}" | ||
) | ||
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target_link_libraries(AlignTool PRIVATE Avogadro::QtOpenGL) |
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/****************************************************************************** | ||
This source file is part of the Avogadro project. | ||
This source code is released under the 3-Clause BSD License, (see "LICENSE"). | ||
******************************************************************************/ | ||
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#include "aligntool.h" | ||
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#include <avogadro/core/vector.h> | ||
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#include <avogadro/qtgui/molecule.h> | ||
#include <avogadro/qtgui/rwmolecule.h> | ||
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#include <avogadro/qtopengl/glwidget.h> | ||
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#include <avogadro/rendering/camera.h> | ||
#include <avogadro/rendering/geometrynode.h> | ||
#include <avogadro/rendering/glrenderer.h> | ||
#include <avogadro/rendering/groupnode.h> | ||
#include <avogadro/rendering/scene.h> | ||
#include <avogadro/rendering/textlabel2d.h> | ||
#include <avogadro/rendering/textlabel3d.h> | ||
#include <avogadro/rendering/textproperties.h> | ||
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#include <QtCore/QDebug> | ||
#include <QtGui/QIcon> | ||
#include <QtGui/QKeyEvent> | ||
#include <QtGui/QMouseEvent> | ||
#include <QtGui/QWheelEvent> | ||
#include <QtWidgets/QAction> | ||
#include <QtWidgets/QComboBox> | ||
#include <QtWidgets/QGridLayout> | ||
#include <QtWidgets/QHBoxLayout> | ||
#include <QtWidgets/QLabel> | ||
#include <QtWidgets/QPushButton> | ||
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using Avogadro::Core::Elements; | ||
using Avogadro::QtGui::Molecule; | ||
using Avogadro::Rendering::GeometryNode; | ||
using Avogadro::Rendering::Identifier; | ||
using Avogadro::Rendering::TextLabel3D; | ||
using Avogadro::Rendering::TextProperties; | ||
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namespace Avogadro::QtPlugins { | ||
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using QtGui::Molecule; | ||
using QtGui::RWAtom; | ||
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AlignTool::AlignTool(QObject* parent_) | ||
: QtGui::ToolPlugin(parent_), m_activateAction(new QAction(this)), | ||
m_molecule(nullptr), m_toolWidget(nullptr) | ||
{ | ||
m_activateAction->setText(tr("Align")); | ||
m_activateAction->setIcon(QIcon(":/icons/align.png")); | ||
m_activateAction->setToolTip( | ||
tr("Align Molecules\n\n" | ||
"Left Mouse: \tSelect up to two atoms.\n" | ||
"\tThe first atom is centered at the origin.\n" | ||
"\tThe second atom is aligned to the selected axis.\n" | ||
"Right Mouse: \tReset alignment.\n" | ||
"Double-Click: \tCenter the atom at the origin.")); | ||
} | ||
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AlignTool::~AlignTool() | ||
{ | ||
if (m_toolWidget) | ||
m_toolWidget->deleteLater(); | ||
} | ||
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QWidget* AlignTool::toolWidget() const | ||
{ | ||
if (!m_toolWidget) { | ||
m_toolWidget = new QWidget; | ||
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QLabel* labelAxis = new QLabel(tr("Axis:"), m_toolWidget); | ||
labelAxis->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Preferred); | ||
labelAxis->setMaximumHeight(15); | ||
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// Combo box to select desired aixs to align to | ||
QComboBox* comboAxis = new QComboBox(m_toolWidget); | ||
m_axis = 0; | ||
comboAxis->addItem("x"); | ||
comboAxis->addItem("y"); | ||
comboAxis->addItem("z"); | ||
comboAxis->setCurrentIndex(m_axis); | ||
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// Button to actually perform actions | ||
QPushButton* buttonAlign = new QPushButton(m_toolWidget); | ||
buttonAlign->setText(tr("Align")); | ||
connect(buttonAlign, SIGNAL(clicked()), this, SLOT(align())); | ||
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QGridLayout* gridLayout = new QGridLayout(); | ||
gridLayout->addWidget(labelAxis, 0, 0, 1, 1, Qt::AlignRight); | ||
QHBoxLayout* hLayout = new QHBoxLayout; | ||
hLayout->addWidget(comboAxis); | ||
hLayout->addStretch(1); | ||
gridLayout->addLayout(hLayout, 0, 1); | ||
