diff --git a/corelib/src/libs/SireIO/biosimspace.cpp b/corelib/src/libs/SireIO/biosimspace.cpp
index c21a92a8e..89dd01ca5 100644
--- a/corelib/src/libs/SireIO/biosimspace.cpp
+++ b/corelib/src/libs/SireIO/biosimspace.cpp
@@ -1687,6 +1687,64 @@ namespace SireIO
         return ion;
     }
 
+    System setCoordinates(System &system, const QVector<QVector<float>> &coordinates, const bool is_lambda1, const PropertyMap &map)
+    {
+        // Make sure that the number of coordinates matches the number of atoms.
+        if (system.nAtoms() != coordinates.size())
+        {
+            throw SireError::incompatible_error(
+                QObject::tr("Number of coordinates (%1) does not match number of atoms in the system (%2)!")
+                    .arg(coordinates.size())
+                    .arg(system.nAtoms()),
+                CODELOC);
+        }
+
+        // Keep track of the current coordinate index.
+        unsigned coord_idx = 0;
+
+        // Loop over all molecules in the system in MolIdx order.
+        for (int i = 0; i < system.nMolecules(); ++i)
+        {
+            // Extract the molecule and make it editable.
+            auto molecule = system.molecule(MolIdx(i)).molecule().edit();
+
+            QString prop_name = "coordinates";
+            if (molecule.hasProperty("is_perturbable"))
+            {
+                if (is_lambda1)
+                    prop_name = "coordinates1";
+                else
+                    prop_name = "coordinates0";
+            }
+
+            // Get the coordinate property.
+            const auto coord_prop = map[prop_name];
+
+            // Loop over all atoms in the molecule.
+            for (int j = 0; j < molecule.nAtoms(); ++j)
+            {
+                // Construct the new coordinate.
+                const auto coord = Vector(coordinates[coord_idx + j][0],
+                                          coordinates[coord_idx + j][1],
+                                          coordinates[coord_idx + j][2]);
+
+                // Set the new coordinates.
+                molecule = molecule.edit()
+                                   .atom(AtomIdx(j))
+                                   .setProperty(coord_prop, coord)
+                                   .molecule();
+            }
+
+            // Update the molecule in the system.
+            system.update(molecule.commit());
+
+            // Update the coordinate index.
+            coord_idx += molecule.nAtoms();
+        }
+
+        return system;
+    }
+
     Vector cross(const Vector &v0, const Vector &v1)
     {
         double nx = v0.y() * v1.z() - v0.z() * v1.y();
diff --git a/corelib/src/libs/SireIO/biosimspace.h b/corelib/src/libs/SireIO/biosimspace.h
index b90c6db8a..081735cff 100644
--- a/corelib/src/libs/SireIO/biosimspace.h
+++ b/corelib/src/libs/SireIO/biosimspace.h
@@ -351,6 +351,26 @@ namespace SireIO
     SIREIO_EXPORT Molecule createChlorineIon(
         const Vector &coords, const QString model, const PropertyMap &map = PropertyMap());
 
+    //! Set the coordinates of the entire system.
+    /* \param system
+            The molecular system of interest.
+
+        \param coordinates
+            The new coordinates for the system.
+
+        \param is_lambda1
+            Whether this is for the lambda = 1 state.
+
+        \param map
+            A dictionary of user-defined molecular property names.
+
+        \retval system
+            The system with updated coordinates.
+     */
+    SIREIO_EXPORT SireSystem::System setCoordinates(
+        SireSystem::System &system, const QVector<QVector<float>> &coordinates,
+        const bool is_lambda1 = false, const PropertyMap &map = PropertyMap());
+
     Vector cross(const Vector &v0, const Vector &v1);
 } // namespace SireIO
 
@@ -366,6 +386,7 @@ SIRE_EXPOSE_FUNCTION(SireIO::updateAndPreserveOrder)
 SIRE_EXPOSE_FUNCTION(SireIO::updateCoordinatesAndVelocities)
 SIRE_EXPOSE_FUNCTION(SireIO::createSodiumIon)
 SIRE_EXPOSE_FUNCTION(SireIO::createChlorineIon)
+SIRE_EXPOSE_FUNCTION(SireIO::setCoordinates)
 
 SIRE_END_HEADER
 
diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
index 8a2759e55..0431accdd 100644
--- a/doc/source/changelog.rst
+++ b/doc/source/changelog.rst
@@ -27,6 +27,8 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Add missing dihedrals for all 1-4 atom paths in ``Sire::MM::AmberParams::validateAndFix``,
   not just the first one found.
 
+* Added :func:`Sire::IO::setCoordinates` function to set atom coordinates of an entire system.
+
 `2025.2.0 <https://github.com/openbiosim/sire/compare/2025.1.0...2025.2.0>`__ - October 2025
 --------------------------------------------------------------------------------------------
 
