Merge pull request #1479 from ghutchis/read-script-properties

Allow scripts to add properties (orbitals, vibrations, cubes)

Author: ghutchis

avogadro/core/molecule.cpp

@@ -9,11 +9,13 @@
 #include "color3f.h"
 #include "cube.h"
 #include "elements.h"
+#include "gaussianset.h"
 #include "layermanager.h"
 #include "mdlvalence_p.h"
 #include "mesh.h"
 #include "neighborperceiver.h"
 #include "residue.h"
+#include "slaterset.h"
 #include "unitcell.h"
 
 #include <algorithm>
@@ -74,6 +76,54 @@ Molecule::Molecule(const Molecule& other)
   }
 }
 
+void Molecule::readProperties(const Molecule& other)
+{
+  m_label = other.m_label;
+  m_colors = other.m_colors;
+  // merge data maps by iterating through other's map
+  for (auto it = other.m_data.constBegin(); it != other.m_data.constEnd(); ++it) {
+    // even if we have the same key, we want to overwrite
+    m_data.setValue(it->first, it->second);
+  }
+  // merge partial charge maps
+  for (auto it = other.m_partialCharges.cbegin();
+       it != other.m_partialCharges.cend(); ++it) {
+    m_partialCharges[it->first] = it->second;
+  }
+
+  // copy orbital information
+  SlaterSet* slaterSet = dynamic_cast<SlaterSet*>(other.m_basisSet);
+  if (slaterSet != nullptr) {
+    m_basisSet = slaterSet->clone();
+    m_basisSet->setMolecule(this);
+  }
+  GaussianSet* gaussianSet = dynamic_cast<GaussianSet*>(other.m_basisSet);
+  if (gaussianSet != nullptr) {
+    m_basisSet = gaussianSet->clone();
+    m_basisSet->setMolecule(this);
+  }
+
+  // copy over spectra information
+  if (other.m_vibrationFrequencies.size() > 0) {
+    m_vibrationFrequencies = other.m_vibrationFrequencies;
+    m_vibrationIRIntensities = other.m_vibrationIRIntensities;
+    m_vibrationRamanIntensities = other.m_vibrationRamanIntensities;
+    m_vibrationLx = other.m_vibrationLx;
+  }
+
+  // Copy over any meshes
+  for (Index i = 0; i < other.meshCount(); ++i) {
+    Mesh* m = addMesh();
+    *m = *other.mesh(i);
+  }
+
+  // Copy over any cubes
+  for (Index i = 0; i < other.cubeCount(); ++i) {
+    Cube* c = addCube();
+    *c = *other.cube(i);
+  }
+}
+
 Molecule::Molecule(Molecule&& other) noexcept
   : m_data(other.m_data), m_partialCharges(std::move(other.m_partialCharges)),
     m_customElementMap(std::move(other.m_customElementMap)),
@@ -277,53 +327,52 @@ void Molecule::setFrozenAtom(Index atomId, bool frozen)
     return;
 
   // check if we need to resize
-  unsigned int size = m_frozenAtomMask.rows();  
-  if (m_frozenAtomMask.rows() != 3*m_atomicNumbers.size())
-    m_frozenAtomMask.conservativeResize(3*m_atomicNumbers.size());
+  unsigned int size = m_frozenAtomMask.rows();
+  if (m_frozenAtomMask.rows() != 3 * m_atomicNumbers.size())
+    m_frozenAtomMask.conservativeResize(3 * m_atomicNumbers.size());
 
   // do we need to initialize new values?
   if (m_frozenAtomMask.rows() > size)
     for (unsigned int i = size; i < m_frozenAtomMask.rows(); ++i)
       m_frozenAtomMask[i] = 1.0;
-  
+
   float value = frozen ? 0.0 : 1.0;
   if (atomId * 3 <= m_frozenAtomMask.rows() - 3) {
-    m_frozenAtomMask[atomId*3] = value;
-    m_frozenAtomMask[atomId*3+1] = value;
-    m_frozenAtomMask[atomId*3+2] = value;
+    m_frozenAtomMask[atomId * 3] = value;
+    m_frozenAtomMask[atomId * 3 + 1] = value;
+    m_frozenAtomMask[atomId * 3 + 2] = value;
   }
 }
 
 bool Molecule::frozenAtom(Index atomId) const
 {
   bool frozen = false;
   if (atomId * 3 <= m_frozenAtomMask.rows() - 3) {
-    frozen = (m_frozenAtomMask[atomId*3] == 0.0 &&
-              m_frozenAtomMask[atomId*3+1] == 0.0 &&
-              m_frozenAtomMask[atomId*3+2] == 0.0);
+    frozen = (m_frozenAtomMask[atomId * 3] == 0.0 &&
+              m_frozenAtomMask[atomId * 3 + 1] == 0.0 &&
+              m_frozenAtomMask[atomId * 3 + 2] == 0.0);
   }
   return frozen;
 }
 
 void Molecule::setFrozenAtomAxis(Index atomId, int axis, bool frozen)
 {
   // check if we need to resize
-  unsigned int size = m_frozenAtomMask.rows();  
-  if (m_frozenAtomMask.rows() != 3*m_atomicNumbers.size())
-    m_frozenAtomMask.conservativeResize(3*m_atomicNumbers.size());
+  unsigned int size = m_frozenAtomMask.rows();
+  if (m_frozenAtomMask.rows() != 3 * m_atomicNumbers.size())
+    m_frozenAtomMask.conservativeResize(3 * m_atomicNumbers.size());
 
