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Update the template tool to place ligands or functional groups #1777

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merged 5 commits into from
Nov 12, 2024
Merged

Update the template tool to place ligands or functional groups #1777

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d136655
Update the template tool to place ligands or functional groups
ghutchis Nov 11, 2024
2dd7a0d
Don't crash if there's only one atom (e.g., a single hydrogen) to con…
ghutchis Nov 11, 2024
48dccd5
Allow clicking dummy atoms for connecting pieces
ghutchis Nov 11, 2024
0dcce7f
Fix warnings
ghutchis Nov 11, 2024
fa12cf2
Missed one
ghutchis Nov 11, 2024
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268 changes: 181 additions & 87 deletions avogadro/qtplugins/templatetool/templatetool.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -269,36 +269,113 @@ void TemplateTool::reset()

void TemplateTool::emptyLeftClick(QMouseEvent* e)
{
QFile templ(":/templates/centers/" + m_toolWidget->coordinationString() +
".cjson");
if (!templ.open(QFile::ReadOnly | QFile::Text))
// Get the coordinates of the clicked position
if (m_renderer == nullptr)
return;
QTextStream templateStream(&templ);

m_toolWidget->selectedUIDs().clear();
Vector2f windowPos(e->localPos().x(), e->localPos().y());
Vector3f atomPos = m_renderer->camera().unProject(windowPos);
// center of inserted template
Vector3 center(0.0f, 0.0f, 0.0f);

CjsonFormat ff;
Molecule templateMolecule;
if (!ff.readString(templateStream.readAll().toStdString(), templateMolecule))
return;

m_toolWidget->selectedUIDs().clear();
// before we do anything, check if it's a metal or a ligand
// in the dialog
int currentTab = m_toolWidget->currentTab();
if (currentTab == 0) { // metal center
QFile templ(":/templates/centers/" + m_toolWidget->coordinationString() +
".cjson");
if (!templ.open(QFile::ReadOnly | QFile::Text))
return;
QTextStream templateStream(&templ);

// Add an atom at the clicked position
Vector2f windowPos(e->localPos().x(), e->localPos().y());
Vector3f atomPos = m_renderer->camera().unProject(windowPos);
if (!ff.readString(templateStream.readAll().toStdString(),
templateMolecule))
return;

// Add hydrogens around it following template
Vector3 center(0.0f, 0.0f, 0.0f);
size_t centerIndex = 0;
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (templateMolecule.atomicNumber(i) != 1) {
center = templateMolecule.atomPosition3d(i);
centerIndex = i;
templateMolecule.setAtomicNumber(i, m_toolWidget->atomicNumber());
templateMolecule.setFormalCharge(i, m_toolWidget->formalCharge());
continue;
// Add the atom and hydrogens around it following template
size_t centerIndex = 0;
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (templateMolecule.atomicNumber(i) != 1) {
center = templateMolecule.atomPosition3d(i);
centerIndex = i;
templateMolecule.setAtomicNumber(i, m_toolWidget->atomicNumber());
templateMolecule.setFormalCharge(i, m_toolWidget->formalCharge());
continue;
}
}
// done with metal center and coordination
} else {
// ligand
// check if it's clipboard first
if (m_toolWidget->ligandString() == tr("Clipboard")) {
const QMimeData* mimeData(QApplication::clipboard()->mimeData());

if (!mimeData) {
return;
}

// Try to find a reader that can handle the available mime-types.
Io::FileFormatManager& mgr = Io::FileFormatManager::instance();
QStringList mimeTypes(mimeData->formats());
Io::FileFormat* pastedFormat = nullptr;
QByteArray pastedData;
Io::FileFormat::Operations ops(Io::FileFormat::Read |
Io::FileFormat::String);
foreach (const QString& mimeType, mimeTypes) {
if ((pastedFormat =
mgr.newFormatFromMimeType(mimeType.toStdString(), ops))) {
pastedData = mimeData->data(mimeType);
break;
}
}