diff --git a/tests/biosimspace/test_set_coordinates.py b/tests/biosimspace/test_set_coordinates.py
new file mode 100644
index 000000000..2a0adba47
--- /dev/null
+++ b/tests/biosimspace/test_set_coordinates.py
@@ -0,0 +1,84 @@
+import sire as sr
+import numpy as np
+
+
+def test_set_coordinates(ala_mols):
+
+    # Clone the input molecules.
+    mols = ala_mols.clone()
+
+    # Store the existing coordinates as a NumPy array.
+    coords = sr.io.get_coords_array(mols)
+
+    # Modify the system to multiply all coordinates by 2.
+    new_mols = sr.legacy.IO.setCoordinates(mols._system, (coords * 2.0).tolist())
+
+    # Get the new coordinates as a NumPy array.
+    new_coords = sr.io.get_coords_array(new_mols)
+
+    # Make sure the new coordinates are as expected.
+    assert (
+        np.sum(np.round(new_coords / coords)) == 6.0 * mols.num_atoms()
+    ), "Coordinates were not set correctly."
+
+
+def test_set_coordinates_perturbable(merged_ethane_methanol):
+
+    # Clone the input molecules.
+    mols = merged_ethane_methanol.clone()
+
+    # First link to the reference state.
+    mols = sr.morph.link_to_reference(mols)
+
+    # Store the existing coordinates as a NumPy array.
+    coords = sr.io.get_coords_array(mols)
+
+    # Modify the system to multiply all coordinates by 2.
+    new_mols = sr.legacy.IO.setCoordinates(mols._system, (coords * 2.0).tolist())
+
+    # Link to the reference state.
+    new_mols = sr.system.System(new_mols)
+    new_mols = sr.morph.link_to_reference(new_mols)
+
+    # Get the new coordinates as a NumPy array.
+    new_coords = sr.io.get_coords_array(new_mols)
+
+    # Divide the new coordinates by the old coordinates.
+    ratio = new_coords / coords
+
+    # Set any NaN values to 2.0 (in case of zero coordinates).
+    ratio = np.where(np.isnan(ratio), 2.0, ratio)
+
+    # Make sure the new coordinates are as expected.
+    assert (
+        np.sum(np.round(ratio)) == 6.0 * mols.num_atoms()
+    ), "Coordinates were not set correctly."
+
+    # Now link to the perturbable state.
+    mols = sr.morph.link_to_perturbed(mols)
+
+    # Store the existing coordinates as a NumPy array.
+    coords = sr.io.get_coords_array(mols)
+
+    # Modify the system to multiply all coordinates by 2.
+    new_mols = sr.legacy.IO.setCoordinates(
+        mols._system, (coords * 2.0).tolist(), is_lambda1=True
+    )
+
+    # Link to the perturbable state.
+    new_mols = sr.system.System(new_mols)
+    new_mols = sr.morph.link_to_perturbed(new_mols)
+
+    # Get the new coordinates as a NumPy array.
+    new_coords = sr.io.get_coords_array(new_mols)
+
+    # Divide the new coordinates by the old coordinates.
+    ratio = new_coords / coords
+
+    # Set any NaN values to 2.0 (in case of zero coordinates).
+    ratio = np.where(np.isnan(ratio), 2.0, ratio)
+
+    # Make sure the new coordinates are as expected.
+    assert (
+        np.sum(np.round(ratio)) == 6.0 * mols.num_atoms()
+    ), "Coordinates were not set correctly."
diff --git a/wrapper/IO/Amber.pypp.cpp b/wrapper/IO/Amber.pypp.cpp
index d321929b6..4cfc341ab 100644
--- a/wrapper/IO/Amber.pypp.cpp
+++ b/wrapper/IO/Amber.pypp.cpp
@@ -87,6 +87,8 @@ namespace bp = boost::python;
 
 SireIO::Amber __copy__(const SireIO::Amber &other){ return SireIO::Amber(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 const char* pvt_get_name(const SireIO::Amber&){ return "SireIO::Amber";}
@@ -197,13 +199,13 @@ void register_Amber_class(){
                 "writeCrd"
                 , writeCrd_function_value
                 , ( bp::arg("mols"), bp::arg("space"), bp::arg("crdfile"), bp::arg("map")=SireBase::PropertyMap() )
-                , "" );
+                , "Write the coordinates of the molecules in the passed MoleculeGroup in the\npassed Space to an Amber7,\nformat coordinaterestart file. The passed property map is used to find\nthe required properties" );
         
         }
         Amber_exposer.staticmethod( "typeName" );
-        Amber_exposer.def( "__copy__", &__copy__);
-        Amber_exposer.def( "__deepcopy__", &__copy__);
-        Amber_exposer.def( "clone", &__copy__);
+        Amber_exposer.def( "__copy__", &__copy__<SireIO::Amber>);
+        Amber_exposer.def( "__deepcopy__", &__copy__<SireIO::Amber>);
+        Amber_exposer.def( "clone", &__copy__<SireIO::Amber>);
         Amber_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::Amber >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         Amber_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::Amber >,
diff --git a/wrapper/IO/AmberPrm.pypp.cpp b/wrapper/IO/AmberPrm.pypp.cpp
index e18672e68..d3ba24c8c 100644
--- a/wrapper/IO/AmberPrm.pypp.cpp
+++ b/wrapper/IO/AmberPrm.pypp.cpp
@@ -11,6 +11,10 @@ namespace bp = boost::python;
 
 #include "SireBase/parallel.h"
 
+#include "SireBase/progressbar.h"
+
+#include "SireBase/propertylist.h"
+
 #include "SireBase/stringproperty.h"
 
 #include "SireBase/tempdir.h"
@@ -37,6 +41,8 @@ namespace bp = boost::python;
 
 #include "SireMM/internalff.h"
 
+#include "SireMM/lj1264parameter.h"
+
 #include "SireMM/ljparameter.h"
 
 #include "SireMaths/maths.h"
@@ -125,6 +131,8 @@ namespace bp = boost::python;
 
 SireIO::AmberPrm __copy__(const SireIO::AmberPrm &other){ return SireIO::AmberPrm(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -142,6 +150,7 @@ void register_AmberPrm_class(){
             .value("INTEGER", SireIO::AmberPrm::INTEGER)
             .value("FLOAT", SireIO::AmberPrm::FLOAT)
             .value("STRING", SireIO::AmberPrm::STRING)
+            .value("FFLOAT", SireIO::AmberPrm::FFLOAT)
             .export_values()
             ;
         AmberPrm_exposer.def( bp::init< QString const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("filename"), bp::arg("map")=SireBase::PropertyMap() ), "Construct by reading from the file called filename") );
@@ -603,6 +612,18 @@ void register_AmberPrm_class(){
                 , bp::release_gil_policy()
                 , "" );
         
+        }
+        { //::SireIO::AmberPrm::warnings
+        
+            typedef ::QStringList ( ::SireIO::AmberPrm::*warnings_function_type)(  ) const;
+            warnings_function_type warnings_function_value( &::SireIO::AmberPrm::warnings );
+            
+            AmberPrm_exposer.def( 
+                "warnings"
+                , warnings_function_value
+                , bp::release_gil_policy()
+                , "" );
+        
         }
         { //::SireIO::AmberPrm::what
         
