Merge pull request #937 from ghutchis/use-cjson-openbabel

Check for Open Babel CJSON support: use it if available

avogadro/qtplugins/openbabel/obfileformat.cpp

@@ -1,29 +1,16 @@
 /******************************************************************************
-
   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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "obfileformat.h"
 
 #include "obprocess.h"
 
-#include <avogadro/io/cmlformat.h>
-#include <avogadro/io/pdbformat.h>
-
 #include <nlohmann/json.hpp>
 
 #include <QtCore/QCoreApplication>
+#include <QtCore/QDebug>
 #include <QtCore/QFileInfo>
 #include <QtCore/QTimer>
 
@@ -81,11 +68,12 @@ OBFileFormat::OBFileFormat(const std::string& name_,
                            const std::string& specificationUrl_,
                            const std::vector<std::string> fileExtensions_,
                            const std::vector<std::string> mimeTypes_,
-                           bool fileOnly_)
+                           const std::string& defaultFormat_, bool fileOnly_)
   : Io::FileFormat(), m_description(description_),
     m_fileExtensions(fileExtensions_), m_mimeTypes(mimeTypes_),
     m_identifier(identifier_), m_name(name_),
-    m_specificationUrl(specificationUrl_), m_fileOnly(fileOnly_)
+    m_specificationUrl(specificationUrl_), m_defaultFormat(defaultFormat_),
+    m_fileOnly(fileOnly_)
 {}
 
 OBFileFormat::~OBFileFormat() {}
@@ -132,8 +120,10 @@ bool OBFileFormat::read(std::istream& in, Core::Molecule& molecule)
   }
 
   // check if we're going to read to a different format
-  // default is CML
-  QString format = QString::fromStdString(opts.value("format", "cml"));
+  // 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
@@ -187,17 +177,22 @@ bool OBFileFormat::read(std::istream& in, Core::Molecule& molecule)
   }
 
   if (format == "cml") {
-    Io::CmlFormat cmlReader;
-    if (!cmlReader.readString(std::string(output.constData()), molecule)) {
+    if (!m_cmlFormat.readString(std::string(output.constData()), molecule)) {
       appendError(std::string("Error while reading OpenBabel-generated CML:"));
-      appendError(cmlReader.error());
+      appendError(m_cmlFormat.error());
+      return false;
+    }
+  } else if (format == "cjson") {
+    if (!m_cjsonFormat.readString(std::string(output.constData()), molecule)) {
+      appendError(
+        std::string("Error while reading OpenBabel-generated CJSON:"));
+      appendError(m_cjsonFormat.error());
       return false;
     }
   } else if (format == "pdb") {
-    Io::PdbFormat pdbReader;
-    if (!pdbReader.readString(std::string(output.constData()), molecule)) {
+    if (!m_pdbFormat.readString(std::string(output.constData()), molecule)) {
       appendError(std::string("Error while reading OpenBabel-generated PDB:"));
-      appendError(pdbReader.error());
+      appendError(m_pdbFormat.error());
       return false;
     }
   } else {
@@ -225,13 +220,22 @@ bool OBFileFormat::write(std::ostream& out, const Core::Molecule& molecule)
     }
   }
 
-  // Generate CML to give to OpenBabel
-  std::string cml;
-  Io::CmlFormat cmlWriter;
-  if (!cmlWriter.writeString(cml, molecule)) {
-    appendError(std::string("Error while writing CML:"));
-    appendError(cmlWriter.error());
-    return false;
+  qDebug() << " writing to " << m_defaultFormat.c_str();
+
+  // Generate CML or CJSON to give to OpenBabel
+  std::string outputString;
+  if (m_defaultFormat == "cml") {
+    if (!m_cmlFormat.writeString(outputString, molecule)) {
+      appendError(std::string("Error while writing CML:"));
+      appendError(m_cmlFormat.error());
+      return false;
+    }
+  } else if (m_defaultFormat == "cjson") {
+    if (!m_cjsonFormat.writeString(outputString, molecule)) {
+      appendError(std::string("Error while writing CJSON:"));
+      appendError(m_cjsonFormat.error());
+      return false;
+    }
   }
 
