Fix 375 and add support for writing trajectory frames to named files

corelib/src/libs/SireIO/gro87.cpp

@@ -693,54 +693,75 @@ Frame Gro87::getFrame(int i) const
 {
     i = SireID::Index(i).map(this->nFrames());
 
-    return SireMol::Frame();
-}
+    QVector<Vector> frame_coords;
+    if (not this->coords.isEmpty())
+    {
+        frame_coords = this->coords[i];
+    }
 
-/** Return the Gro87 object that contains only the information for the ith
-    frame. This allows you to extract and create a system for the ith frame
-    from a trajectory */
-Gro87 Gro87::operator[](int i) const
-{
-    i = Index(i).map(this->nFrames());
+    QVector<Velocity3D> frame_vels;
 
-    if (nFrames() == 1)
-        return *this;
+    if (not this->vels.isEmpty())
+    {
+        const auto velocities = this->vels[i];
+        const int nats = frame_vels.count();
 
-    Gro87 ret(*this);
+        frame_vels = QVector<Velocity3D>(nats);
 
-    if (not coords.isEmpty())
-    {
-        ret.coords = {coords[i]};
-    }
+        auto velocities_data = frame_vels.data();
+        const auto vels_data = velocities.constData();
 
-    if (not vels.isEmpty())
-    {
-        ret.vels = {vels[i]};
-    }
+        // velocity is Angstroms per 1/20.455 ps
+        const auto vel_unit = (1.0 / 20.455) * angstrom / picosecond;
 
-    if (not current_time.isEmpty())
-    {
-        ret.current_time = {current_time[i]};
+        for (int i = 0; i < nats; ++i)
+        {
+            const Vector &vel = vels_data[i];
+            velocities_data[i] = Velocity3D(vel.x() * vel_unit, vel.y() * vel_unit, vel.z() * vel_unit);
+        }
     }
 
-    if (not box_v1.isEmpty())
+    // Convert the box vectors into a Space object.
+    SpacePtr space;
+    if (not this->box_v1.isEmpty() and not this->box_v2.isEmpty() and not this->box_v3.isEmpty())
     {
-        ret.box_v1 = {box_v1[i]};
-    }
+        Vector v1 = this->box_v1[i];
+        Vector v2 = this->box_v2[i];
+        Vector v3 = this->box_v3[i];
 
-    if (not box_v2.isEmpty())
+        if (v1.y() == 0 and v1.z() == 0 and v2.x() == 0 and v2.z() == 0 and v3.x() == 0 and v3.y() == 0)
+        {
+            // PeridicBox
+            space = SpacePtr(new PeriodicBox(Vector(v1.x(), v2.y(), v3.z())));
+        }
+        else
+        {
+            // TriclinicBox
+            space = SpacePtr(new TriclinicBox(v1, v2, v3));
+        }
+    }
+    else
     {
-        ret.box_v2 = {box_v2[i]};
+        // no box information
+        space = SpacePtr(new Cartesian());
     }
 
-    if (not box_v3.isEmpty())
+    Time frame_time;
+    if (not this->current_time.isEmpty())
     {
-        ret.box_v3 = {box_v3[i]};
+        frame_time = this->current_time[i] * SireUnits::picosecond;
     }
 
-    ret.assertSane();
+    return SireMol::Frame(frame_coords, frame_vels, space.read(), frame_time);
+}
 
-    return ret;
+/** Return the Gro87 object that contains only the information for the ith
+    frame. This allows you to extract and create a system for the ith frame
+    from a trajectory */
+Gro87 Gro87::operator[](int i) const
+{
+    throw SireError::unsupported(
+        QObject::tr("Gro87::operator[] is not yet implemented!"), CODELOC);
 }
 
 /** Return the parser that has been constructed by reading in the passed

corelib/src/libs/SireIO/moleculeparser.cpp

@@ -1669,7 +1669,35 @@ QStringList MoleculeParser::writeToFile(const QString &filename) const
 
     QStringList written_files;
 
-    createDirectoryForFile(filename);
+    // Check whether list of trajectory frames have been specified via the map.
+    // If so, then the name will be prefixed with "frames_names:"
+    QStringList frame_names;
+    if (filename.contains("frames_names:"))
+    {
+        // Split the part of the string following "frames_names:" by commas to get
+        // individual frame names.
+        const QString frames_names_str = filename.section("frames_names:", 1);
+        frame_names = frames_names_str.split(",", Qt::SkipEmptyParts);
+
+        // Convert to absolute paths.
+        for (auto &frame_name : frame_names)
+        {
+            frame_name = QFileInfo(frame_name.trimmed()).absoluteFilePath();
+        }
+
+        if (frame_names.size() != frames_to_write.size())
+        {
+            throw SireError::program_bug(
+                QObject::tr("The number of frame names provided (%1) does not match the number of frames to write (%2).")
+                    .arg(frame_names.size())
+                    .arg(frames_to_write.size()),
+                CODELOC);
+        }
+    }
+    else
+    {
+        createDirectoryForFile(filename);
+    }
 
     if (this->writingTrajectory() and this->isFrame())
     {
@@ -1694,51 +1722,61 @@ QStringList MoleculeParser::writeToFile(const QString &filename) const
 
         const int padding = QString::number(largest_frame).length();
 
