Enhanced molecular properties dialog

avogadro/io/CMakeLists.txt

@@ -9,12 +9,13 @@ avogadro_headers(IO
   fileformatmanager.h
   gromacsformat.h
   mdlformat.h
-  vaspformat.h
+  lammpsformat.h
   pdbformat.h
-  xyzformat.h
+  sdfformat.h
   trrformat.h
   turbomoleformat.h
-  lammpsformat.h
+  vaspformat.h
+  xyzformat.h
 )
 
 target_sources(IO PRIVATE
@@ -25,13 +26,14 @@ target_sources(IO PRIVATE
   fileformat.cpp
   fileformatmanager.cpp
   gromacsformat.cpp
+  lammpsformat.cpp
   mdlformat.cpp
-  vaspformat.cpp
   pdbformat.cpp
-  xyzformat.cpp
+  sdfformat.cpp
   trrformat.cpp
   turbomoleformat.cpp
-  lammpsformat.cpp
+  vaspformat.cpp
+  xyzformat.cpp
 )
 
 if(USE_HDF5)

avogadro/io/fileformatmanager.cpp

@@ -15,6 +15,7 @@
 #include "lammpsformat.h"
 #include "mdlformat.h"
 #include "pdbformat.h"
+#include "sdfformat.h"
 #include "trrformat.h"
 #include "turbomoleformat.h"
 #include "vaspformat.h"
@@ -293,6 +294,7 @@ FileFormatManager::FileFormatManager()
   addFormat(new OutcarFormat);
   addFormat(new PdbFormat);
   addFormat(new PoscarFormat);
+  addFormat(new SdfFormat);
   addFormat(new TrrFormat);
   addFormat(new TurbomoleFormat);
   addFormat(new XyzFormat);

avogadro/io/mdlformat.cpp

@@ -40,6 +40,25 @@ MdlFormat::MdlFormat() {}
 
 MdlFormat::~MdlFormat() {}
 
+void handlePartialCharges(Core::Molecule& mol, std::string data)
+{
+  // the string starts with the number of charges
+  // then atom index  charge
+  MatrixX charges(mol.atomCount(), 1);
+  std::istringstream iss(data);
+  size_t numCharges;
+  iss >> numCharges;
+  for (size_t i = 0; i < numCharges; ++i) {
+    size_t index;
+    Real charge;
+    iss >> index >> charge;
+    // prints with atom index 1, not zero
+    charges(index - 1, 0) = charge;
+  }
+
+  mol.setPartialCharges("MMFF94", charges);
+}
+
 bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
 {
   string buffer;
@@ -182,7 +201,7 @@ bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
   }
 
   // Apply charges.
-  for (auto & i : chargeList) {
+  for (auto& i : chargeList) {
     size_t index = i.first;
     signed int charge = i.second;
     mol.setFormalCharge(index, charge);
@@ -208,7 +227,11 @@ bool MdlFormat::read(std::istream& in, Core::Molecule& mol)
       return true;
     if (inValue) {
       if (buffer.empty() && dataName.length() > 0) {
-        mol.setData(dataName, dataValue);
+        // check for partial charges
+        if (dataName == "PUBCHEM_MMFF94_PARTIAL_CHARGES")
+          handlePartialCharges(mol, dataValue);
+        else
+          mol.setData(dataName, dataValue);
         dataName.clear();
         dataValue.clear();
         inValue = false;
@@ -260,13 +283,23 @@ bool MdlFormat::write(std::ostream& out, const Core::Molecule& mol)
         << "  0  0  0  0\n";
   }
   // Properties block.
-  for (auto & i : chargeList) {
+  for (auto& i : chargeList) {
     Index atomIndex = i.first;
     signed int atomCharge = i.second;
     out << "M  CHG  1 " << setw(3) << std::right << atomIndex + 1 << " "
         << setw(3) << atomCharge << "\n";
   }
+  // TODO: isotopes, etc.
   out << "M  END\n";
+  // Data block
+  if (m_writeProperties) {
+    const auto dataMap = mol.dataMap();
+    for (const auto& key : dataMap.names()) {
+      out << "> <" << key << ">\n";
+      out << dataMap.value(key).toString() << "\n";
+      out << "\n"; // empty line between data blocks
+    }
+  }
 
   if (isMode(FileFormat::MultiMolecule))
     out << "$$$$\n";
@@ -278,7 +311,6 @@ std::vector<std::string> MdlFormat::fileExtensions() const
 {
   std::vector<std::string> ext;
   ext.emplace_back("mol");
-  ext.emplace_back("sdf");
   return ext;
 }
 
