Support for reading AMBER mdcrd trajectories

avogadro/io/CMakeLists.txt

@@ -31,6 +31,7 @@ set(HEADERS
   fileformat.h
   fileformatmanager.h
   gromacsformat.h
+  mdcrdformat.h
   mdlformat.h
   pdbformat.h
   poscarformat.h
@@ -46,6 +47,7 @@ set(SOURCES
   fileformat.cpp
   fileformatmanager.cpp
   gromacsformat.cpp
+  mdcrdformat.cpp
   mdlformat.cpp
   pdbformat.cpp
   poscarformat.cpp

avogadro/io/fileformatmanager.cpp

@@ -23,6 +23,7 @@
 #include "dcdformat.h"
 #include "gromacsformat.h"
 #include "lammpsformat.h"
+#include "mdcrdformat.h"
 #include "mdlformat.h"
 #include "pdbformat.h"
 #include "poscarformat.h"
@@ -162,7 +163,7 @@ bool FileFormatManager::addFormat(FileFormat* format)
 namespace {
 // Lookup each key from "keys" in "map", and remove "val" from the Map's
 // data value (which is a vector of ValueType)
-template<typename Map, typename VectorOfKeys, typename ValueType>
+template <typename Map, typename VectorOfKeys, typename ValueType>
 void removeFromMap(Map& map, const VectorOfKeys& keys, const ValueType& val)
 {
   typedef typename VectorOfKeys::const_iterator KeysIter;
@@ -180,7 +181,7 @@ void removeFromMap(Map& map, const VectorOfKeys& keys, const ValueType& val)
     }
   }
 }
-}
+} // namespace
 
 bool FileFormatManager::removeFormat(const std::string& identifier)
 {
@@ -291,6 +292,7 @@ FileFormatManager::FileFormatManager()
   addFormat(new CmlFormat);
   addFormat(new CjsonFormat);
   addFormat(new GromacsFormat);
+  addFormat(new MdcrdFormat);
   addFormat(new MdlFormat);
   addFormat(new PdbFormat);
   addFormat(new PoscarFormat);
@@ -385,5 +387,5 @@ void FileFormatManager::appendError(const std::string& errorMessage)
   m_error += errorMessage + "\n";
 }
 
-} // end Io namespace
-} // end Avogadro namespace
+} // namespace Io
+} // namespace Avogadro

avogadro/io/mdcrdformat.cpp

@@ -0,0 +1,103 @@
+/******************************************************************************
+
+  This source file is part of the Avogadro project.
+
+  Copyright 2013 Kitware, Inc.
+
+  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.
+
+******************************************************************************/
+
+#include "mdcrdformat.h"
+
+#include <avogadro/core/elements.h>
+#include <avogadro/core/molecule.h>
+#include <avogadro/core/unitcell.h>
+#include <avogadro/core/utilities.h>
+#include <avogadro/core/vector.h>
+
+#include <iomanip>
+#include <iostream>
+#include <istream>
+#include <ostream>
+#include <sstream>
+#include <string>
+
+using std::endl;
+using std::getline;
+using std::map;
+using std::string;
+using std::to_string;
+using std::vector;
+
+namespace Avogadro {
+namespace Io {
+
+using Core::Array;
+using Core::Atom;
+using Core::Elements;
+using Core::lexicalCast;
+using Core::Molecule;
+using Core::split;
+using Core::trimmed;
+using Core::UnitCell;
+
+#ifndef _WIN32
+using std::isalpha;
+#endif
+
+#define MDCRD_EOF -1
+
+MdcrdFormat::MdcrdFormat() {}
+
+MdcrdFormat::~MdcrdFormat() {}
+
+bool MdcrdFormat::read(std::istream& inStream, Core::Molecule& mol)
+{
+  string title;
+  float x, y, z;
+
+  typedef map<string, unsigned char> AtomTypeMap;
+  AtomTypeMap atomTypes;
+
+  Array<Vector3> positions;
+
+  getline(inStream, title);
+  mol.setData("name", title);
+
+  while (inStream >> x >> y >> z) {
+    Vector3 pos(x, y, z);
+    positions.push_back(pos);
+  }
+
+  mol.setCoordinate3d(positions, 0);
+  return true;
+}
+
+bool MdcrdFormat::write(std::ostream& outStream, const Core::Molecule& mol)
+{
+  return false;
+}
+
+std::vector<std::string> MdcrdFormat::fileExtensions() const
+{
+  std::vector<std::string> ext;
+  ext.push_back("mdcrd");
+  return ext;
+}
+
+std::vector<std::string> MdcrdFormat::mimeTypes() const
+{
+  std::vector<std::string> mime;
+  mime.push_back("N/A");
+  return mime;
+}
+
+} // namespace Io
+} // namespace Avogadro

avogadro/io/mdcrdformat.h

@@ -0,0 +1,62 @@
+/******************************************************************************
+
+  This source file is part of the Avogadro project.
+
+  Copyright 2013 Kitware, Inc.
+
+  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.
+
+******************************************************************************/
+
+#ifndef AVOGADRO_IO_MDCRDFORMAT_H
+#define AVOGADRO_IO_MDCRDFORMAT_H
+
+#include "fileformat.h"
+
+namespace Avogadro {
+namespace Io {
+
+/**
+ * @class MdcrdFormat mdcrdformat.h <avogadro/io/mdcrdformat.h>
+ * @brief Implementation of the generic mdcrd format.
+ * @author David C. Lonie
+ */
+
+class AVOGADROIO_EXPORT MdcrdFormat : public FileFormat
+{
+public:
+  MdcrdFormat();
+  ~MdcrdFormat() override;
+
+  Operations supportedOperations() const override
+  {
+    return ReadWrite | MultiMolecule | File | Stream | String;
+  }
+
+  FileFormat* newInstance() const override { return new MdcrdFormat; }
+  std::string identifier() const override { return "Avogadro: AMBER MDCRD"; }
+  std::string name() const override { return "MDCRD"; }
+  std::string description() const override
+  {
+    return "Generic format that tabulates atomic symbols and 3D positions.";
+  }
+
+  std::string specificationUrl() const override { return ""; }
+
+  std::vector<std::string> fileExtensions() const override;
+  std::vector<std::string> mimeTypes() const override;
+
+  bool read(std::istream& inStream, Core::Molecule& molecule) override;
+  bool write(std::ostream& outStream, const Core::Molecule& molecule) override;
+};
+
+} // namespace Io
+} // namespace Avogadro
+
+#endif // AVOGADRO_IO_MDCRDFORMAT_H

avogadro/qtgui/CMakeLists.txt

@@ -44,6 +44,7 @@ set(HEADERS
   interfacewidget.h
   meshgenerator.h
   molecule.h
+  moleculeinfodialog.h
   moleculemodel.h
   multiviewwidget.h
   periodictableview.h
@@ -74,6 +75,7 @@ set(SOURCES
   interfacewidget.cpp
   meshgenerator.cpp
   molecule.cpp
+  moleculeinfodialog.cpp
   moleculemodel.cpp
   multiviewwidget.cpp
   periodictablescene_p.cpp
@@ -90,6 +92,7 @@ set(SOURCES
 
 set(UIS
   customelementdialog.ui
+  moleculeinfodialog.ui
 )
 qt5_wrap_ui(UI_SOURCES ${UIS})
 list(APPEND SOURCES ${UI_SOURCES})