   // do we need to initialize new values?
   if (m_frozenAtomMask.rows() > size)
     for (unsigned int i = size; i < m_frozenAtomMask.rows(); ++i)
       m_frozenAtomMask[i] = 1.0;
-  
+
   float value = frozen ? 0.0 : 1.0;
   if (atomId * 3 <= m_frozenAtomMask.rows() - 3) {
-    m_frozenAtomMask[atomId*3 + axis] = value;
+    m_frozenAtomMask[atomId * 3 + axis] = value;
   }
 }
 
-
 void Molecule::setData(const std::string& name, const Variant& value)
 {
   m_data.setValue(name, value);

avogadro/core/molecule.h

@@ -73,6 +73,13 @@ class AVOGADROCORE_EXPORT Molecule
   /** Destroys the molecule object. */
   virtual ~Molecule();
 
+  /**
+   * Adds the properties from the supplied
+   * molecule to this molecule. Does not otherwise
+   * modify atoms / bonds / residues, etc.
+   */
+  void readProperties(const Molecule& other);
+
   /** Sets the data value with @p name to @p value. */
   void setData(const std::string& name, const Variant& value);
 
@@ -695,20 +702,20 @@ class AVOGADROCORE_EXPORT Molecule
 
   /**
    * Freeze or unfreeze an atom for optimization
-  */
+   */
   void setFrozenAtom(Index atomId, bool frozen);
 
   /**
    * Get the frozen status of an atom
-  */
+   */
   bool frozenAtom(Index atomId) const;
 
   /**
    * Freeze or unfreeze X, Y, or Z coordinate of an atom for optimization
    * @param atomId The index of the atom to modify.
    * @param axis The axis to freeze (0, 1, or 2 for X, Y, or Z)
    * @param frozen True to freeze, false to unfreeze
-  */
+   */
   void setFrozenAtomAxis(Index atomId, int axis, bool frozen);
 
   Eigen::VectorXd frozenAtomMask() const { return m_frozenAtomMask; }

avogadro/qtgui/interfacescript.cpp

@@ -252,8 +252,11 @@ bool InterfaceScript::processCommand(Core::Molecule* mol)
       newMol.perceiveBondOrders();
     }
 
-    // just append some new bits
-    if (obj["append"].toBool()) {
+    // how do we handle this result?
+    if (obj["readProperties"].toBool()) {
+      guiMol->readProperties(newMol);
+      guiMol->emitChanged(Molecule::Properties | Molecule::Added);
+    } else if (obj["append"].toBool()) {
       guiMol->undoMolecule()->appendMolecule(newMol, m_displayName);
     } else { // replace the whole molecule
       Molecule::MoleculeChanges changes = (Molecule::Atoms | Molecule::Bonds |

avogadro/qtgui/molecule.h

@@ -73,6 +73,7 @@ class AVOGADROQTGUI_EXPORT Molecule : public QObject, public Core::Molecule
     UnitCell = 0x04,
     Selection = 0x08,
     Layers = 0x16,
+    Properties = 0x32,
     /** Operations that can affect the above types. */
     Added = 0x1024,
     Removed = 0x2048,
@@ -93,7 +94,8 @@ class AVOGADROQTGUI_EXPORT Molecule : public QObject, public Core::Molecule
    */
   virtual AtomType addAtom(unsigned char atomicNumber, Index uniqueId);
 
-  AtomType addAtom(unsigned char number, Vector3 position3d, Index uniqueId = MaxIndex);
+  AtomType addAtom(unsigned char number, Vector3 position3d,
+                   Index uniqueId = MaxIndex);
 
   /**
    * @brief Remove the specified atom from the molecule.

avogadro/qtplugins/openbabel/obfileformat.cpp

@@ -12,6 +12,7 @@
 #include <QtCore/QCoreApplication>
 #include <QtCore/QDebug>
 #include <QtCore/QFileInfo>
+#include <QtCore/QTemporaryFile>
 #include <QtCore/QTimer>
 
 using json = nlohmann::json;
@@ -73,7 +74,8 @@ OBFileFormat::OBFileFormat(const std::string& name_,
     m_identifier(identifier_), m_name(name_),
     m_specificationUrl(specificationUrl_), m_defaultFormat(defaultFormat_),
     m_fileOnly(fileOnly_)
-{}
+{
+}
 
