Merge pull request #1452 from ghutchis/add-msgpack

Add new MessagePack version of CJSON

avogadro/io/CMakeLists.txt

@@ -3,6 +3,7 @@ add_library(IO)
 avogadro_headers(IO
   cjsonformat.h
   cmlformat.h
+  cmsgpackformat.h
   dcdformat.h
   fileformat.h
   fileformatmanager.h
@@ -19,6 +20,7 @@ avogadro_headers(IO
 target_sources(IO PRIVATE
   cjsonformat.cpp
   cmlformat.cpp
+  cmsgpackformat.cpp
   dcdformat.cpp
   fileformat.cpp
   fileformatmanager.cpp

avogadro/io/cjsonformat.cpp

@@ -82,7 +82,18 @@ bool isBooleanArray(json& j)
 
 bool CjsonFormat::read(std::istream& file, Molecule& molecule)
 {
-  json jsonRoot = json::parse(file, nullptr, false);
+  return deserialize(file, molecule, true);
+}
+
+bool CjsonFormat::deserialize(std::istream& file, Molecule& molecule,
+                              bool isJson)
+{
+  json jsonRoot;
+  if (isJson)
+    jsonRoot = json::parse(file, nullptr, false);
+  else // msgpack
+    jsonRoot = json::from_msgpack(file);
+
   if (jsonRoot.is_discarded()) {
     appendError("Error reading CJSON file.");
     return false;
@@ -634,6 +645,12 @@ bool CjsonFormat::read(std::istream& file, Molecule& molecule)
 }
 
 bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
+{
+  return serialize(file, molecule, true);
+}
+
+bool CjsonFormat::serialize(std::ostream& file, const Molecule& molecule,
+                            bool isJson)
 {
   json opts;
   if (!options().empty())
@@ -1015,7 +1032,8 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
       modes.push_back(static_cast<unsigned int>(i) + 1);
       freqs.push_back(molecule.vibrationFrequencies()[i]);
       inten.push_back(molecule.vibrationIRIntensities()[i]);
-      raman.push_back(molecule.vibrationRamanIntensities()[i]);
+      if (molecule.vibrationRamanIntensities().size() > i)
+        raman.push_back(molecule.vibrationRamanIntensities()[i]);
       Core::Array<Vector3> atomDisplacements = molecule.vibrationLx(i);
       json eigenVector;
       for (auto pos : atomDisplacements) {
@@ -1028,7 +1046,8 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
     root["vibrations"]["modes"] = modes;
     root["vibrations"]["frequencies"] = freqs;
     root["vibrations"]["intensities"] = inten;
-    root["vibrations"]["ramanIntensities"] = raman;
+    if (molecule.vibrationRamanIntensities().size() > 0)
+      root["vibrations"]["ramanIntensities"] = raman;
     root["vibrations"]["eigenVectors"] = eigenVectors;
   }
 
@@ -1059,8 +1078,11 @@ bool CjsonFormat::write(std::ostream& file, const Molecule& molecule)
     root["layer"]["settings"][settings.first] = setting;
   }
 
-  // Write out the file, use a two space indent to "pretty print".
-  file << std::setw(2) << root;
+  if (isJson)
+    file << std::setw(2) << root;
+  else { // write msgpack
+    json::to_msgpack(root, file);
+  }
 
   return true;
 }

avogadro/io/cjsonformat.h

@@ -41,17 +41,21 @@ class AVOGADROIO_EXPORT CjsonFormat : public FileFormat
 
   std::string specificationUrl() const override
   {
-    return "http://wiki.openchemistry.org/Chemical_JSON";
+    return "https://github.com/openchemistry/chemicaljson";
   }
 
   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;
+
+  // internal - to allow JSON or MsgPack to be written
+  bool deserialize(std::istream& in, Core::Molecule& molecule, bool json);
+  bool serialize(std::ostream& out, const Core::Molecule& molecule, bool json);
 };
 
-} // end Io namespace
-} // end Avogadro namespace
+} // namespace Io
+} // namespace Avogadro
 
 #endif // AVOGADRO_IO_CJSONFORMAT_H

avogadro/io/cmsgpackformat.cpp

@@ -0,0 +1,45 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#include "cmsgpackformat.h"
+
+#include <iostream>
+
+using namespace std;
+
+namespace Avogadro::Io {
+
+CMsgPackFormat::CMsgPackFormat() : CjsonFormat()
+{
+  m_json = false;
+}
+
+CMsgPackFormat::~CMsgPackFormat() = default;
+
+vector<std::string> CMsgPackFormat::fileExtensions() const
+{
+  vector<std::string> ext;
+  ext.emplace_back("cmpk");
+  return ext;
+}
+
+vector<std::string> CMsgPackFormat::mimeTypes() const
+{
+  vector<std::string> mime;
+  mime.emplace_back("chemical/x-cmpack");
+  return mime;
+}
+
+bool CMsgPackFormat::read(std::istream& in, Core::Molecule& molecule)
+{
+  return CjsonFormat::deserialize(in, molecule, false);
+}
+
+bool CMsgPackFormat::write(std::ostream& out, const Core::Molecule& molecule)
+{
+  return CjsonFormat::serialize(out, molecule, false);
+}
+
+} // namespace Avogadro::Io

