From ca33dce11113b64bf90895138e72ccbcf0887a4c Mon Sep 17 00:00:00 2001
From: Geoff Hutchison <geoff.hutchison@gmail.com>
Date: Tue, 16 Aug 2022 14:14:26 -0400
Subject: [PATCH] Fetch molecule names from PubChem PUG interface

Fix #342

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
---
 .../molecularpropertiesdialog.cpp             | 68 ++++++++++++++++++-
 .../molecularpropertiesdialog.h               | 13 ++++
 .../molecularpropertiesdialog.ui              | 37 +++++++---
 3 files changed, 107 insertions(+), 11 deletions(-)

diff --git a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.cpp b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.cpp
index 48be6f5ae5..26cf67ed57 100644
--- a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.cpp
+++ b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.cpp
@@ -7,8 +7,13 @@
 #include "ui_molecularpropertiesdialog.h"
 
 #include <avogadro/core/elements.h>
+#include <avogadro/io/fileformatmanager.h>
 #include <avogadro/qtgui/molecule.h>
 
+#include <QtCore/QRegExp>
+#include <QtNetwork/QNetworkAccessManager>
+#include <QtNetwork/QNetworkReply>
+
 using Avogadro::QtGui::Molecule;
 
 namespace Avogadro::QtPlugins {
@@ -20,6 +25,10 @@ MolecularPropertiesDialog::MolecularPropertiesDialog(QtGui::Molecule* mol,
 {
   m_ui->setupUi(this);
 
+  m_network = new QNetworkAccessManager(this);
+  connect(m_network, SIGNAL(finished(QNetworkReply*)), this,
+          SLOT(replyFinished(QNetworkReply*)));
+
   setMolecule(mol);
 }
 
@@ -51,6 +60,7 @@ void MolecularPropertiesDialog::updateLabels()
   if (m_molecule) {
     updateMassLabel();
     updateFormulaLabel();
+    updateName();
     m_ui->atomCountLabel->setText(QString::number(m_molecule->atomCount()));
     m_ui->bondCountLabel->setText(QString::number(m_molecule->bondCount()));
   } else {
@@ -61,6 +71,62 @@ void MolecularPropertiesDialog::updateLabels()
   }
 }
 
+void MolecularPropertiesDialog::updateName()
+{
+  QString name = tr("(pending)", "asking server for molecule name");
+
+  if (!m_molecule || m_molecule->atomCount() == 0) {
+    m_ui->moleculeNameLabel->clear();
+    return;
+  }
+
+  m_ui->moleculeNameLabel->setText(name); // while we wait
+
+  // InChI is intentionally designed to avoid issues with URL encoding
+  std::string smiles;
+  Io::FileFormatManager::instance().writeString(*m_molecule, smiles, "smi");
+  QString smilesString = QString::fromStdString(smiles);
+  smilesString.remove(QRegExp("\\s+.*"));
+  QString requestURL =
+    QString("https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/" +
+            QUrl::toPercentEncoding(smilesString) + "/property/IUPACName/TXT");
+
+  // qDebug() << "Requesting" << requestURL;
+
+  m_network->get(QNetworkRequest(QUrl(requestURL)));
+
+  // TODO: fetch and parse JSON eventually
+  // https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/…/json
+}
+
+void MolecularPropertiesDialog::replyFinished(QNetworkReply* reply)
+{
+  // Read in all the data
+  if (!reply->isReadable()) {
+    reply->deleteLater();
+    m_ui->moleculeNameLabel->setText(tr("unknown molecule"));
+    return;
+  }
+
+  // check if the data came through
+  QByteArray data = reply->readAll();
+  if (data.contains("Error report") || data.contains("<h1>")) {
+    reply->deleteLater();
+    m_ui->moleculeNameLabel->setText(tr("unknown molecule"));
+    return;
+  }
+
+  QString name = QString(data).trimmed().toLower();
+  if (!name.isEmpty()) {
+    m_ui->moleculeNameLabel->setText(name);
+    // TODO: set the name in the molecule
+  } else {
+    m_ui->moleculeNameLabel->setText(tr("unknown molecule"));
+  }
+
+  reply->deleteLater();
+}
+
 void MolecularPropertiesDialog::updateMassLabel()
 {
   double mass = 0.0;
@@ -90,4 +156,4 @@ void MolecularPropertiesDialog::moleculeDestroyed()
   updateLabels();
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtPlugins
diff --git a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.h b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.h
index fc1b16ebc2..f5cb30f721 100644
--- a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.h
+++ b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.h
@@ -8,6 +8,10 @@
 