@@ -618,9 +639,9 @@ void register_AmberPrm_class(){
         }
         AmberPrm_exposer.staticmethod( "parse" );
         AmberPrm_exposer.staticmethod( "typeName" );
-        AmberPrm_exposer.def( "__copy__", &__copy__);
-        AmberPrm_exposer.def( "__deepcopy__", &__copy__);
-        AmberPrm_exposer.def( "clone", &__copy__);
+        AmberPrm_exposer.def( "__copy__", &__copy__<SireIO::AmberPrm>);
+        AmberPrm_exposer.def( "__deepcopy__", &__copy__<SireIO::AmberPrm>);
+        AmberPrm_exposer.def( "clone", &__copy__<SireIO::AmberPrm>);
         AmberPrm_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::AmberPrm >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         AmberPrm_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::AmberPrm >,
diff --git a/wrapper/IO/AmberRst.pypp.cpp b/wrapper/IO/AmberRst.pypp.cpp
index 70b9cdf5b..30fb1f37e 100644
--- a/wrapper/IO/AmberRst.pypp.cpp
+++ b/wrapper/IO/AmberRst.pypp.cpp
@@ -69,6 +69,8 @@ namespace bp = boost::python;
 
 SireIO::AmberRst __copy__(const SireIO::AmberRst &other){ return SireIO::AmberRst(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -338,9 +340,9 @@ void register_AmberRst_class(){
         }
         AmberRst_exposer.staticmethod( "parse" );
         AmberRst_exposer.staticmethod( "typeName" );
-        AmberRst_exposer.def( "__copy__", &__copy__);
-        AmberRst_exposer.def( "__deepcopy__", &__copy__);
-        AmberRst_exposer.def( "clone", &__copy__);
+        AmberRst_exposer.def( "__copy__", &__copy__<SireIO::AmberRst>);
+        AmberRst_exposer.def( "__deepcopy__", &__copy__<SireIO::AmberRst>);
+        AmberRst_exposer.def( "clone", &__copy__<SireIO::AmberRst>);
         AmberRst_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::AmberRst >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         AmberRst_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::AmberRst >,
diff --git a/wrapper/IO/AmberRst7.pypp.cpp b/wrapper/IO/AmberRst7.pypp.cpp
index 28ebd62a3..85e6a1619 100644
--- a/wrapper/IO/AmberRst7.pypp.cpp
+++ b/wrapper/IO/AmberRst7.pypp.cpp
@@ -55,6 +55,8 @@ namespace bp = boost::python;
 
 SireIO::AmberRst7 __copy__(const SireIO::AmberRst7 &other){ return SireIO::AmberRst7(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -345,9 +347,9 @@ void register_AmberRst7_class(){
         }
         AmberRst7_exposer.staticmethod( "parse" );
         AmberRst7_exposer.staticmethod( "typeName" );
-        AmberRst7_exposer.def( "__copy__", &__copy__);
-        AmberRst7_exposer.def( "__deepcopy__", &__copy__);
-        AmberRst7_exposer.def( "clone", &__copy__);
+        AmberRst7_exposer.def( "__copy__", &__copy__<SireIO::AmberRst7>);
+        AmberRst7_exposer.def( "__deepcopy__", &__copy__<SireIO::AmberRst7>);
+        AmberRst7_exposer.def( "clone", &__copy__<SireIO::AmberRst7>);
         AmberRst7_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::AmberRst7 >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         AmberRst7_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::AmberRst7 >,
diff --git a/wrapper/IO/AmberTraj.pypp.cpp b/wrapper/IO/AmberTraj.pypp.cpp
index 123670eff..18a058145 100644
--- a/wrapper/IO/AmberTraj.pypp.cpp
+++ b/wrapper/IO/AmberTraj.pypp.cpp
@@ -67,6 +67,8 @@ namespace bp = boost::python;
 
 SireIO::AmberTraj __copy__(const SireIO::AmberTraj &other){ return SireIO::AmberTraj(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -322,9 +324,9 @@ void register_AmberTraj_class(){
         }
         AmberTraj_exposer.staticmethod( "parse" );
         AmberTraj_exposer.staticmethod( "typeName" );
-        AmberTraj_exposer.def( "__copy__", &__copy__);
-        AmberTraj_exposer.def( "__deepcopy__", &__copy__);
-        AmberTraj_exposer.def( "clone", &__copy__);
+        AmberTraj_exposer.def( "__copy__", &__copy__<SireIO::AmberTraj>);
+        AmberTraj_exposer.def( "__deepcopy__", &__copy__<SireIO::AmberTraj>);
+        AmberTraj_exposer.def( "clone", &__copy__<SireIO::AmberTraj>);
         AmberTraj_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::AmberTraj >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         AmberTraj_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::AmberTraj >,
diff --git a/wrapper/IO/BrokenParser.pypp.cpp b/wrapper/IO/BrokenParser.pypp.cpp
index 6ec0406a4..fa14b0f03 100644
--- a/wrapper/IO/BrokenParser.pypp.cpp
+++ b/wrapper/IO/BrokenParser.pypp.cpp
@@ -79,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::BrokenParser __copy__(const SireIO::BrokenParser &other){ return SireIO::BrokenParser(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -260,9 +262,9 @@ void register_BrokenParser_class(){
         