 OBFileFormat::~OBFileFormat() {}
 
@@ -122,7 +124,6 @@ bool OBFileFormat::read(std::istream& in, Core::Molecule& molecule)
   // default is CML or CJSON
   QString format =
     QString::fromStdString(opts.value("format", m_defaultFormat));
-  qDebug() << "Reading to format: " << format << m_defaultFormat.c_str();
 
   if (!m_fileOnly) {
     // Determine length of data
@@ -149,6 +150,26 @@ bool OBFileFormat::read(std::istream& in, Core::Molecule& molecule)
   } else {
     // Can only read files. Need absolute path.
     QString filename = QString::fromStdString(fileName());
+    if (filename.isEmpty()) {
+      // no choice but to write to a temporary file
+      in.seekg(0, std::ios_base::end);
+      std::istream::pos_type length = in.tellg();
+      in.seekg(0, std::ios_base::beg);
+      in.clear();
+
+      // Extract data, hope it's not big
+      QByteArray input;
+      input.resize(static_cast<int>(length));
+      in.read(input.data(), length);
+
+      QTemporaryFile tmpFile;
+      tmpFile.setAutoRemove(false);
+      tmpFile.open();
+      tmpFile.write(input.data());
+      tmpFile.close();
+      filename = tmpFile.fileName();
+    }
+
     if (!QFileInfo(filename).isAbsolute()) {
       appendError("Internal error -- filename must be absolute! " +
                   filename.toStdString());
@@ -281,6 +302,6 @@ Io::FileFormat* OBFileFormat::newInstance() const
                           m_defaultFormat, m_fileOnly);
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtPlugins
 
 #include "obfileformat.moc"

avogadro/qtplugins/spectra/spectra.cpp

@@ -45,6 +45,9 @@ QStringList Spectra::menuPath(QAction*) const
 
 void Spectra::setMolecule(QtGui::Molecule* mol)
 {
+  if (m_molecule != nullptr)
+    m_molecule->disconnect(this);
+
   bool isVibrational(false);
   if (mol->vibrationFrequencies().size())
     isVibrational = true;
@@ -56,6 +59,25 @@ void Spectra::setMolecule(QtGui::Molecule* mol)
 
   if (isVibrational)
     openDialog();
+
+  connect(m_molecule, SIGNAL(changed(unsigned int)),
+          SLOT(moleculeChanged(unsigned int)));
+}
+
+void Spectra::moleculeChanged(unsigned int changes)
+{
+  if (m_molecule == nullptr)
+    return;
+
+  bool currentVibrational = m_actions[0]->isEnabled();
+  bool isVibrational = (m_molecule->vibrationFrequencies().size() > 0);
+  if (currentVibrational != isVibrational) {
+    m_actions[0]->setEnabled(isVibrational);
+    if (m_dialog)
+      m_dialog->setMolecule(m_molecule); // update the dialog
+    if (isVibrational)
+      openDialog();
+  }
 }
 
 void Spectra::registerCommands()

avogadro/qtplugins/spectra/spectra.h

@@ -53,6 +53,7 @@ public slots:
   void startVibrationAnimation();
   void stopVibrationAnimation();
   void openDialog();
+  void moleculeChanged(unsigned int changes);
 
 private slots:
   void advanceFrame();

avogadro/qtplugins/surfaces/surfaces.cpp

@@ -224,6 +224,10 @@ bool Surfaces::handleCommand(const QString& command, const QVariantMap& options)
 
 void Surfaces::setMolecule(QtGui::Molecule* mol)
 {
+  if (m_molecule != nullptr) {
+    m_molecule->disconnect(this);
+  }
+
   if (mol->basisSet()) {
     m_basis = mol->basisSet();
   } else if (mol->cubes().size() != 0) {
@@ -234,6 +238,18 @@ void Surfaces::setMolecule(QtGui::Molecule* mol)
   m_mesh1 = nullptr;
   m_mesh2 = nullptr;
   m_molecule = mol;
+
+  if (m_molecule != nullptr) {
+    connect(m_molecule, SIGNAL(changed(uint)), SLOT(moleculeChanged(uint)));
+  }
+}
+
+void Surfaces::moleculeChanged(unsigned int changes)
+{
+  if (changes & Molecule::Added || changes & Molecule::Removed) {
+    m_cubes = m_molecule->cubes();
+    m_basis = m_molecule->basisSet();
+  }
 }
 
 QList<QAction*> Surfaces::actions() const

avogadro/qtplugins/surfaces/surfaces.h

@@ -85,6 +85,7 @@ class Surfaces : public QtGui::ExtensionPlugin
 public slots:
   bool handleCommand(const QString& command,
                      const QVariantMap& options) override;
+  void moleculeChanged(unsigned int changes);
 
 private slots:
   void surfacesActivated();