avogadro/io/cmsgpackformat.h

@@ -0,0 +1,62 @@
+/******************************************************************************
+  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_CMSGPACKFORMAT_H
+#define AVOGADRO_IO_CMSGPACKFORMAT_H
+
+#include "cjsonformat.h"
+#include "fileformat.h"
+
+namespace Avogadro {
+namespace Core {
+class GaussianSet;
+}
+namespace Io {
+
+/**
+ * @class CMsgPackFormat cmsgpackformat.h <avogadro/io/cmsgpackformat.h>
+ * @brief Implementation of the Chemical MessagePack format.
+ */
+
+class AVOGADROIO_EXPORT CMsgPackFormat : public CjsonFormat
+{
+public:
+  CMsgPackFormat();
+  ~CMsgPackFormat() override;
+
+  Operations supportedOperations() const override
+  {
+    return ReadWrite | File | Stream | String;
+  }
+
+  FileFormat* newInstance() const override { return new CMsgPackFormat; }
+  std::string identifier() const override { return "Avogadro: CMsgPack"; }
+  std::string name() const override { return "Chemical MessagePack"; }
+  std::string description() const override
+  {
+    return "CMsgPack format is a lightweight intermediate format used to "
+           "exchange "
+           "information between Avogadro and other data parsing applications";
+  }
+
+  std::string specificationUrl() const override
+  {
+    return "https://github.com/openchemistry/chemicaljson";
+  }
+
+  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;
+
+  // write MessagePack
+  bool m_json = false;
+};
+
+} // namespace Io
+} // namespace Avogadro
+
+#endif // AVOGADRO_IO_CMSGPACKFORMAT_H

avogadro/io/fileformatmanager.cpp

@@ -9,6 +9,7 @@
 
 #include "cjsonformat.h"
 #include "cmlformat.h"
+#include "cmsgpackformat.h"
 #include "dcdformat.h"
 #include "gromacsformat.h"
 #include "lammpsformat.h"
@@ -134,7 +135,7 @@ bool FileFormatManager::addFormat(FileFormat* format)
     appendError("Format " + format->identifier() + " already loaded.");
     return false;
   }
-  for (auto & m_format : m_formats) {
+  for (auto& m_format : m_formats) {
     if (m_format == format) {
       appendError("The format object was already loaded.");
       return false;
@@ -146,11 +147,11 @@ bool FileFormatManager::addFormat(FileFormat* format)
   m_formats.push_back(format);
   m_identifiers[format->identifier()].push_back(index);
   std::vector<std::string> mimes = format->mimeTypes();
-  for (auto & mime : mimes) {
+  for (auto& mime : mimes) {
     m_mimeTypes[mime].push_back(index);
   }
   std::vector<std::string> extensions = format->fileExtensions();
-  for (auto & extension : extensions) {
+  for (auto& extension : extensions) {
     m_fileExtensions[extension].push_back(index);
   }
 
@@ -160,7 +161,7 @@ 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)
 {
   for (auto key = keys.begin(), keyEnd = keys.end(); key != keyEnd; ++key) {
@@ -171,13 +172,12 @@ void removeFromMap(Map& map, const VectorOfKeys& keys, const ValueType& val)
     if (vec.size() <= 1) {
       map.erase(*key);
     } else {
-      auto newEnd =
-        std::remove(vec.begin(), vec.end(), val);
+      auto newEnd = std::remove(vec.begin(), vec.end(), val);
       vec.resize(newEnd - vec.begin());
     }
   }
 }
-}
+} // namespace
 
 bool FileFormatManager::removeFormat(const std::string& identifier)
 {
@@ -284,6 +284,7 @@ FileFormatManager::FileFormatManager()
 {
   addFormat(new CmlFormat);
   addFormat(new CjsonFormat);
+  addFormat(new CMsgPackFormat);
   addFormat(new DcdFormat);
   addFormat(new GromacsFormat);
   addFormat(new LammpsTrajectoryFormat);
@@ -303,7 +304,7 @@ FileFormatManager::FileFormatManager()
 FileFormatManager::~FileFormatManager()
 {
   // Delete the file formats that were loaded.
-  for (auto & m_format : m_formats) {
+  for (auto& m_format : m_formats) {
     delete m_format;
   }
   m_formats.clear();
@@ -314,9 +315,9 @@ std::vector<std::string> FileFormatManager::filteredKeysFromFormatMap(
   const FileFormatManager::FormatIdMap& fmap) const
 {
   std::vector<std::string> result;
-  for (const auto & it : fmap) {
-    for (auto formatIt = it.second.begin();
-         formatIt != it.second.end(); ++formatIt) {
+  for (const auto& it : fmap) {
+    for (auto formatIt = it.second.begin(); formatIt != it.second.end();
+         ++formatIt) {
       if (filter == FileFormat::None ||
           (m_formats[*formatIt]->supportedOperations() & filter) == filter) {
         result.push_back(it.first);
@@ -383,4 +384,4 @@ void FileFormatManager::appendError(const std::string& errorMessage)
   m_error += errorMessage + "\n";
 }
 
-} // end Avogadro namespace
+} // namespace Avogadro::Io