-        // in this case, we are going to create a directory named after the
-        // filename, into which all the frames will be written
-        auto fileinfo = QFileInfo(filename);
+        QDir framedir;
+        QFileInfo fileinfo;
+        bool write_to_frame_dir = false;
 
-        if (fileinfo.exists())
+        if (frame_names.isEmpty())
         {
-            // by default, we support overwriting of files - so remove this if it is a file
-            if (fileinfo.isDir())
-            {
-                _check_and_remove_frame_dir(fileinfo);
+            fileinfo = QFileInfo(filename);
+            write_to_frame_dir = true;
 
-                // rebuild so it is not cached
-                fileinfo = QFileInfo(filename);
+            // in this case, we are going to create a directory named after the
+            // filename, into which all the frames will be written
+            fileinfo = QFileInfo(filename);
 
-                if (fileinfo.exists())
-                    throw SireError::file_error(QObject::tr(
-                                                    "Could not write the trajectory for file '%1' as there "
-                                                    "is already a directory with this name that contains "
-                                                    "files that don't appear to have been created by sire.")
-                                                    .arg(filename),
-                                                CODELOC);
-            }
-            else
+            if (fileinfo.exists())
             {
-                auto dir = fileinfo.absoluteDir();
-
-                if (not dir.remove(fileinfo.fileName()))
-                    throw SireError::file_error(QObject::tr(
-                                                    "Could not write the trajectory for file '%1' as "
-                                                    "we don't have permission to remove the existing "
-                                                    "file with this name.")
-                                                    .arg(filename),
-                                                CODELOC);
+                // by default, we support overwriting of files - so remove this if it is a file
+                if (fileinfo.isDir())
+                {
+                    _check_and_remove_frame_dir(fileinfo);
+
+                    // rebuild so it is not cached
+                    fileinfo = QFileInfo(filename);
+
+                    if (fileinfo.exists())
+                        throw SireError::file_error(QObject::tr(
+                                                        "Could not write the trajectory for file '%1' as there "
+                                                        "is already a directory with this name that contains "
+                                                        "files that don't appear to have been created by sire.")
+                                                        .arg(filename),
+                                                    CODELOC);
+                }
+                else
+                {
+                    auto dir = fileinfo.absoluteDir();
+
+                    if (not dir.remove(fileinfo.fileName()))
+                        throw SireError::file_error(QObject::tr(
+                                                        "Could not write the trajectory for file '%1' as "
+                                                        "we don't have permission to remove the existing "
+                                                        "file with this name.")
+                                                        .arg(filename),
+                                                    CODELOC);
+                }
             }
-        }
 
-        QDir framedir(fileinfo.absoluteFilePath());
+            framedir = QDir(fileinfo.absoluteFilePath());
 
-        if (not framedir.mkpath("."))
-            throw SireError::file_error(QObject::tr(
-                                            "Could not create the directory into which to write the "
-                                            "trajectory for '%1'. Check that there is enough space "
-                                            "and you have the correct permissions.")
-                                            .arg(framedir.absolutePath()),
-                                        CODELOC);
+            if (not framedir.mkpath("."))
+                throw SireError::file_error(QObject::tr(
+                                                "Could not create the directory into which to write the "
+                                                "trajectory for '%1'. Check that there is enough space "
+                                                "and you have the correct permissions.")
+                                                .arg(framedir.absolutePath()),
+                                            CODELOC);
+        }
 
         const auto suffix = fileinfo.completeSuffix();
 
@@ -1765,13 +1803,26 @@ QStringList MoleculeParser::writeToFile(const QString &filename) const
                     // construct a copy of this parser for this frame
                     auto parser = this->construct(thread_s, m);
 