         }
         BrokenParser_exposer.staticmethod( "typeName" );
-        BrokenParser_exposer.def( "__copy__", &__copy__);
-        BrokenParser_exposer.def( "__deepcopy__", &__copy__);
-        BrokenParser_exposer.def( "clone", &__copy__);
+        BrokenParser_exposer.def( "__copy__", &__copy__<SireIO::BrokenParser>);
+        BrokenParser_exposer.def( "__deepcopy__", &__copy__<SireIO::BrokenParser>);
+        BrokenParser_exposer.def( "clone", &__copy__<SireIO::BrokenParser>);
         BrokenParser_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::BrokenParser >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         BrokenParser_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::BrokenParser >,
diff --git a/wrapper/IO/CMakeAutogenFile.txt b/wrapper/IO/CMakeAutogenFile.txt
index 4695ffe6b..b5ccdb7dc 100644
--- a/wrapper/IO/CMakeAutogenFile.txt
+++ b/wrapper/IO/CMakeAutogenFile.txt
@@ -1,45 +1,45 @@
 # WARNING - AUTOGENERATED FILE - CONTENTS WILL BE OVERWRITTEN!
 set ( PYPP_SOURCES
-       PerturbationsTemplate.pypp.cpp
-       ProtoMSParameters.pypp.cpp
-       AmberPrm.pypp.cpp
-       PDB2.pypp.cpp
-       SDF.pypp.cpp
-       TinkerParameters.pypp.cpp
-       CharmmPSF.pypp.cpp
        Gro87.pypp.cpp
+       TRR.pypp.cpp
+       ZmatrixMaker.pypp.cpp
+       GroMolType.pypp.cpp
+       GroAtom.pypp.cpp
+       NullIO.pypp.cpp
+       MoleculeParser.pypp.cpp
+       Tinker.pypp.cpp
+       CharmmPSF.pypp.cpp
+       PDBParameters.pypp.cpp
+       IOParametersBase.pypp.cpp
+       SDF.pypp.cpp
+       BrokenParser.pypp.cpp
+       XTC.pypp.cpp
+       Cube.pypp.cpp
+       GroSystem.pypp.cpp
+       NullParser.pypp.cpp
+       AmberPrm.pypp.cpp
+       PerturbationsTemplate.pypp.cpp
        _IO_free_functions.pypp.cpp
-       PDB.pypp.cpp
-       IOBase.pypp.cpp
+       PDB2.pypp.cpp
        PDBx.pypp.cpp
+       AmberRst7.pypp.cpp
+       IOBase.pypp.cpp
+       Supplementary.pypp.cpp
+       TinkerParameters.pypp.cpp
        FlexibilityTemplate.pypp.cpp
-       GroSystem.pypp.cpp
        DCD.pypp.cpp
-       AmberRst.pypp.cpp
-       PDBParameters.pypp.cpp
+       FileTrajectoryParser.pypp.cpp
+       PerturbationsLibrary.pypp.cpp
+       AmberTraj.pypp.cpp
+       ProtoMSParameters.pypp.cpp
+       PDB.pypp.cpp
        GroTop.pypp.cpp
-       ZmatrixMaker.pypp.cpp
-       NullIO.pypp.cpp
-       NullParser.pypp.cpp
-       TRR.pypp.cpp
-       Supplementary.pypp.cpp
-       IOParametersBase.pypp.cpp
        Amber.pypp.cpp
-       GroMolType.pypp.cpp
-       Tinker.pypp.cpp
-       GroAtom.pypp.cpp
-       AmberRst7.pypp.cpp
        TrajectoryMonitor.pypp.cpp
-       PerturbationsLibrary.pypp.cpp
-       Cube.pypp.cpp
-       Mol2.pypp.cpp
-       FileTrajectoryParser.pypp.cpp
-       MoleculeParser.pypp.cpp
+       AmberRst.pypp.cpp
        ProtoMS.pypp.cpp
+       Mol2.pypp.cpp
        FlexibilityLibrary.pypp.cpp
-       AmberTraj.pypp.cpp
-       BrokenParser.pypp.cpp
-       XTC.pypp.cpp
        SireIO_containers.cpp
        SireIO_properties.cpp
        SireIO_registrars.cpp
diff --git a/wrapper/IO/CharmmPSF.pypp.cpp b/wrapper/IO/CharmmPSF.pypp.cpp
index 99a1be45d..c41747441 100644
--- a/wrapper/IO/CharmmPSF.pypp.cpp
+++ b/wrapper/IO/CharmmPSF.pypp.cpp
@@ -73,6 +73,8 @@ namespace bp = boost::python;
 
 SireIO::CharmmPSF __copy__(const SireIO::CharmmPSF &other){ return SireIO::CharmmPSF(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -452,9 +454,9 @@ void register_CharmmPSF_class(){
         
         }
         CharmmPSF_exposer.staticmethod( "typeName" );
-        CharmmPSF_exposer.def( "__copy__", &__copy__);
-        CharmmPSF_exposer.def( "__deepcopy__", &__copy__);
-        CharmmPSF_exposer.def( "clone", &__copy__);
+        CharmmPSF_exposer.def( "__copy__", &__copy__<SireIO::CharmmPSF>);
+        CharmmPSF_exposer.def( "__deepcopy__", &__copy__<SireIO::CharmmPSF>);
+        CharmmPSF_exposer.def( "clone", &__copy__<SireIO::CharmmPSF>);
         CharmmPSF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::CharmmPSF >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         CharmmPSF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::CharmmPSF >,
diff --git a/wrapper/IO/Cube.pypp.cpp b/wrapper/IO/Cube.pypp.cpp
index 172377b01..1129c1ebe 100644
--- a/wrapper/IO/Cube.pypp.cpp
+++ b/wrapper/IO/Cube.pypp.cpp
@@ -31,6 +31,8 @@ namespace bp = boost::python;
 
 SireIO::Cube __copy__(const SireIO::Cube &other){ return SireIO::Cube(other); }
 
+#include "Helpers/copy.hpp"
+
 const char* pvt_get_name(const SireIO::Cube&){ return "SireIO::Cube";}
 
 #include "Helpers/release_gil_policy.hpp"
@@ -94,9 +96,9 @@ void register_Cube_class(){
                 , "" );
         
         }
-        Cube_exposer.def( "__copy__", &__copy__);
-        Cube_exposer.def( "__deepcopy__", &__copy__);
-        Cube_exposer.def( "clone", &__copy__);
+        Cube_exposer.def( "__copy__", &__copy__<SireIO::Cube>);
+        Cube_exposer.def( "__deepcopy__", &__copy__<SireIO::Cube>);
+        Cube_exposer.def( "clone", &__copy__<SireIO::Cube>);
         Cube_exposer.def( "__str__", &pvt_get_name);
         Cube_exposer.def( "__repr__", &pvt_get_name);
     }
diff --git a/wrapper/IO/DCD.pypp.cpp b/wrapper/IO/DCD.pypp.cpp
index 3c6c65ef5..6b0326cb2 100644
--- a/wrapper/IO/DCD.pypp.cpp
+++ b/wrapper/IO/DCD.pypp.cpp
@@ -83,6 +83,8 @@ namespace bp = boost::python;
 
