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Allow semi-transparent ball-and-sticks and vdw rendering #1783

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merged 6 commits into from
Nov 15, 2024
Merged

Allow semi-transparent ball-and-sticks and vdw rendering #1783

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313204f
Allow semi-transparent ball-and-sticks and vdw rendering
ghutchis Nov 14, 2024
a37e2f5
Some progress, but can't set per-layer settings?
ghutchis Nov 14, 2024
2f9ed9e
Ball and sticks work
ghutchis Nov 14, 2024
68c9667
Remove commented unused code
ghutchis Nov 15, 2024
ceb9e23
Handle cloning settings for layer-specific options
ghutchis Nov 15, 2024
039e5ac
Ensure VdW settings can be changed for each layer
ghutchis Nov 15, 2024
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16 changes: 13 additions & 3 deletions avogadro/qtgui/pluginlayermanager.h
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@

#include <avogadro/core/layermanager.h>
#include <cassert>
#include <iostream>

namespace Avogadro {
namespace QtGui {
Expand Down Expand Up @@ -79,22 +80,31 @@ class AVOGADROQTGUI_EXPORT PluginLayerManager : protected Core::LayerManager
/** @return custom data T derived from LayerData. if @p layer is equal to
* MaxIndex returns activeLayer */
template <typename T>
T& getSetting(size_t layer = MaxIndex)
T* getSetting(size_t layer = MaxIndex)
{
auto info = m_molToInfo[m_activeMolecule];

if (layer == MaxIndex) {
layer = info->layer.activeLayer();
}

// std::cout << "name: " << m_name << " layer " << layer << " " <<
// info->layer.activeLayer() << std::endl;

assert(layer <= info->layer.maxLayer());
if (info->settings.find(m_name) == info->settings.end()) {
std::cout << " hit the end? " << std::endl;
info->settings[m_name] = Core::Array<Core::LayerData*>();
}

// do we need to create new layers in the array?
while (info->settings[m_name].size() < layer + 1) {
std::cout << " loop " << info->settings[m_name].size() << " " << layer
<< std::endl;
info->settings[m_name].push_back(new T());
}
auto result = static_cast<T*>(info->settings[m_name][layer]);
return *result;
auto* result = static_cast<T*>(info->settings[m_name][layer]);
return result;
}

private:
Expand Down
126 changes: 98 additions & 28 deletions avogadro/qtplugins/ballandstick/ballandstick.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,8 @@
#include <QtWidgets/QVBoxLayout>
#include <QtWidgets/QWidget>

#include <iostream>

namespace Avogadro::QtPlugins {

using Core::Elements;
Expand All @@ -37,15 +39,19 @@
bool showHydrogens;
float atomScale;
float bondRadius;
float opacity;

LayerBallAndStick()
{
widget = nullptr;
QSettings settings;
std::cout << " new settings " << std::endl;

atomScale = settings.value("ballandstick/atomScale", 0.3).toDouble();
bondRadius = settings.value("ballandstick/bondRadius", 0.1).toDouble();
multiBonds = settings.value("ballandstick/multiBonds", true).toBool();
showHydrogens = settings.value("ballandstick/showHydrogens", true).toBool();
opacity = settings.value("ballandstick/opacity", 1.0).toDouble();
}

~LayerBallAndStick() override
Expand All @@ -56,12 +62,17 @@

std::string serialize() final
{
std::cout << " serialize " << std::endl;

return boolToString(multiBonds) + " " + boolToString(showHydrogens) + " " +
std::to_string(atomScale) + " " + std::to_string(bondRadius);
std::to_string(atomScale) + " " + std::to_string(bondRadius) + " " +
std::to_string(opacity);
}

void deserialize(std::string text) final
{
std::cout << " deserialize " << text << std::endl;

std::stringstream ss(text);
std::string aux;
ss >> aux;
Expand All @@ -72,6 +83,9 @@
atomScale = std::stof(aux);
ss >> aux;
bondRadius = std::stof(aux);
ss >> aux;
if (!aux.empty())
opacity = std::stof(aux); // backwards compatibility
}

void setupWidget(BallAndStick* slot)
Expand All @@ -98,6 +112,16 @@
QObject::connect(bondRadiusSlider, &QSlider::valueChanged, slot,
&BallAndStick::bondRadiusChanged);
f->addRow(QObject::tr("Bond scale"), bondRadiusSlider);