// No mime-type match, default to cjson.
if (!pastedFormat && mimeData->hasText()) {
pastedFormat = new Io::CjsonFormat;
pastedData = mimeData->text().toLatin1();
}

if (pastedFormat == nullptr)
return;

// we have a format, so try to insert the new bits into the molecule
bool success = pastedFormat->readString(
std::string(pastedData.constData(), pastedData.size()),
templateMolecule);

if (!success)
return;

center = templateMolecule.centerOfGeometry();
// done with clipboard ligands
} else { // a ligand file
QString path;
if (m_toolWidget->ligandString().endsWith(".cjson")) {
// we already have the full path .. from the insert browser
path = m_toolWidget->ligandString();
} else {
path = ":/templates/ligands/" + m_toolWidget->ligandString() + ".cjson";
}

QFile templ(path);
if (!templ.open(QFile::ReadOnly | QFile::Text))
return;
QTextStream templateStream(&templ);

if (!ff.readString(templateStream.readAll().toStdString(),
templateMolecule))
return;

center = templateMolecule.centerOfGeometry();
// done with ligand
}
}

// move the template to the clicked position
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
Vector3 pos =
templateMolecule.atomPosition3d(i) - center + atomPos.cast<double>();
Expand All @@ -317,7 +394,7 @@ void TemplateTool::emptyLeftClick(QMouseEvent* e)
// Update the clicked object
m_clickedObject.type = Rendering::AtomType;
m_clickedObject.molecule = m_molecule;
m_clickedObject.index = firstIndex + centerIndex;
m_clickedObject.index = firstIndex;

// Emit changed signal
m_molecule->emitChanged(changes);
Expand Down Expand Up @@ -371,8 +448,10 @@ Matrix3 applyKabsch(std::vector<Vector3> templatePoints,
void TemplateTool::atomLeftClick(QMouseEvent*)
{
size_t selectedIndex = m_clickedObject.index;
// if it's a valid selected atom and a hydrogen or dummy atom
if (m_molecule->atom(selectedIndex).isValid() &&
m_molecule->atomicNumber(selectedIndex) == 1) {
(m_molecule->atomicNumber(selectedIndex) == 1 ||
m_molecule->atomicNumber(selectedIndex) == 0)) {
m_toolWidget->selectedUIDs().push_back(
m_molecule->atomUniqueId(selectedIndex));
if (static_cast<int>(m_toolWidget->selectedUIDs().size()) !=
Expand All @@ -384,7 +463,7 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
// - otherwise use the template
Molecule templateMolecule;

if (m_toolWidget->ligandString() == "Clipboard") {
if (m_toolWidget->ligandString() == tr("Clipboard")) {
const QMimeData* mimeData(QApplication::clipboard()->mimeData());

if (!mimeData) {
Expand Down Expand Up @@ -461,36 +540,46 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
}

// Find center atom in molecule and get all necessary info
size_t moleculeCenterIndex =
m_molecule->bonds(selectedIndex)[0].getOtherAtom(selectedIndex).index();
size_t moleculeCenterUID = m_molecule->atomUniqueId(moleculeCenterIndex);
// - first check to see if there is a bond
Vector3 moleculeLigandOutVector(0.0, 0.0, 0.0);
for (size_t UID : m_toolWidget->selectedUIDs()) {
size_t index = m_molecule->atomByUniqueId(UID).index();
Vector3 newPos = m_molecule->atomPosition3d(index);
moleculeLigandOutVector +=
newPos - m_molecule->atomPosition3d(moleculeCenterIndex);
}

