Merge remote-tracking branch 'origin/devel'

Merging from 2023.5.0.dev into 2023.5.0 for the release
OpenBioSim · Dec 15, 2023 · 16421d9 · 16421d9
2 parents 5412f1c + 1e9a6b9
commit 16421d9
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Showing 64 changed files with 4,614 additions and 423 deletions.
diff --git a/corelib/src/libs/SireIO/CMakeLists.txt b/corelib/src/libs/SireIO/CMakeLists.txt
@@ -48,6 +48,7 @@ set ( SIREIO_HEADERS
       netcdffile.h
       pdb.h
       pdb2.h
+      pdbx.h
       perturbationslibrary.h
       protoms.h
       sdf.h
@@ -95,6 +96,7 @@ set ( SIREIO_SOURCES
       netcdffile.cpp
       pdb.cpp
       pdb2.cpp
+      pdbx.cpp
       perturbationslibrary.cpp
       protoms.cpp
       sdf.cpp

diff --git a/corelib/src/libs/SireIO/mol2.cpp b/corelib/src/libs/SireIO/mol2.cpp
@@ -2380,6 +2380,9 @@ void Mol2::addToSystem(System &system, const PropertyMap &map) const
     // you should loop through each molecule in the system and work out
     // which ones are described in the file, and then add data from the file
     // to thise molecules.
+    throw SireError::unsupported(QObject::tr(
+                                     "You cannot add data from a mol2 file to an existing system!"),
+                                 CODELOC);
 }
 
 /** Internal function used to get the molecule structure for molecule 'imol'. */

diff --git a/corelib/src/libs/SireIO/moleculeparser.cpp b/corelib/src/libs/SireIO/moleculeparser.cpp
@@ -1929,8 +1929,19 @@ MoleculeParserPtr MoleculeParser::parse(const System &system, const QString &for
     cannot be recognised, or if there is an error in parsing. */
 MoleculeParserPtr MoleculeParser::parse(const QString &filename, const PropertyMap &map)
 {
-    MoleculeParserPtr parser = MoleculeParser::_pvt_parse(filename, map);
-    getFileCache()->clear();
+    MoleculeParserPtr parser;
+
+    try
+    {
+        parser = MoleculeParser::_pvt_parse(filename, map);
+        getFileCache()->clear();
+    }
+    catch (...)
+    {
+        getFileCache()->clear();
+        throw;
+    }
+
     return parser;
 }
 
@@ -1939,48 +1950,56 @@ QList<MoleculeParserPtr> MoleculeParser::parse(const QStringList &filenames, con
 {
     QList<MoleculeParserPtr> result;
 
-    if (filenames.count() == 1)
-    {
-        result.append(MoleculeParser::_pvt_parse(filenames[0], map));
-    }
-    else
+    try
     {
-        QVector<MoleculeParserPtr> parsers(filenames.count());
-
-        bool run_parallel = true;
-
-        if (map["parallel"].hasValue())
+        if (filenames.count() == 1)
         {
-            run_parallel = map["parallel"].value().asA<BooleanProperty>().value();
-        }
-
-        if (run_parallel)
-        {
-            // parse the files in parallel - we use a grain size of 1
-            // as each file can be pretty big, and there won't be many of them
-            tbb::parallel_for(
-                tbb::blocked_range<int>(0, filenames.count(), 1),
-                [&](tbb::blocked_range<int> r)
-                {
-                    for (int i = r.begin(); i < r.end(); ++i)
-                    {
-                        parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
-                    }
-                },
-                tbb::simple_partitioner());
+            result.append(MoleculeParser::_pvt_parse(filenames[0], map));
         }
         else
         {
-            for (int i = 0; i < filenames.count(); ++i)
+            QVector<MoleculeParserPtr> parsers(filenames.count());
+
+            bool run_parallel = true;
+
+            if (map["parallel"].hasValue())
+            {
+                run_parallel = map["parallel"].value().asA<BooleanProperty>().value();
+            }
+
+            if (run_parallel)
             {
-                parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                // parse the files in parallel - we use a grain size of 1
+                // as each file can be pretty big, and there won't be many of them
+                tbb::parallel_for(
+                    tbb::blocked_range<int>(0, filenames.count(), 1),
+                    [&](tbb::blocked_range<int> r)
+                    {
+                        for (int i = r.begin(); i < r.end(); ++i)
+                        {
+                            parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                        }
+                    },
+                    tbb::simple_partitioner());
             }
+            else
+            {
+                for (int i = 0; i < filenames.count(); ++i)
+                {
+                    parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                }
+            }
+
+            result = parsers.toList();
         }
 
-        result = parsers.toList();
+        getFileCache()->clear();
+    }
+    catch (...)
+    {
+        getFileCache()->clear();
+        throw;
     }
-
-    getFileCache()->clear();
 
     return result;
 }