auto* opacitySlider = new QSlider(Qt::Horizontal);
opacitySlider->setMinimum(0);
opacitySlider->setMaximum(100);
opacitySlider->setTickInterval(1);
opacitySlider->setValue(static_cast<int>(opacity * 100));
QObject::connect(opacitySlider, &QSlider::valueChanged, slot,
&BallAndStick::opacityChanged);
f->addRow(QObject::tr("Opacity"), opacitySlider);

v->addLayout(f);

auto* check = new QCheckBox(QObject::tr("Show multiple bonds"));
Expand Down Expand Up @@ -134,11 +158,22 @@
auto* geometry = new GeometryNode;
node.addChild(geometry);
auto* spheres = new SphereGeometry;
auto selectedSpheres = new SphereGeometry;
selectedSpheres->setOpacity(0.42);
spheres->identifier().molecule = reinterpret_cast<const void*>(&molecule);
spheres->identifier().type = Rendering::AtomType;
geometry->addDrawable(spheres);

// if we have to draw any translucent spheres, we need to add a separate
// geometry node for them
auto translucentSpheres = new SphereGeometry;
translucentSpheres->setRenderPass(Rendering::TranslucentPass);
translucentSpheres->identifier().molecule =
reinterpret_cast<const void*>(&molecule);
translucentSpheres->identifier().type = Rendering::AtomType;
geometry->addDrawable(translucentSpheres);

// for the selected atoms
auto selectedSpheres = new SphereGeometry;
selectedSpheres->setOpacity(0.42);
geometry->addDrawable(selectedSpheres);

for (Index i = 0; i < molecule.atomCount(); ++i) {
Expand All @@ -147,17 +182,28 @@
continue;
}
unsigned char atomicNumber = atom.atomicNumber();
auto& interface = m_layerManager.getSetting<LayerBallAndStick>(

auto* interface = m_layerManager.getSetting<LayerBallAndStick>(
m_layerManager.getLayerID(i));
if (atomicNumber == 1 && !interface.showHydrogens)
if (atomicNumber == 1 && !interface->showHydrogens)
continue;

Vector3ub color = atom.color();
auto radius = static_cast<float>(Elements::radiusVDW(atomicNumber));
float scale = interface.atomScale;
spheres->addSphere(atom.position3d().cast<float>(), color, radius * scale,
i);
float scale = interface->atomScale;
std::cout << " atom " << i << " radius " << radius << " scale " << scale
<< " opacity " << interface->opacity << std::endl;

if (interface->opacity < 1.0f) {
translucentSpheres->addSphere(atom.position3d().cast<float>(), color,
radius * scale, i);
translucentSpheres->setOpacity(interface->opacity);
} else
spheres->addSphere(atom.position3d().cast<float>(), color, radius * scale,
i);

if (atom.selected()) {
// add the selected indicator
color = Vector3ub(0, 0, 255);
radius *= 1.2;
selectedSpheres->addSphere(atom.position3d().cast<float>(), color,
Expand All @@ -169,25 +215,32 @@
cylinders->identifier().molecule = &molecule;
cylinders->identifier().type = Rendering::BondType;
geometry->addDrawable(cylinders);

auto* translucentBonds = new CylinderGeometry;
translucentBonds->setRenderPass(Rendering::TranslucentPass);
translucentBonds->identifier().molecule = &molecule;
translucentBonds->identifier().type = Rendering::BondType;
geometry->addDrawable(translucentBonds);

for (Index i = 0; i < molecule.bondCount(); ++i) {
Core::Bond bond = molecule.bond(i);
if (!m_layerManager.bondEnabled(bond.atom1().index(),
bond.atom2().index())) {
continue;
}

auto& interface1 = m_layerManager.getSetting<LayerBallAndStick>(
auto* interface1 = m_layerManager.getSetting<LayerBallAndStick>(
m_layerManager.getLayerID(bond.atom1().index()));
auto& interface2 = m_layerManager.getSetting<LayerBallAndStick>(
auto* interface2 = m_layerManager.getSetting<LayerBallAndStick>(
m_layerManager.getLayerID(bond.atom2().index()));

if (!interface1.showHydrogens && !interface2.showHydrogens &&
if (!interface1->showHydrogens && !interface2->showHydrogens &&
(bond.atom1().atomicNumber() == 1 ||
bond.atom2().atomicNumber() == 1)) {
continue;
}

float bondRadius = (interface1.bondRadius + interface2.bondRadius) * 0.5f;
float bondRadius = (interface1->bondRadius + interface2->bondRadius) * 0.5f;