// Estimate and try to realize bond distances
Vector3 displacement(0.0, 0.0, 0.0);
for (size_t i = 0; i < templateLigandIndices.size(); i++) {
unsigned char ligandAtomicNumber =
templateMolecule.atomicNumber(templateLigandIndices[i]);
ligandAtomicNumber = (ligandAtomicNumber == 0) ? 6 : ligandAtomicNumber;
// Estimate as the sum of covalent radii
double bondDistance =
Elements::radiusCovalent(ligandAtomicNumber) +
Elements::radiusCovalent(m_molecule->atomicNumber(moleculeCenterIndex));
Vector3 inVector =
templateMolecule.atomPosition3d(templateDummyIndex) -
templateMolecule.atomPosition3d(templateLigandIndices[i]);
Vector3 correctionVector = inVector;
correctionVector.normalize();
correctionVector *= bondDistance - inVector.norm();
displacement += correctionVector;
Vector3 centerPosition = m_molecule->atomPosition3d(selectedIndex);
size_t moleculeCenterIndex = selectedIndex;
size_t moleculeCenterUID = m_molecule->atomUniqueId(moleculeCenterIndex);

if (m_molecule->bonds(selectedIndex).size() != 0) {
moleculeCenterIndex =
m_molecule->bonds(selectedIndex)[0].getOtherAtom(selectedIndex).index();
moleculeCenterUID = m_molecule->atomUniqueId(moleculeCenterIndex);
for (size_t UID : m_toolWidget->selectedUIDs()) {
size_t index = m_molecule->atomByUniqueId(UID).index();
Vector3 newPos = m_molecule->atomPosition3d(index);
moleculeLigandOutVector +=
newPos - m_molecule->atomPosition3d(moleculeCenterIndex);
}

// Estimate and try to realize bond distances
for (size_t i = 0; i < templateLigandIndices.size(); i++) {
unsigned char ligandAtomicNumber =
templateMolecule.atomicNumber(templateLigandIndices[i]);
ligandAtomicNumber = (ligandAtomicNumber == 0) ? 6 : ligandAtomicNumber;
// Estimate as the sum of covalent radii
double bondDistance = Elements::radiusCovalent(ligandAtomicNumber) +
Elements::radiusCovalent(
m_molecule->atomicNumber(moleculeCenterIndex));
Vector3 inVector =
templateMolecule.atomPosition3d(templateDummyIndex) -
templateMolecule.atomPosition3d(templateLigandIndices[i]);
Vector3 correctionVector = inVector;
correctionVector.normalize();
correctionVector *= bondDistance - inVector.norm();
displacement += correctionVector;
}
displacement *= 1.0 / templateLigandIndices.size();
} else {
// direction can be random
displacement = Eigen::Vector3d::Random();
}
displacement *= 1.0 / templateLigandIndices.size();
Vector3 newPos =
templateMolecule.atomPosition3d(templateDummyIndex) + displacement;
templateMolecule.setAtomPosition3d(templateDummyIndex, newPos);
Expand All @@ -505,43 +594,45 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
}
}

// Create arrays with the points to align and apply Kabsch algorithm
std::vector<Vector3> templateLigandPositions;
for (size_t index : templateLigandIndices)
templateLigandPositions.push_back(
templateMolecule.atomPosition3d(index) -
m_molecule->atomPosition3d(moleculeCenterIndex));
std::vector<Vector3> moleculeLigandPositions;
for (size_t UID : m_toolWidget->selectedUIDs())
moleculeLigandPositions.push_back(
m_molecule->atomPosition3d(m_molecule->atomByUniqueId(UID).index()) -
m_molecule->atomPosition3d(moleculeCenterIndex));
Matrix3 rotation =
applyKabsch(templateLigandPositions, moleculeLigandPositions);
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (i != templateDummyIndex) {
templateMolecule.setAtomPosition3d(
i, rotation * (templateMolecule.atomPosition3d(i) -
m_molecule->atomPosition3d(moleculeCenterIndex)) +
m_molecule->atomPosition3d(moleculeCenterIndex));
if (m_molecule->bonds(selectedIndex).size() != 0) {
// Create arrays with the points to align and apply Kabsch algorithm
std::vector<Vector3> templateLigandPositions;
for (size_t index : templateLigandIndices)
templateLigandPositions.push_back(
templateMolecule.atomPosition3d(index) -
m_molecule->atomPosition3d(moleculeCenterIndex));
std::vector<Vector3> moleculeLigandPositions;
for (size_t UID : m_toolWidget->selectedUIDs())
moleculeLigandPositions.push_back(
m_molecule->atomPosition3d(m_molecule->atomByUniqueId(UID).index()) -
m_molecule->atomPosition3d(moleculeCenterIndex));
Matrix3 rotation =
applyKabsch(templateLigandPositions, moleculeLigandPositions);
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (i != templateDummyIndex) {
templateMolecule.setAtomPosition3d(
i, rotation * (templateMolecule.atomPosition3d(i) -
m_molecule->atomPosition3d(moleculeCenterIndex)) +
m_molecule->atomPosition3d(moleculeCenterIndex));
}
}
}