@@ -289,4 +321,4 @@ std::vector<std::string> MdlFormat::mimeTypes() const
   return mime;
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::Io

avogadro/io/mdlformat.h

@@ -40,7 +40,8 @@ class AVOGADROIO_EXPORT MdlFormat : public FileFormat
 
   std::string specificationUrl() const override
   {
-    return "http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/direct/"
+    return "http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/"
+           "direct/"
            "reference/ctfileformats2016.pdf";
     /* for previous (2011) version, see:
     https://web.archive.org/web/20180329184712/http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip
@@ -52,9 +53,12 @@ class AVOGADROIO_EXPORT MdlFormat : public FileFormat
 
   bool read(std::istream& in, Core::Molecule& molecule) override;
   bool write(std::ostream& out, const Core::Molecule& molecule) override;
+
+protected:
+  bool m_writeProperties = false;
 };
 
-} // end Io namespace
-} // end Avogadro namespace
+} // namespace Io
+} // namespace Avogadro
 
 #endif // AVOGADRO_IO_MDLFORMAT_H

avogadro/io/sdfformat.cpp

@@ -0,0 +1,41 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#include "sdfformat.h"
+
+namespace Avogadro::Io {
+
+SdfFormat::SdfFormat() : MdlFormat()
+{
+  m_writeProperties = true;
+}
+
+SdfFormat::~SdfFormat() {}
+
+bool SdfFormat::read(std::istream& in, Core::Molecule& mol)
+{
+  return MdlFormat::read(in, mol);
+}
+
+bool SdfFormat::write(std::ostream& out, const Core::Molecule& mol)
+{
+  return MdlFormat::write(out, mol);
+}
+
+std::vector<std::string> SdfFormat::fileExtensions() const
+{
+  std::vector<std::string> ext;
+  ext.emplace_back("sdf");
+  return ext;
+}
+
+std::vector<std::string> SdfFormat::mimeTypes() const
+{
+  std::vector<std::string> mime;
+  mime.emplace_back("chemical/x-mdl-molfile");
+  return mime;
+}
+
+} // namespace Avogadro::Io

avogadro/io/sdfformat.h

@@ -0,0 +1,64 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#ifndef AVOGADRO_IO_SDFFORMAT_H
+#define AVOGADRO_IO_SDFFORMAT_H
+
+#include "fileformat.h"
+#include "mdlformat.h"
+
+namespace Avogadro {
+namespace Io {
+
+/**
+ * @class SdfFormat sdfformat.h <avogadro/io/sdfformat.h>
+ * @brief Implementation of the generic SDF format.
+ * @author Marcus D. Hanwell
+ *
+ * Differs from the MDL / Mol format in that it includes properties
+ *
+ * Currently just supports V2000 of the format.
+ */
+
+class AVOGADROIO_EXPORT SdfFormat : public MdlFormat
+{
+public:
+  SdfFormat();
+  ~SdfFormat() override;
+
+  Operations supportedOperations() const override
+  {
+    return ReadWrite | MultiMolecule | File | Stream | String;
+  }
+
+  FileFormat* newInstance() const override { return new SdfFormat; }
+  std::string identifier() const override { return "Avogadro: SDF"; }
+  std::string name() const override { return "SDF"; }
+  std::string description() const override
+  {
+    return "Generic format that contains atoms, bonds, positions.";
+  }
+
+  std::string specificationUrl() const override
+  {
+    return "http://help.accelrysonline.com/ulm/onelab/1.0/content/ulm_pdfs/"
+           "direct/"
+           "reference/ctfileformats2016.pdf";
+    /* for previous (2011) version, see:
+    https://web.archive.org/web/20180329184712/http://download.accelrys.com/freeware/ctfile-formats/ctfile-formats.zip
+    */
+  }
+
+  std::vector<std::string> fileExtensions() const override;
+  std::vector<std::string> mimeTypes() const override;
+
+  bool read(std::istream& in, Core::Molecule& molecule) override;
+  bool write(std::ostream& out, const Core::Molecule& molecule) override;
+};
+
+} // namespace Io
+} // namespace Avogadro
+
+#endif // AVOGADRO_IO_MDLFORMAT_H

avogadro/qtgui/richtextdelegate.cpp

@@ -1,21 +1,12 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2015 Marcus Johansson <[email protected]>
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "richtextdelegate.h"
 