 SireIO::DCD __copy__(const SireIO::DCD &other){ return SireIO::DCD(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -352,9 +354,9 @@ void register_DCD_class(){
         }
         DCD_exposer.staticmethod( "parse" );
         DCD_exposer.staticmethod( "typeName" );
-        DCD_exposer.def( "__copy__", &__copy__);
-        DCD_exposer.def( "__deepcopy__", &__copy__);
-        DCD_exposer.def( "clone", &__copy__);
+        DCD_exposer.def( "__copy__", &__copy__<SireIO::DCD>);
+        DCD_exposer.def( "__deepcopy__", &__copy__<SireIO::DCD>);
+        DCD_exposer.def( "clone", &__copy__<SireIO::DCD>);
         DCD_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::DCD >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         DCD_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::DCD >,
diff --git a/wrapper/IO/FileTrajectoryParser.pypp.cpp b/wrapper/IO/FileTrajectoryParser.pypp.cpp
index 1084fbcb8..c5b550aa3 100644
--- a/wrapper/IO/FileTrajectoryParser.pypp.cpp
+++ b/wrapper/IO/FileTrajectoryParser.pypp.cpp
@@ -65,6 +65,8 @@ namespace bp = boost::python;
 
 SireIO::FileTrajectoryParser __copy__(const SireIO::FileTrajectoryParser &other){ return SireIO::FileTrajectoryParser(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -320,9 +322,9 @@ void register_FileTrajectoryParser_class(){
         }
         FileTrajectoryParser_exposer.staticmethod( "parse" );
         FileTrajectoryParser_exposer.staticmethod( "typeName" );
-        FileTrajectoryParser_exposer.def( "__copy__", &__copy__);
-        FileTrajectoryParser_exposer.def( "__deepcopy__", &__copy__);
-        FileTrajectoryParser_exposer.def( "clone", &__copy__);
+        FileTrajectoryParser_exposer.def( "__copy__", &__copy__<SireIO::FileTrajectoryParser>);
+        FileTrajectoryParser_exposer.def( "__deepcopy__", &__copy__<SireIO::FileTrajectoryParser>);
+        FileTrajectoryParser_exposer.def( "clone", &__copy__<SireIO::FileTrajectoryParser>);
         FileTrajectoryParser_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::FileTrajectoryParser >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         FileTrajectoryParser_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::FileTrajectoryParser >,
diff --git a/wrapper/IO/FlexibilityLibrary.pypp.cpp b/wrapper/IO/FlexibilityLibrary.pypp.cpp
index 80c95c87f..f2ff6fca8 100644
--- a/wrapper/IO/FlexibilityLibrary.pypp.cpp
+++ b/wrapper/IO/FlexibilityLibrary.pypp.cpp
@@ -49,6 +49,8 @@ namespace bp = boost::python;
 
 SireIO::FlexibilityLibrary __copy__(const SireIO::FlexibilityLibrary &other){ return SireIO::FlexibilityLibrary(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -157,9 +159,9 @@ void register_FlexibilityLibrary_class(){
         
         }
         FlexibilityLibrary_exposer.staticmethod( "typeName" );
-        FlexibilityLibrary_exposer.def( "__copy__", &__copy__);
-        FlexibilityLibrary_exposer.def( "__deepcopy__", &__copy__);
-        FlexibilityLibrary_exposer.def( "clone", &__copy__);
+        FlexibilityLibrary_exposer.def( "__copy__", &__copy__<SireIO::FlexibilityLibrary>);
+        FlexibilityLibrary_exposer.def( "__deepcopy__", &__copy__<SireIO::FlexibilityLibrary>);
+        FlexibilityLibrary_exposer.def( "clone", &__copy__<SireIO::FlexibilityLibrary>);
         FlexibilityLibrary_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::FlexibilityLibrary >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         FlexibilityLibrary_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::FlexibilityLibrary >,
diff --git a/wrapper/IO/FlexibilityTemplate.pypp.cpp b/wrapper/IO/FlexibilityTemplate.pypp.cpp
index 5246be7cc..0b6751379 100644
--- a/wrapper/IO/FlexibilityTemplate.pypp.cpp
+++ b/wrapper/IO/FlexibilityTemplate.pypp.cpp
@@ -49,6 +49,8 @@ namespace bp = boost::python;
 
 SireIO::FlexibilityTemplate __copy__(const SireIO::FlexibilityTemplate &other){ return SireIO::FlexibilityTemplate(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 const char* pvt_get_name(const SireIO::FlexibilityTemplate&){ return "SireIO::FlexibilityTemplate";}
@@ -342,9 +344,9 @@ void register_FlexibilityTemplate_class(){
         
         }
         FlexibilityTemplate_exposer.staticmethod( "typeName" );
-        FlexibilityTemplate_exposer.def( "__copy__", &__copy__);
-        FlexibilityTemplate_exposer.def( "__deepcopy__", &__copy__);
-        FlexibilityTemplate_exposer.def( "clone", &__copy__);
+        FlexibilityTemplate_exposer.def( "__copy__", &__copy__<SireIO::FlexibilityTemplate>);
+        FlexibilityTemplate_exposer.def( "__deepcopy__", &__copy__<SireIO::FlexibilityTemplate>);
+        FlexibilityTemplate_exposer.def( "clone", &__copy__<SireIO::FlexibilityTemplate>);
         FlexibilityTemplate_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::FlexibilityTemplate >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         FlexibilityTemplate_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::FlexibilityTemplate >,
diff --git a/wrapper/IO/Gro87.pypp.cpp b/wrapper/IO/Gro87.pypp.cpp
index d749f44e4..444c30e7d 100644
--- a/wrapper/IO/Gro87.pypp.cpp
+++ b/wrapper/IO/Gro87.pypp.cpp
@@ -69,6 +69,8 @@ namespace bp = boost::python;
 
 SireIO::Gro87 __copy__(const SireIO::Gro87 &other){ return SireIO::Gro87(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -569,9 +571,9 @@ void register_Gro87_class(){
         
