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Fetch molecule names from PubChem PUG interface #1103

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Aug 16, 2022
Merged

Fetch molecule names from PubChem PUG interface #1103

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68 changes: 67 additions & 1 deletion avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand All @@ -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);
}

Expand Down Expand Up @@ -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 {
Expand All @@ -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;
Expand Down Expand Up @@ -90,4 +156,4 @@ void MolecularPropertiesDialog::moleculeDestroyed()
updateLabels();
}

} // namespace Avogadro
} // namespace Avogadro::QtPlugins
13 changes: 13 additions & 0 deletions avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.h
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,10 @@

#include <QtWidgets/QDialog>

// Forward declarations
class QNetworkAccessManager;
class QNetworkReply;

namespace Avogadro {

namespace QtGui {
Expand Down Expand Up @@ -44,6 +48,7 @@ public slots:
void setMolecule(QtGui::Molecule* mol);

private slots:
void updateName();
void updateLabels();
void updateMassLabel();
void updateFormulaLabel();
Expand All @@ -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
Expand Down
37 changes: 27 additions & 10 deletions avogadro/qtplugins/molecularproperties/molecularpropertiesdialog.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -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">
Expand All @@ -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>
Expand Down