 #include <QtWidgets/QDialog>
 
+// Forward declarations
+class QNetworkAccessManager;
+class QNetworkReply;
+
 namespace Avogadro {
 
 namespace QtGui {
@@ -44,6 +48,7 @@ public slots:
   void setMolecule(QtGui::Molecule* mol);
 
 private slots:
+  void updateName();
   void updateLabels();
   void updateMassLabel();
   void updateFormulaLabel();
@@ -52,6 +57,14 @@ private slots:
 private:
   QtGui::Molecule* m_molecule;
   Ui::MolecularPropertiesDialog* m_ui;
+
+  QString m_inchi;
+  QNetworkAccessManager *m_network;
+  bool m_nameRequestPending;
+  
+private slots:
+  void replyFinished(QNetworkReply*);
+
 };
 
 } // namespace QtPlugins
diff --git a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.ui b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.ui
index 65733db5a5..cff87ed91d 100644
--- a/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.ui
+++ b/avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.ui
@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>316</width>
-    <height>107</height>
+    <width>405</width>
+    <height>183</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -19,62 +19,79 @@
      <property name="fieldGrowthPolicy">
       <enum>QFormLayout::ExpandingFieldsGrow</enum>
      </property>
-     <item row="0" column="0">
+     <property name="formAlignment">
+      <set>Qt::AlignHCenter|Qt::AlignTop</set>
+     </property>
+     <item row="0" column="1">
+      <widget class="QLabel" name="moleculeNameLabel">
+       <property name="text">
+        <string>TODO</string>
+       </property>
+      </widget>
+     </item>
+     <item row="1" column="0">
       <widget class="QLabel" name="label_4">
        <property name="text">
         <string>Molecular Mass (g/mol):</string>
        </property>
       </widget>
      </item>
-     <item row="0" column="1">
+     <item row="1" column="1">
       <widget class="QLabel" name="molMassLabel">
        <property name="text">
         <string>TODO</string>
        </property>
       </widget>
      </item>
-     <item row="1" column="0">
+     <item row="2" column="0">
       <widget class="QLabel" name="label_2">
        <property name="text">
         <string>Chemical Formula:</string>
        </property>
       </widget>
      </item>
-     <item row="1" column="1">
+     <item row="2" column="1">
       <widget class="QLabel" name="formulaLabel">
        <property name="text">
         <string>TODO</string>
        </property>
       </widget>
      </item>
-     <item row="2" column="0">
+     <item row="3" column="0">
       <widget class="QLabel" name="label_7">
        <property name="text">
         <string>Number of Atoms:</string>
        </property>
       </widget>
      </item>
-     <item row="2" column="1">
+     <item row="3" column="1">
       <widget class="QLabel" name="atomCountLabel">
        <property name="text">
         <string>TODO</string>
        </property>
       </widget>
      </item>
-     <item row="3" column="0">
+     <item row="4" column="0">
       <widget class="QLabel" name="label_8">
        <property name="text">
         <string>Number of Bonds:</string>
        </property>
       </widget>
      </item>
-     <item row="3" column="1">
+     <item row="4" column="1">
       <widget class="QLabel" name="bondCountLabel">
        <property name="text">
         <string>TODO</string>
        </property>
       </widget>
      </item>
+     <item row="0" column="0">
+      <widget class="QLabel" name="label_3">
+       <property name="text">
+        <string>Molecule Name:</string>
+       </property>
+      </widget>
+     </item>
     </layout>
    </item>
    <item>