         }
         Gro87_exposer.staticmethod( "typeName" );
-        Gro87_exposer.def( "__copy__", &__copy__);
-        Gro87_exposer.def( "__deepcopy__", &__copy__);
-        Gro87_exposer.def( "clone", &__copy__);
+        Gro87_exposer.def( "__copy__", &__copy__<SireIO::Gro87>);
+        Gro87_exposer.def( "__deepcopy__", &__copy__<SireIO::Gro87>);
+        Gro87_exposer.def( "clone", &__copy__<SireIO::Gro87>);
         Gro87_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::Gro87 >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         Gro87_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::Gro87 >,
diff --git a/wrapper/IO/GroAtom.pypp.cpp b/wrapper/IO/GroAtom.pypp.cpp
index c3e5aa3de..e3dc7a7e0 100644
--- a/wrapper/IO/GroAtom.pypp.cpp
+++ b/wrapper/IO/GroAtom.pypp.cpp
@@ -23,6 +23,8 @@ namespace bp = boost::python;
 
 #include "SireMM/cljnbpairs.h"
 
+#include "SireMM/cmapfunctions.h"
+
 #include "SireMM/fouratomfunctions.h"
 
 #include "SireMM/internalff.h"
@@ -77,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::GroAtom __copy__(const SireIO::GroAtom &other){ return SireIO::GroAtom(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -404,9 +408,9 @@ void register_GroAtom_class(){
         
         }
         GroAtom_exposer.staticmethod( "typeName" );
-        GroAtom_exposer.def( "__copy__", &__copy__);
-        GroAtom_exposer.def( "__deepcopy__", &__copy__);
-        GroAtom_exposer.def( "clone", &__copy__);
+        GroAtom_exposer.def( "__copy__", &__copy__<SireIO::GroAtom>);
+        GroAtom_exposer.def( "__deepcopy__", &__copy__<SireIO::GroAtom>);
+        GroAtom_exposer.def( "clone", &__copy__<SireIO::GroAtom>);
         GroAtom_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::GroAtom >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         GroAtom_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::GroAtom >,
diff --git a/wrapper/IO/GroMolType.pypp.cpp b/wrapper/IO/GroMolType.pypp.cpp
index dffc1affa..aa131f21d 100644
--- a/wrapper/IO/GroMolType.pypp.cpp
+++ b/wrapper/IO/GroMolType.pypp.cpp
@@ -23,6 +23,8 @@ namespace bp = boost::python;
 
 #include "SireMM/cljnbpairs.h"
 
+#include "SireMM/cmapfunctions.h"
+
 #include "SireMM/fouratomfunctions.h"
 
 #include "SireMM/internalff.h"
@@ -77,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::GroMolType __copy__(const SireIO::GroMolType &other){ return SireIO::GroMolType(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -150,6 +154,18 @@ void register_GroMolType_class(){
                 , ( bp::arg("bonds"), bp::arg("is_lambda1")=(bool)(false) )
                 , "Add the passed bonds to the molecule" );
         
+        }
+        { //::SireIO::GroMolType::addCMAPs
+        
+            typedef void ( ::SireIO::GroMolType::*addCMAPs_function_type)( ::QHash< SireMol::CMAPID, QString > const &,bool ) ;
+            addCMAPs_function_type addCMAPs_function_value( &::SireIO::GroMolType::addCMAPs );
+            
+            GroMolType_exposer.def( 
+                "addCMAPs"
+                , addCMAPs_function_value
+                , ( bp::arg("cmaps"), bp::arg("is_lambda1")=(bool)(false) )
+                , "Add the passed CMAPs to the molecule" );
+        
         }
         { //::SireIO::GroMolType::addDihedral
         
@@ -307,6 +323,18 @@ void register_GroMolType_class(){
                 , ( bp::arg("is_lambda1")=(bool)(false) )
                 , "Return all of the bonds" );
         
+        }
+        { //::SireIO::GroMolType::cmaps
+        
+            typedef ::QHash< SireMol::CMAPID, QString > ( ::SireIO::GroMolType::*cmaps_function_type)( bool ) const;
+            cmaps_function_type cmaps_function_value( &::SireIO::GroMolType::cmaps );
+            
+            GroMolType_exposer.def( 
+                "cmaps"
+                , cmaps_function_value
+                , ( bp::arg("is_lambda1")=(bool)(false) )
+                , "Return all of the cmaps" );
+        
         }
         { //::SireIO::GroMolType::dihedrals
         
@@ -454,6 +482,30 @@ void register_GroMolType_class(){
                 , ( bp::arg("elecstyle"), bp::arg("vdwstyle"), bp::arg("combrule"), bp::arg("elec14"), bp::arg("vdw14"), bp::arg("is_lambda1")=(bool)(false) )
                 , "Sanitise this moleculetype. This assumes that the moleculetype has\nbeen fully specified, so it collects everything together and checks that the\nmolecule makes sense. Any warnings generated can be retrieved using the\nwarnings function. It also uses the passed defaults from the top file,\ntogether with the information in the molecule to guess the forcefield for\nthe molecule" );
         
+        }
+        { //::SireIO::GroMolType::sanitiseCMAPs
+        
+            typedef void ( ::SireIO::GroMolType::*sanitiseCMAPs_function_type)( bool ) ;
+            sanitiseCMAPs_function_type sanitiseCMAPs_function_value( &::SireIO::GroMolType::sanitiseCMAPs );
+            
+            GroMolType_exposer.def( 
+                "sanitiseCMAPs"
+                , sanitiseCMAPs_function_value
+                , ( bp::arg("is_lambda1")=(bool)(false) )
+                , "Sanitise all of the CMAP terms - this sets the string equal to 1,\n  as the information contained previously has already been read\n" );
+        
+        }
+        { //::SireIO::GroMolType::setAtomType
+        
+            typedef void ( ::SireIO::GroMolType::*setAtomType_function_type)( ::SireMol::AtomIdx const &,::QString const &,bool ) ;
+            setAtomType_function_type setAtomType_function_value( &::SireIO::GroMolType::setAtomType );
+            
+            GroMolType_exposer.def( 
+                "setAtomType"
+                , setAtomType_function_value
+                , ( bp::arg("atomidx"), bp::arg("atomtype"), bp::arg("is_lambda1")=(bool)(false) )
+                , "Set the atom type of the specified atom" );
+        
         }
         { //::SireIO::GroMolType::setAtoms
         