+#include <cmath>
+
 namespace Avogadro::QtGui {
 
 // See for example
@@ -44,39 +35,21 @@ QSize RichTextDelegate::sizeHint(const QStyleOptionViewItem& o,
   doc.setHtml(ov.text);
   doc.setTextWidth(ov.rect.width());
   doc.setDefaultFont(ov.font);
-  doc.setDocumentMargin(1);
 
-  return QSize(doc.idealWidth(), doc.size().height());
+  return QSize(std::ceil(doc.idealWidth()), std::ceil(doc.size().height()));
 }
 
 void RichTextDelegate::paint(QPainter* p, const QStyleOptionViewItem& o,
                              const QModelIndex& index) const
 {
-  if (o.text.isEmpty()) {
-    // no need to do anything if the text is empty
-    QStyledItemDelegate::paint(p, o, index);
-
-    return;
-  }
-
   QStyleOptionViewItem ov = o;
   initStyleOption(&ov, index);
 
   p->save();
 
   QTextDocument doc;
   doc.setHtml(ov.text);
-
-  QTextOption textOption;
-  textOption.setWrapMode(ov.features & QStyleOptionViewItem::WrapText
-                           ? QTextOption::WordWrap
-                           : QTextOption::ManualWrap);
-  textOption.setTextDirection(ov.direction);
-  doc.setDefaultTextOption(textOption);
   doc.setDefaultFont(ov.font);
-  doc.setDocumentMargin(1);
-  doc.setTextWidth(ov.rect.width());
-  doc.adjustSize();
 
   ov.text = "";
   ov.widget->style()->drawControl(QStyle::CE_ItemViewItem, &ov, p);

avogadro/qtgui/richtextdelegate.h

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   This source file is part of the Avogadro project.
-
-  Copyright 2015 Marcus Johansson <[email protected]>
-
-  This source code is released under the New BSD License, (the "License").
-
-  Unless required by applicable law or agreed to in writing, software
-  distributed under the License is distributed on an "AS IS" BASIS,
-  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-  See the License for the specific language governing permissions and
-  limitations under the License.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTPLUGINS_RICHTEXTDELEGATE_H

avogadro/qtplugins/forcefield/scriptenergy.cpp

@@ -13,6 +13,7 @@
 #include <avogadro/io/cmlformat.h>
 #include <avogadro/io/mdlformat.h>
 #include <avogadro/io/pdbformat.h>
+#include <avogadro/io/sdfformat.h>
 #include <avogadro/io/xyzformat.h>
 
 #include <QtCore/QDebug>
@@ -191,10 +192,12 @@ ScriptEnergy::Format ScriptEnergy::stringToFormat(const std::string& str)
     return Cjson;
   else if (str == "cml")
     return Cml;
-  else if (str == "mdl" || str == "mol" || str == "sdf" || str == "sd")
+  else if (str == "mdl" || str == "mol")
     return Mdl;
   else if (str == "pdb")
     return Pdb;
+  else if (str == "sdf")
+    return Sdf;
   else if (str == "xyz")
     return Xyz;
   return NotUsed;
@@ -211,6 +214,8 @@ Io::FileFormat* ScriptEnergy::createFileFormat(ScriptEnergy::Format fmt)
       return new Io::MdlFormat;
     case Pdb:
       return new Io::PdbFormat;
+    case Sdf:
+      return new Io::SdfFormat;
     case Xyz:
       return new Io::XyzFormat;
     default:

avogadro/qtplugins/forcefield/scriptenergy.h

@@ -39,8 +39,9 @@ class ScriptEnergy : public Avogadro::Calc::EnergyCalculator
     NotUsed,
     Cjson,
     Cml,
-    Mdl, // sdf
+    Mdl,
     Pdb,
+    Sdf,
     Xyz
   };