-                    // now write it to the file, numbered by the frame number and time
-                    QString frame_filename = framedir.filePath(
-                        "frame_" +
-                        QString::number(i).rightJustified(padding, '0') +
-                        "_" +
-                        QString::number(time).replace(".", "-") +
-                        "." + suffix);
+                    QString frame_filename;
+
+                    if (write_to_frame_dir)
+                    {
+                        // now write it to the file, numbered by the frame number and time
+                        QDir framedir(fileinfo.absoluteFilePath());
+
+                        frame_filename = framedir.filePath(
+                            "frame_" +
+                            QString::number(i).rightJustified(padding, '0') +
+                            "_" +
+                            QString::number(time).replace(".", "-") +
+                            "." + suffix);
+                    }
+                    else
+                    {
+                        // write to the specified frame name
+                        frame_filename = frame_names[i];
+                        createDirectoryForFile(frame_filename);
+                    }
 
                     parser.read().writeToFile(frame_filename);
 
@@ -1792,13 +1843,26 @@ QStringList MoleculeParser::writeToFile(const QString &filename) const
                 // construct a copy of this parser for this frame
                 auto parser = this->construct(s, m);
 
-                // now write it to the file, numbered by the frame number
-                QString frame_filename = framedir.filePath(
-                    "frame_" +
-                    QString::number(i).rightJustified(padding, '0') +
-                    "_" +
-                    QString::number(time).replace(".", "-") +
-                    "." + suffix);
+                QString frame_filename;
+
+                if (write_to_frame_dir)
+                {
+                    // now write it to the file, numbered by the frame number
+                    QDir framedir(fileinfo.absoluteFilePath());
+
+                    frame_filename = framedir.filePath(
+                        "frame_" +
+                        QString::number(i).rightJustified(padding, '0') +
+                        "_" +
+                        QString::number(time).replace(".", "-") +
+                        "." + suffix);
+                }
+                else
+                {
+                    // write to the specified frame name
+                    frame_filename = frame_names[i];
+                    createDirectoryForFile(frame_filename);
+                }
 
                 parser.read().writeToFile(frame_filename);
 
@@ -1810,7 +1874,14 @@ QStringList MoleculeParser::writeToFile(const QString &filename) const
 
         // only return the directory name, as we can handle
         // reading all the frames contained therein
-        written_files.append(framedir.absolutePath());
+        if (write_to_frame_dir)
+        {
+            written_files.append(framedir.absolutePath());
+        }
+        else
+        {
+            written_files.append(frame_names);
+        }
     }
     else
     {
@@ -2452,6 +2523,38 @@ QStringList MoleculeParser::write(const System &system, const QString &filename,
         }
     }
 
+    // Check for a frame_names property in the map, which is used to control the naming of
+    // specific frames when writing trajectories.
+    if (map.specified("frame_names"))
+    {
+        const auto frame_names_property = map["frame_names"];
+
+        QStringList frame_names;
+
+        if (frame_names_property.hasSource())
+        {
+            frame_names = frame_names_property.source().split(",");
+        }
+        else
+        {
+            try
+            {
+                frame_names = frame_names_property.value().asA<StringProperty>().toString().split(",");
+            }
+            catch (...)
+            {
+                throw SireError::incompatible_error(
+                    QObject::tr("The 'frame_names' property must be a StringProperty containing "
+                                "a comma-separated list of filenames to use for each frame when "
+                                "writing trajectories."),
+                    CODELOC);
+            }
+        }
+
+        // add the special prefix to the first filename
+        filenames[0] = "frames_names:" + frame_names.join(",");
+    }
+
     // now we have a list of filenames and associated formats, actually
     // write the files
     return ::pvt_write(system, filenames, fileformats, map);

doc/source/changelog.rst

@@ -33,6 +33,11 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
 * Added support for saving crash reports during Sire dynamics runs.
 
+* Fix missing ``Sire::IO::Gro87::getFrame`` implementation to allow creation of
+  trajectory frames from GROMACS coordinate file data.
+
+* Add support for writing trajectory frames to user-defined file names.
+
 `2025.2.0 <https://github.com/openbiosim/sire/compare/2025.1.0...2025.2.0>`__ - October 2025
 --------------------------------------------------------------------------------------------
 

doc/source/tutorial/part01/06_trajectories.rst

@@ -157,5 +157,17 @@ System( name=output num_molecules=1 num_residues=3 num_atoms=22 ) 1000
    The individual frame files are named using the frame number plus
    the time in picoseconds for that frame.
 
+Rather than writing to a frame directory, it is also possible to use specific
+names for each frame file by passing a list of filenames to :func:`sire.save`,
+e.g.:
+
+>>> f = sr.save(mols[0].trajectory()[:2], ["cat.pdb", "dog.pdb"])
+>>> print(f)
+['cat.pdb', 'dog.pdb']
+
+When specifying frame names, the number of names provided must match the
+number of frames being saved. In addition, the frames must have a common
+file format (e.g. all PDB, or all GRO etc).
+
 :mod:`sire` has extensive support for trajectories. To learn more,
 check out the :doc:`detailed guide <../../cheatsheet/trajectory>`.