@@ -553,9 +605,9 @@ void register_GroMolType_class(){
         
         }
         GroMolType_exposer.staticmethod( "typeName" );
-        GroMolType_exposer.def( "__copy__", &__copy__);
-        GroMolType_exposer.def( "__deepcopy__", &__copy__);
-        GroMolType_exposer.def( "clone", &__copy__);
+        GroMolType_exposer.def( "__copy__", &__copy__<SireIO::GroMolType>);
+        GroMolType_exposer.def( "__deepcopy__", &__copy__<SireIO::GroMolType>);
+        GroMolType_exposer.def( "clone", &__copy__<SireIO::GroMolType>);
         GroMolType_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::GroMolType >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         GroMolType_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::GroMolType >,
diff --git a/wrapper/IO/GroSystem.pypp.cpp b/wrapper/IO/GroSystem.pypp.cpp
index f71c52165..28efe6652 100644
--- a/wrapper/IO/GroSystem.pypp.cpp
+++ b/wrapper/IO/GroSystem.pypp.cpp
@@ -23,6 +23,8 @@ namespace bp = boost::python;
 
 #include "SireMM/cljnbpairs.h"
 
+#include "SireMM/cmapfunctions.h"
+
 #include "SireMM/fouratomfunctions.h"
 
 #include "SireMM/internalff.h"
@@ -77,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::GroSystem __copy__(const SireIO::GroSystem &other){ return SireIO::GroSystem(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -279,9 +283,9 @@ void register_GroSystem_class(){
         
         }
         GroSystem_exposer.staticmethod( "typeName" );
-        GroSystem_exposer.def( "__copy__", &__copy__);
-        GroSystem_exposer.def( "__deepcopy__", &__copy__);
-        GroSystem_exposer.def( "clone", &__copy__);
+        GroSystem_exposer.def( "__copy__", &__copy__<SireIO::GroSystem>);
+        GroSystem_exposer.def( "__deepcopy__", &__copy__<SireIO::GroSystem>);
+        GroSystem_exposer.def( "clone", &__copy__<SireIO::GroSystem>);
         GroSystem_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::GroSystem >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         GroSystem_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::GroSystem >,
diff --git a/wrapper/IO/GroTop.pypp.cpp b/wrapper/IO/GroTop.pypp.cpp
index 633f279b8..50a05a9ec 100644
--- a/wrapper/IO/GroTop.pypp.cpp
+++ b/wrapper/IO/GroTop.pypp.cpp
@@ -23,6 +23,8 @@ namespace bp = boost::python;
 
 #include "SireMM/cljnbpairs.h"
 
+#include "SireMM/cmapfunctions.h"
+
 #include "SireMM/fouratomfunctions.h"
 
 #include "SireMM/internalff.h"
@@ -77,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::GroTop __copy__(const SireIO::GroTop &other){ return SireIO::GroTop(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -193,6 +197,19 @@ void register_GroTop_class(){
                 , bp::release_gil_policy()
                 , "Return the bond potential data for the passed pair of atoms. This returns\na list of all associated parameters" );
         
+        }
+        { //::SireIO::GroTop::cmaps
+        
+            typedef ::QList< SireMM::CMAPParameter > ( ::SireIO::GroTop::*cmaps_function_type)( ::QString const &,::QString const &,::QString const &,::QString const &,::QString const &,int ) const;
+            cmaps_function_type cmaps_function_value( &::SireIO::GroTop::cmaps );
+            
+            GroTop_exposer.def( 
+                "cmaps"
+                , cmaps_function_value
+                , ( bp::arg("atm0"), bp::arg("atm1"), bp::arg("atm2"), bp::arg("atm3"), bp::arg("atm4"), bp::arg("func") )
+                , bp::release_gil_policy()
+                , "Return all of the CMAP potentials for the passed quint of atom types, for the\n  passed function type. This returns a list of all associated parameters\n  (or an empty list if none exist)" );
+        
         }
         { //::SireIO::GroTop::combiningRules
         
@@ -528,9 +545,9 @@ void register_GroTop_class(){
         
         }
         GroTop_exposer.staticmethod( "typeName" );
-        GroTop_exposer.def( "__copy__", &__copy__);
-        GroTop_exposer.def( "__deepcopy__", &__copy__);
-        GroTop_exposer.def( "clone", &__copy__);
+        GroTop_exposer.def( "__copy__", &__copy__<SireIO::GroTop>);
+        GroTop_exposer.def( "__deepcopy__", &__copy__<SireIO::GroTop>);
+        GroTop_exposer.def( "clone", &__copy__<SireIO::GroTop>);
         GroTop_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::GroTop >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         GroTop_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::GroTop >,
diff --git a/wrapper/IO/IOParametersBase.pypp.cpp b/wrapper/IO/IOParametersBase.pypp.cpp
index 2e4f41165..c50593441 100644
--- a/wrapper/IO/IOParametersBase.pypp.cpp
+++ b/wrapper/IO/IOParametersBase.pypp.cpp
@@ -29,6 +29,8 @@ namespace bp = boost::python;
 
 SireIO::IOParametersBase __copy__(const SireIO::IOParametersBase &other){ return SireIO::IOParametersBase(other); }
 
+#include "Helpers/copy.hpp"
+
 const char* pvt_get_name(const SireIO::IOParametersBase&){ return "SireIO::IOParametersBase";}
 
 #include "Helpers/release_gil_policy.hpp"
@@ -75,9 +77,9 @@ void register_IOParametersBase_class(){
                 , "Return the default source of the property into which\nthe chemical elements of each atom will be placed\n\ndefault == element\n" );
         
