Add a generic output reader - use internal, then cclib, then OB (#1347)

* Add a generic output reader - use internal, then cclib, then OB

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>

avogadro/qtplugins/surfaces/surfaces.cpp

@@ -38,6 +38,7 @@ namespace {
 #include <avogadro/quantumio/gamessus.h>
 #include <avogadro/quantumio/gaussiancube.h>
 #include <avogadro/quantumio/gaussianfchk.h>
+#include <avogadro/quantumio/genericoutput.h>
 #include <avogadro/quantumio/molden.h>
 #include <avogadro/quantumio/mopacaux.h>
 #include <avogadro/quantumio/nwchemjson.h>
@@ -89,6 +90,7 @@ Surfaces::Surfaces(QObject* p) : ExtensionPlugin(p), d(new PIMPL())
   Io::FileFormatManager::registerFormat(new QuantumIO::GAMESSUSOutput);
   Io::FileFormatManager::registerFormat(new QuantumIO::GaussianFchk);
   Io::FileFormatManager::registerFormat(new QuantumIO::GaussianCube);
+  Io::FileFormatManager::registerFormat(new QuantumIO::GenericOutput);
   Io::FileFormatManager::registerFormat(new QuantumIO::MoldenFile);
   Io::FileFormatManager::registerFormat(new QuantumIO::MopacAux);
   Io::FileFormatManager::registerFormat(new QuantumIO::NWChemJson);

avogadro/quantumio/CMakeLists.txt

@@ -4,6 +4,7 @@ avogadro_headers(QuantumIO
   gamessus.h
   gaussianfchk.h
   gaussiancube.h
+  genericoutput.h
   molden.h
   mopacaux.h
   nwchemjson.h
@@ -16,6 +17,7 @@ target_sources(QuantumIO PRIVATE
   gamessus.cpp
   gaussianfchk.cpp
   gaussiancube.cpp
+  genericoutput.cpp
   molden.cpp
   mopacaux.cpp
   nwchemjson.cpp

avogadro/quantumio/gamessus.cpp

@@ -33,8 +33,6 @@ std::vector<std::string> GAMESSUSOutput::fileExtensions() const
   std::vector<std::string> extensions;
   extensions.emplace_back("gamout");
   extensions.emplace_back("gamess");
-  extensions.emplace_back("log");
-  extensions.emplace_back("out");
   return extensions;
 }
 

avogadro/quantumio/genericoutput.cpp

@@ -0,0 +1,96 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#include "genericoutput.h"
+
+#include <avogadro/io/fileformat.h>
+#include <avogadro/io/fileformatmanager.h>
+
+#include "gamessus.h"
+#include "nwchemlog.h"
+#include "orca.h"
+
+#include <iostream>
+
+namespace Avogadro::QuantumIO {
+
+GenericOutput::GenericOutput() {}
+
+GenericOutput::~GenericOutput() {}
+
+std::vector<std::string> GenericOutput::fileExtensions() const
+{
+  std::vector<std::string> extensions;
+  extensions.emplace_back("out");
+  extensions.emplace_back("output");
+  extensions.emplace_back("log");
+  return extensions;
+}
+
+std::vector<std::string> GenericOutput::mimeTypes() const
+{
+  return std::vector<std::string>();
+}
+
+bool GenericOutput::read(std::istream& in, Core::Molecule& molecule)
+{
+  // check the stream line-by-line until we see the program name
+  FileFormat* reader = nullptr;
+
+  std::string line;
+  while (std::getline(in, line)) {
+    if (line.find("Northwest Computational Chemistry Package") !=
+        std::string::npos) {
+      // NWChem
+      reader = new NWChemLog;
+      break;
+    } else if (line.find("GAMESS VERSION") != std::string::npos) {
+      // GAMESS-US .. don't know if we can read Firefly or GAMESS-UK
+      reader = new GAMESSUSOutput;
+      break;
+    } else if (line.find("O   R   C   A") != std::string::npos) {
+      // ORCA reader
+      reader = new ORCAOutput;
+      break;
+    }
+  }
+
+  // if we didn't find a program name, check for cclib or OpenBabel
+  // prefer cclib if it's available
+  if (reader == nullptr) {
+    // check what output is available
+    std::vector<const FileFormat*> readers =
+      Io::FileFormatManager::instance().fileFormatsFromFileExtension(
+        "out", FileFormat::File | FileFormat::Read);
+
+    // loop through writers to check for "cclib" or "Open Babel"
+    for (const FileFormat* r : readers) {
+      if (r->name() == "cclib") {
+        reader = r->newInstance();
+        break;
+      } else if (r->identifier().compare(0, 9, "OpenBabel") == 0) {
+        reader = r->newInstance();
+        break;
+      }
+    }
+  }
+
+  // rewind the stream
+  in.seekg(0, std::ios::beg);
+  in.clear();
+
+  if (reader) {
+    bool success = reader->readFile(fileName(), molecule);
+    delete reader;
+    return success;
+  } else {
+    appendError(
+      "Could not determine the program used to generate this output file.");
+    delete reader;
+    return false;
+  }
+}
+
+} // namespace Avogadro::QuantumIO

avogadro/quantumio/genericoutput.h

@@ -0,0 +1,50 @@
+/******************************************************************************
+  This source file is part of the Avogadro project.
+  This source code is released under the 3-Clause BSD License, (see "LICENSE").
+******************************************************************************/
+
+#ifndef AVOGADRO_QUANTUMIO_GENERICOUTPUT_H
+#define AVOGADRO_QUANTUMIO_GENERICOUTPUT_H
+
+#include "avogadroquantumioexport.h"
+#include <avogadro/io/fileformat.h>
+
+#include <map>
+#include <vector>
+
+namespace Avogadro {
+namespace QuantumIO {
+
+class AVOGADROQUANTUMIO_EXPORT GenericOutput : public Io::FileFormat
+{
+public:
+  GenericOutput();
+  ~GenericOutput() override;
+
+  Operations supportedOperations() const override
+  {
+    return Read | File | Stream | String;
+  }
+
+  FileFormat* newInstance() const override { return new GenericOutput; }
+  std::string identifier() const override { return "Avogadro: Generic Output"; }
+  std::string name() const override { return "Generic Output"; }
+  std::string description() const override { return "Generic output format."; }
+
+  std::string specificationUrl() const override { return ""; }
+
+  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&, const Core::Molecule&) override
+  {
+    // Empty, as we do not write output files.
+    return false;
+  }
+};
+
+} // namespace QuantumIO
+} // namespace Avogadro
+
+#endif

avogadro/quantumio/nwchemlog.cpp

@@ -29,8 +29,6 @@ NWChemLog::~NWChemLog()
 std::vector<std::string> NWChemLog::fileExtensions() const
 {
   std::vector<std::string> extensions;
-  extensions.emplace_back("log");
-  extensions.emplace_back("out");
   extensions.emplace_back("nwchem");
   return extensions;
 }

avogadro/quantumio/orca.cpp

@@ -30,8 +30,7 @@ ORCAOutput::~ORCAOutput() {}
 std::vector<std::string> ORCAOutput::fileExtensions() const
 {
   std::vector<std::string> extensions;
-  extensions.emplace_back("log");
-  extensions.emplace_back("out");
+  extensions.emplace_back("orca");
   return extensions;
 }