Vector3f pos1 = bond.atom1().position3d().cast<float>();
Vector3f pos2 = bond.atom2().position3d().cast<float>();
Expand All @@ -197,7 +250,8 @@
float bondLength = bondVector.norm();
bondVector /= bondLength;

switch (interface1.multiBonds || interface2.multiBonds ? bond.order() : 1) {
switch (interface1->multiBonds || interface2->multiBonds ? bond.order()
: 1) {
case 3: {
Vector3f delta = bondVector.unitOrthogonal();
// Rotate 45 degrees around the bond vector.
Expand Down Expand Up @@ -232,18 +286,34 @@

QWidget* BallAndStick::setupWidget()
{
auto& interface = m_layerManager.getSetting<LayerBallAndStick>();
interface.setupWidget(this);
return interface.widget;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
interface->setupWidget(this);
return interface->widget;
}

void BallAndStick::opacityChanged(int opacity)
{
m_opacity = static_cast<float>(opacity) / 100.0f;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
if (m_opacity != interface->opacity) {
Fixed Show fixed Hide fixed
Dismissed Show dismissed Hide dismissed
std::cout << " previous opacity " << interface->opacity << " new opacity "
<< m_opacity << std::endl;

interface->opacity = m_opacity;
emit drawablesChanged();
}

QSettings settings;
settings.setValue("ballandstick/opacity", m_opacity);
}

void BallAndStick::atomRadiusChanged(int value)
{
m_atomScale = static_cast<float>(value) / 10.0f;

auto& interface = m_layerManager.getSetting<LayerBallAndStick>();
if (m_atomScale != interface.atomScale) {
interface.atomScale = m_atomScale;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
if (m_atomScale != interface->atomScale) {
Dismissed Show dismissed Hide dismissed
interface->atomScale = m_atomScale;
emit drawablesChanged();
}

Expand All @@ -255,9 +325,9 @@
{
m_bondRadius = static_cast<float>(value) / 10.0f;

auto& interface = m_layerManager.getSetting<LayerBallAndStick>();
if (m_bondRadius != interface.bondRadius) {
interface.bondRadius = m_bondRadius;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
if (m_bondRadius != interface->bondRadius) {
Dismissed Show dismissed Hide dismissed
interface->bondRadius = m_bondRadius;
emit drawablesChanged();
}

Expand All @@ -267,9 +337,9 @@

void BallAndStick::multiBonds(bool show)
{
auto& interface = m_layerManager.getSetting<LayerBallAndStick>();
if (show != interface.multiBonds) {
interface.multiBonds = show;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
if (show != interface->multiBonds) {
interface->multiBonds = show;
emit drawablesChanged();
}
QSettings settings;
Expand All @@ -278,9 +348,9 @@

void BallAndStick::showHydrogens(bool show)
{
auto& interface = m_layerManager.getSetting<LayerBallAndStick>();
if (show != interface.showHydrogens) {
interface.showHydrogens = show;
auto* interface = m_layerManager.getSetting<LayerBallAndStick>();
if (show != interface->showHydrogens) {
interface->showHydrogens = show;
emit drawablesChanged();
}
QSettings settings;
Expand Down
2 changes: 2 additions & 0 deletions avogadro/qtplugins/ballandstick/ballandstick.h
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Original file line number Diff line number Diff line change
Expand Up @@ -46,12 +46,14 @@ public slots:
void bondRadiusChanged(int value);
void multiBonds(bool show);
void showHydrogens(bool show);
void opacityChanged(int value);

private:
Rendering::GroupNode* m_group;
std::string m_name = "Ball and Stick";
float m_atomScale = 0.3f;
float m_bondRadius = 0.1f;
float m_opacity = 1.0f;
};

} // end namespace QtPlugins
Expand Down
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