   // Block until the OpenBabel conversion finishes:
@@ -246,7 +250,8 @@ bool OBFileFormat::write(std::ostream& out, const Core::Molecule& molecule)
     appendError("Internal error: No file extensions set.");
     return false;
   }
-  proc.convert(QByteArray(cml.c_str()), "cml",
+
+  proc.convert(QByteArray(outputString.c_str()), m_defaultFormat.c_str(),
                QString::fromStdString(m_fileExtensions.front()), options);
 
   QByteArray output;
@@ -274,7 +279,7 @@ Io::FileFormat* OBFileFormat::newInstance() const
 {
   return new OBFileFormat(m_name, m_identifier, m_description,
                           m_specificationUrl, m_fileExtensions, m_mimeTypes,
-                          m_fileOnly);
+                          m_defaultFormat, m_fileOnly);
 }
 
 } // namespace QtPlugins

avogadro/qtplugins/openbabel/obfileformat.h

@@ -1,24 +1,17 @@
 /******************************************************************************
-
   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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTPLUGINS_OBFILEFORMAT_H
 #define AVOGADRO_QTPLUGINS_OBFILEFORMAT_H
 
 #include <avogadro/io/fileformat.h>
 
+#include <avogadro/io/cjsonformat.h>
+#include <avogadro/io/cmlformat.h>
+#include <avogadro/io/pdbformat.h>
+
 namespace Avogadro {
 namespace QtPlugins {
 
@@ -34,6 +27,7 @@ class OBFileFormat : public Avogadro::Io::FileFormat
                const std::string& specificationUrl_,
                const std::vector<std::string> fileExtensions_,
                const std::vector<std::string> mimeTypes_,
+               const std::string& defaultFormat_,
                bool fileOnly_ = false);
   ~OBFileFormat() override;
 
@@ -81,7 +75,13 @@ class OBFileFormat : public Avogadro::Io::FileFormat
   std::string m_identifier;
   std::string m_name;
   std::string m_specificationUrl;
+  std::string m_defaultFormat;
   bool m_fileOnly;
+
+  // internal format objects for interchange with obabel
+  Io::CjsonFormat m_cjsonFormat;
+  Io::CmlFormat m_cmlFormat;
+  Io::PdbFormat m_pdbFormat;
 };
 
 } // namespace QtPlugins

avogadro/qtplugins/openbabel/obforcefielddialog.cpp

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #include "obforcefielddialog.h"

avogadro/qtplugins/openbabel/obforcefielddialog.h

@@ -1,17 +1,6 @@
 /******************************************************************************
-
   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.
-
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
 ******************************************************************************/
 
 #ifndef AVOGADRO_QTPLUGINS_OBFORCEFIELDDIALOG_H

avogadro/qtplugins/openbabel/obprocess.cpp

@@ -325,17 +325,23 @@ void OBProcess::queryChargesPrepare()
 }
 
 bool OBProcess::optimizeGeometry(const QByteArray& mol,
-                                 const QStringList& options)
+                                 const QStringList& options,
+                                 const std::string format)
 {
   if (!tryLockProcess()) {
     qWarning() << "OBProcess::optimizeGeometry(): process already in use.";
     return false;
   }
 
   QStringList realOptions;
-  realOptions << "-icml"
-              << "-ocml"
-              << "--minimize"
+  if (format == "cjson") {
+    realOptions << "-icjson"
+                << "-ocjson";
+  } else {
+    realOptions << "-icml"
+                << "-ocml";
+  }
+  realOptions << "--minimize"
               << "--noh" // new in OB 3.0.1
               << "--log" << options;
 

avogadro/qtplugins/openbabel/obprocess.h

@@ -269,7 +269,7 @@ public slots:
    * optimization finishes, optimizeGeometryFinished will be emitted with the
    * result of the optimization.
    *
-   * The optimization is started with
+   * The optimization is started with, e.g. 
    * `obabel -icml -ocml --minimize <options>`
    *
    * The standard output is recorded and returned by optimizeGeometryFinished.
@@ -279,7 +279,7 @@ public slots:
    *
    * @return True if the process started successfully, false otherwise.
    */
-  bool optimizeGeometry(const QByteArray& cml, const QStringList& options);
+  bool optimizeGeometry(const QByteArray& cml, const QStringList& options, std::string format = "cml");
 signals:
   /**
    * Emitted with the standard output of the process when it finishes.