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QHBoxLayout* hLayout3 = new QHBoxLayout(); | ||
hLayout3->addStretch(1); | ||
hLayout3->addWidget(buttonAlign); | ||
hLayout3->addStretch(1); | ||
QVBoxLayout* layout = new QVBoxLayout(); | ||
layout->addLayout(gridLayout); | ||
layout->addLayout(hLayout3); | ||
layout->addStretch(1); | ||
m_toolWidget->setLayout(layout); | ||
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connect(comboAxis, SIGNAL(currentIndexChanged(int)), this, | ||
SLOT(axisChanged(int))); | ||
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connect(m_toolWidget, SIGNAL(destroyed()), this, | ||
SLOT(toolWidgetDestroyed())); | ||
} | ||
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return m_toolWidget; | ||
} | ||
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void AlignTool::axisChanged(int axis) | ||
{ | ||
// Axis to use - x=0, y=1, z=2 | ||
m_axis = axis; | ||
} | ||
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void AlignTool::alignChanged(int align) | ||
{ | ||
// Type of alignment - 0=everything, 1=molecule | ||
m_alignType = align; | ||
} | ||
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void AlignTool::align() | ||
{ | ||
if (m_atoms.size() == 0) | ||
return; | ||
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if (m_atoms.size() >= 1) | ||
shiftAtomToOrigin(m_atoms[0].index); | ||
if (m_atoms.size() == 2) | ||
alignAtomToAxis(m_atoms[1].index, m_axis); | ||
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m_atoms.clear(); | ||
} | ||
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void AlignTool::shiftAtomToOrigin(Index atomIndex) | ||
{ | ||
// Shift the atom to the origin | ||
Vector3 shift = m_molecule->atom(atomIndex).position3d(); | ||
const Core::Array<Vector3>& coords = m_molecule->atomPositions3d(); | ||
Core::Array<Vector3> newCoords(coords.size()); | ||
for (Index i = 0; i < coords.size(); ++i) | ||
newCoords[i] = coords[i] - shift; | ||
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m_molecule->setAtomPositions3d(newCoords, tr("Align at Origin")); | ||
m_molecule->emitChanged(QtGui::Molecule::Atoms); | ||
} | ||
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void AlignTool::alignAtomToAxis(Index atomIndex, int axis) | ||
{ | ||
// Align the atom to the specified axis | ||
Vector3 align = m_molecule->atom(atomIndex).position3d(); | ||
const Core::Array<Vector3>& coords = m_molecule->atomPositions3d(); | ||
Core::Array<Vector3> newCoords(coords.size()); | ||
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double alpha, beta, gamma; | ||
alpha = beta = gamma = 0.0; | ||
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Vector3 pos = m_molecule->atom(atomIndex).position3d(); | ||
pos.normalize(); | ||
Vector3 axisVector; | ||
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if (axis == 0) // x-axis | ||
axisVector = Vector3(1., 0., 0.); | ||
else if (axis == 1) // y-axis | ||
axisVector = Vector3(0., 1., 0.); | ||
else if (axis == 2) // z-axis | ||
axisVector = Vector3(0., 0., 1.); | ||
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// Calculate the angle of the atom from the axis | ||
double angle = acos(axisVector.dot(pos)); | ||
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// Get the vector for the rotation | ||
axisVector = axisVector.cross(pos); | ||
axisVector.normalize(); | ||
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// Now to rotate the fragment | ||
for (Index i = 0; i < coords.size(); ++i) | ||
newCoords[i] = Eigen::AngleAxisd(-angle, axisVector) * coords[i]; | ||
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m_molecule->setAtomPositions3d(newCoords, tr("Align to Axis")); | ||
m_molecule->emitChanged(QtGui::Molecule::Atoms); | ||
} | ||
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void AlignTool::toolWidgetDestroyed() | ||
{ | ||
m_toolWidget = nullptr; | ||
} | ||
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QUndoCommand* AlignTool::mousePressEvent(QMouseEvent* e) | ||
{ | ||
// If the click is released on an atom, add it to the list | ||
if (e->button() != Qt::LeftButton || !m_renderer) | ||
return nullptr; | ||
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Identifier hit = m_renderer->hit(e->pos().x(), e->pos().y()); | ||
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// Now add the atom on release. | ||