// Rotate partially aligned template to align "out" vectors
Vector3 templateLigandOutVector(0.0, 0.0, 0.0);
for (size_t index : templateLigandIndices) {
Vector3 pos = templateMolecule.atomPosition3d(index);
templateLigandOutVector +=
pos - m_molecule->atomPosition3d(moleculeCenterIndex);
}
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (templateMolecule.atomicNumber(i) != 0) {
templateMolecule.setAtomPosition3d(
i,
rotateLigandCoords(templateMolecule.atomPosition3d(i) -
m_molecule->atomPosition3d(moleculeCenterIndex),
templateLigandOutVector, moleculeLigandOutVector) +
m_molecule->atomPosition3d(moleculeCenterIndex));
// Rotate partially aligned template to align "out" vectors
Vector3 templateLigandOutVector(0.0, 0.0, 0.0);
for (size_t index : templateLigandIndices) {
Vector3 pos = templateMolecule.atomPosition3d(index);
templateLigandOutVector +=
pos - m_molecule->atomPosition3d(moleculeCenterIndex);
}
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (templateMolecule.atomicNumber(i) != 0) {
templateMolecule.setAtomPosition3d(
i, rotateLigandCoords(
templateMolecule.atomPosition3d(i) -
m_molecule->atomPosition3d(moleculeCenterIndex),
templateLigandOutVector, moleculeLigandOutVector) +
m_molecule->atomPosition3d(moleculeCenterIndex));
}
}
}

Expand All @@ -561,8 +652,11 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
}

// Remove selected atoms and insert ligand
for (size_t UID : m_toolWidget->selectedUIDs())
m_molecule->removeAtom(m_molecule->atomByUniqueId(UID).index());
// (unless there wasn't a bond to begin with)
if (m_molecule->bonds(selectedIndex).size() != 0) {
for (size_t UID : m_toolWidget->selectedUIDs())
m_molecule->removeAtom(m_molecule->atomByUniqueId(UID).index());
}
size_t moleculeBaseIndex = m_molecule->atomCount();
m_molecule->appendMolecule(templateMolecule, tr("Insert Ligand"));

Expand Down
5 changes: 5 additions & 0 deletions avogadro/qtplugins/templatetool/templatetoolwidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -156,6 +156,11 @@ QString TemplateToolWidget::coordinationString() const
return m_centers.at(m_ui->coordinationComboBox->currentIndex());
}

int TemplateToolWidget::currentTab() const
{
return m_ui->tabWidget->currentIndex();
}

unsigned char TemplateToolWidget::ligand() const
{
return static_cast<unsigned char>(m_ui->ligandComboBox->currentIndex());
Expand Down
2 changes: 2 additions & 0 deletions avogadro/qtplugins/templatetool/templatetoolwidget.h
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Expand Up @@ -43,6 +43,8 @@ class TemplateToolWidget : public QWidget
int denticity() const;
std::vector<size_t>& selectedUIDs();

int currentTab() const;

private slots:
void elementChanged(int index);
void updateElementCombo();
Expand Down
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