From c1ea51ed7310258e10d55db2e5aca4bb3f87ba99 Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Sat, 18 Nov 2023 23:45:40 -0500
Subject: [PATCH] Add support for inserting fragments from library

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 .../qtplugins/templatetool/templatetool.cpp   | 11 ++-
 .../templatetool/templatetoolwidget.cpp       | 67 +++++++++++++++++--
 .../templatetool/templatetoolwidget.h         |  2 +
 3 files changed, 74 insertions(+), 6 deletions(-)

diff --git a/avogadro/qtplugins/templatetool/templatetool.cpp b/avogadro/qtplugins/templatetool/templatetool.cpp
index c40bbd79d8..863026428d 100644
--- a/avogadro/qtplugins/templatetool/templatetool.cpp
+++ b/avogadro/qtplugins/templatetool/templatetool.cpp
@@ -408,8 +408,15 @@ void TemplateTool::atomLeftClick(QMouseEvent*)
         return;
 
     } else {
-      QFile templ(":/templates/ligands/" + m_toolWidget->ligandString() +
-                  ".cjson");
+      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);
diff --git a/avogadro/qtplugins/templatetool/templatetoolwidget.cpp b/avogadro/qtplugins/templatetool/templatetoolwidget.cpp
index fc4d6a1c3b..2eeee329e6 100644
--- a/avogadro/qtplugins/templatetool/templatetoolwidget.cpp
+++ b/avogadro/qtplugins/templatetool/templatetoolwidget.cpp
@@ -156,6 +156,10 @@ QString TemplateToolWidget::ligandString() const
   // tell us if we are using the clipboard
   if (m_ui->typeComboBox->currentIndex() == LigandType::Clipboard)
     return "Clipboard";
+  // check if it's "other"
+  if (m_ligands.at(m_ui->ligandComboBox->currentIndex()).endsWith("other"))
+    return m_ligandPath;
+
   return m_ligands.at(m_ui->ligandComboBox->currentIndex());
 }
 
@@ -181,11 +185,43 @@ void TemplateToolWidget::ligandChanged(int index)
   QString iconName = m_ligands[index];
 
   // check if it's "other"
-  if (iconName.endsWith("-other")) {
-    if (!m_fragmentDialog) {
-      m_fragmentDialog = new QtGui::InsertFragmentDialog(this);
-      connect(m_fragmentDialog, SIGNAL(accepted()), this, SLOT(accepted()));
+  if (iconName.endsWith("other")) {
+
+    // figure out the ligand type and the resulting path
+    // to the fragment files
+    int ligandType = m_ui->typeComboBox->currentIndex();
+    QString path = "fragments";
+
+    switch (ligandType) {
+      case LigandType::Monodentate:
+        path += "/ligands/monodentate";
+        break;
+      case LigandType::Bidentate:
+        path += "/ligands/bidentate";
+        break;
+      case LigandType::Tridentate:
+        path += "/ligands/tridentate";
+        break;
+      case LigandType::Tetradentate:
+        path += "/ligands/tetradentate";
+        break;
+      case LigandType::Hexadentate:
+        path += "/ligands/hexadentate";
+        break;
+      case LigandType::Haptic:
+        path += "/ligands/haptic";
+        break;
+      case LigandType::FunctionalGroup:
+        path += "/groups";
+        break;
     }
+
+    if (m_fragmentDialog != nullptr)
+      m_fragmentDialog->deleteLater();
+
+    m_fragmentDialog = new QtGui::InsertFragmentDialog(this, path);
+    connect(m_fragmentDialog, SIGNAL(performInsert(const QString&, bool)), this,
+            SLOT(otherLigandInsert(const QString&, bool)));
     m_fragmentDialog->show();
     return;
   }
@@ -193,6 +229,27 @@ void TemplateToolWidget::ligandChanged(int index)
   m_ui->ligandPreview->setIcon(QIcon(":/icons/ligands/" + iconName + ".png"));
 }
 
+void TemplateToolWidget::otherLigandInsert(const QString& fileName, bool crystal)
+{
+  if (m_fragmentDialog == nullptr)
+    return;
+
+  // get the ligand name
+  QString ligandName = m_fragmentDialog->fileName();
+  m_ligandPath = ligandName;
+
+  m_fragmentDialog->hide();
+  // it will be deleted later
+
+  // update the icon from the filename (so check for .png)
+  QString iconName = fileName;
+  if (iconName.endsWith(".cjson"))
+    iconName.chop(6);
+  iconName += ".png";
+  m_ui->ligandPreview->setIcon(QIcon(iconName));
+}
+
+
 void TemplateToolWidget::typeChanged(int index)
 {
   QSettings settings;
@@ -270,6 +327,8 @@ void TemplateToolWidget::typeChanged(int index)
                   << "phenyl"
                   << "sulfonate" << tr("Other…");
       m_ligands = ligandNames;
+      // make sure last one is "other"
+      m_ligands.last() = "1-other";
       m_denticity = 1;
       break;
     case LigandType::Clipboard: // Clipboard
diff --git a/avogadro/qtplugins/templatetool/templatetoolwidget.h b/avogadro/qtplugins/templatetool/templatetoolwidget.h
index 8fe7451d55..5f209c96a0 100644
--- a/avogadro/qtplugins/templatetool/templatetoolwidget.h
+++ b/avogadro/qtplugins/templatetool/templatetoolwidget.h
@@ -55,6 +55,8 @@ private slots:
   void typeChanged(int index);
   void ligandChanged(int index);
 
+  void otherLigandInsert(const QString& fileName, bool crystal);
+
 private:
   void buildElements();
   void buildBondOrders();