if (hit.type == Rendering::AtomType) { | ||
if (toggleAtom(hit)) | ||
emit drawablesChanged(); | ||
e->accept(); | ||
} | ||
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return nullptr; | ||
} | ||
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QUndoCommand* AlignTool::mouseDoubleClickEvent(QMouseEvent* e) | ||
{ | ||
// Reset the atom list | ||
if (e->button() == Qt::LeftButton && !m_atoms.isEmpty()) { | ||
m_atoms.clear(); | ||
emit drawablesChanged(); | ||
e->accept(); | ||
} | ||
return nullptr; | ||
} | ||
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bool AlignTool::toggleAtom(const Rendering::Identifier& atom) | ||
{ | ||
int ind = m_atoms.indexOf(atom); | ||
if (ind >= 0) { | ||
m_atoms.remove(ind); | ||
return true; | ||
} | ||
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if (m_atoms.size() >= 2) | ||
return false; | ||
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m_atoms.push_back(atom); | ||
return true; | ||
} | ||
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inline Vector3ub AlignTool::contrastingColor(const Vector3ub& rgb) const | ||
{ | ||
// If we're far 'enough' (+/-32) away from 128, just invert the component. | ||
// If we're close to 128, inverting the color will end up too close to the | ||
// input -- adjust the component before inverting. | ||
const unsigned char minVal = 32; | ||
const unsigned char maxVal = 223; | ||
Vector3ub result; | ||
for (size_t i = 0; i < 3; ++i) { | ||
unsigned char input = rgb[i]; | ||
if (input > 160 || input < 96) | ||
result[i] = static_cast<unsigned char>(255 - input); | ||
else | ||
result[i] = static_cast<unsigned char>(255 - (input / 4)); | ||
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// Clamp to 32-->223 to prevent pure black/white | ||
result[i] = std::min(maxVal, std::max(minVal, result[i])); | ||
} | ||
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return result; | ||
} | ||
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void AlignTool::draw(Rendering::GroupNode& node) | ||
{ | ||
if (m_atoms.size() == 0) | ||
return; | ||
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auto* geo = new GeometryNode; | ||
node.addChild(geo); | ||
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// Add labels, extract positions | ||
QVector<Vector3> positions(m_atoms.size(), Vector3()); | ||
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TextProperties atomLabelProp; | ||
atomLabelProp.setFontFamily(TextProperties::SansSerif); | ||
atomLabelProp.setAlign(TextProperties::HCenter, TextProperties::VCenter); | ||
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for (int i = 0; i < m_atoms.size(); ++i) { | ||
Identifier& ident = m_atoms[i]; | ||
Q_ASSERT(ident.type == Rendering::AtomType); | ||
Q_ASSERT(ident.molecule != nullptr); | ||
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auto atom = m_molecule->atom(ident.index); | ||
Q_ASSERT(atom.isValid()); | ||
unsigned char atomicNumber(atom.atomicNumber()); | ||
positions[i] = atom.position3d(); | ||
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// get the color of the atom | ||
const unsigned char* color = Elements::color(atomicNumber); | ||
atomLabelProp.setColorRgb(contrastingColor(Vector3ub(color)).data()); | ||
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auto* label = new TextLabel3D; | ||
label->setText(QString("#%1").arg(i + 1).toStdString()); | ||
label->setTextProperties(atomLabelProp); | ||
label->setAnchor(positions[i].cast<float>()); | ||
label->setRadius( | ||
static_cast<float>(Elements::radiusCovalent(atomicNumber)) + 0.1f); | ||
geo->addDrawable(label); | ||
} | ||
} | ||
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void AlignTool::registerCommands() | ||
{ | ||
emit registerCommand("centerAtom", tr("Center the atom at the origin.")); | ||
emit registerCommand( | ||
"alignAtom", | ||
tr("Rotate the molecule to align the atom to the specified axis.")); | ||
} | ||
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bool AlignTool::handleCommand(const QString& command, | ||
const QVariantMap& options) | ||
{ | ||
if (m_molecule == nullptr) | ||
return false; // No molecule to handle the command. | ||
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return true; | ||
} | ||
} // namespace Avogadro::QtPlugins |
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