         }
-        IOParametersBase_exposer.def( "__copy__", &__copy__);
-        IOParametersBase_exposer.def( "__deepcopy__", &__copy__);
-        IOParametersBase_exposer.def( "clone", &__copy__);
+        IOParametersBase_exposer.def( "__copy__", &__copy__<SireIO::IOParametersBase>);
+        IOParametersBase_exposer.def( "__deepcopy__", &__copy__<SireIO::IOParametersBase>);
+        IOParametersBase_exposer.def( "clone", &__copy__<SireIO::IOParametersBase>);
         IOParametersBase_exposer.def( "__str__", &pvt_get_name);
         IOParametersBase_exposer.def( "__repr__", &pvt_get_name);
     }
diff --git a/wrapper/IO/Mol2.pypp.cpp b/wrapper/IO/Mol2.pypp.cpp
index ad9e66c94..15dee02cd 100644
--- a/wrapper/IO/Mol2.pypp.cpp
+++ b/wrapper/IO/Mol2.pypp.cpp
@@ -45,6 +45,8 @@ namespace bp = boost::python;
 
 SireIO::Mol2 __copy__(const SireIO::Mol2 &other){ return SireIO::Mol2(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -372,9 +374,9 @@ void register_Mol2_class(){
         
         }
         Mol2_exposer.staticmethod( "typeName" );
-        Mol2_exposer.def( "__copy__", &__copy__);
-        Mol2_exposer.def( "__deepcopy__", &__copy__);
-        Mol2_exposer.def( "clone", &__copy__);
+        Mol2_exposer.def( "__copy__", &__copy__<SireIO::Mol2>);
+        Mol2_exposer.def( "__deepcopy__", &__copy__<SireIO::Mol2>);
+        Mol2_exposer.def( "clone", &__copy__<SireIO::Mol2>);
         Mol2_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::Mol2 >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         Mol2_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::Mol2 >,
diff --git a/wrapper/IO/NullIO.pypp.cpp b/wrapper/IO/NullIO.pypp.cpp
index a3a0926ae..c40d0fb3a 100644
--- a/wrapper/IO/NullIO.pypp.cpp
+++ b/wrapper/IO/NullIO.pypp.cpp
@@ -29,6 +29,8 @@ namespace bp = boost::python;
 
 SireIO::NullIO __copy__(const SireIO::NullIO &other){ return SireIO::NullIO(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -70,9 +72,9 @@ void register_NullIO_class(){
         
         }
         NullIO_exposer.staticmethod( "typeName" );
-        NullIO_exposer.def( "__copy__", &__copy__);
-        NullIO_exposer.def( "__deepcopy__", &__copy__);
-        NullIO_exposer.def( "clone", &__copy__);
+        NullIO_exposer.def( "__copy__", &__copy__<SireIO::NullIO>);
+        NullIO_exposer.def( "__deepcopy__", &__copy__<SireIO::NullIO>);
+        NullIO_exposer.def( "clone", &__copy__<SireIO::NullIO>);
         NullIO_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::NullIO >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         NullIO_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::NullIO >,
diff --git a/wrapper/IO/NullParser.pypp.cpp b/wrapper/IO/NullParser.pypp.cpp
index 24e8cc5a0..56b2c551a 100644
--- a/wrapper/IO/NullParser.pypp.cpp
+++ b/wrapper/IO/NullParser.pypp.cpp
@@ -79,6 +79,8 @@ namespace bp = boost::python;
 
 SireIO::NullParser __copy__(const SireIO::NullParser &other){ return SireIO::NullParser(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -231,9 +233,9 @@ void register_NullParser_class(){
         
         }
         NullParser_exposer.staticmethod( "typeName" );
-        NullParser_exposer.def( "__copy__", &__copy__);
-        NullParser_exposer.def( "__deepcopy__", &__copy__);
-        NullParser_exposer.def( "clone", &__copy__);
+        NullParser_exposer.def( "__copy__", &__copy__<SireIO::NullParser>);
+        NullParser_exposer.def( "__deepcopy__", &__copy__<SireIO::NullParser>);
+        NullParser_exposer.def( "clone", &__copy__<SireIO::NullParser>);
         NullParser_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::NullParser >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         NullParser_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::NullParser >,
diff --git a/wrapper/IO/PDB.pypp.cpp b/wrapper/IO/PDB.pypp.cpp
index 96033a623..b0a1e9147 100644
--- a/wrapper/IO/PDB.pypp.cpp
+++ b/wrapper/IO/PDB.pypp.cpp
@@ -85,6 +85,8 @@ namespace bp = boost::python;
 
 SireIO::PDB __copy__(const SireIO::PDB &other){ return SireIO::PDB(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -151,9 +153,9 @@ void register_PDB_class(){
         }
         PDB_exposer.staticmethod( "parameters" );
         PDB_exposer.staticmethod( "typeName" );
-        PDB_exposer.def( "__copy__", &__copy__);
-        PDB_exposer.def( "__deepcopy__", &__copy__);
-        PDB_exposer.def( "clone", &__copy__);
+        PDB_exposer.def( "__copy__", &__copy__<SireIO::PDB>);
+        PDB_exposer.def( "__deepcopy__", &__copy__<SireIO::PDB>);
+        PDB_exposer.def( "clone", &__copy__<SireIO::PDB>);
         PDB_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::PDB >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         PDB_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::PDB >,
diff --git a/wrapper/IO/PDB2.pypp.cpp b/wrapper/IO/PDB2.pypp.cpp
index dfc299654..f5e96f58e 100644
--- a/wrapper/IO/PDB2.pypp.cpp
+++ b/wrapper/IO/PDB2.pypp.cpp
@@ -41,6 +41,10 @@ namespace bp = boost::python;
 
 #include "SireUnits/units.h"
 
+#include "SireVol/periodicbox.h"
+
+#include "SireVol/triclinicbox.h"
+
 #include "pdb2.h"
 
 #include <QFile>
@@ -51,6 +55,8 @@ namespace bp = boost::python;
 
 SireIO::PDB2 __copy__(const SireIO::PDB2 &other){ return SireIO::PDB2(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -355,9 +361,9 @@ void register_PDB2_class(){
         
         }
         PDB2_exposer.staticmethod( "typeName" );
-        PDB2_exposer.def( "__copy__", &__copy__);
-        PDB2_exposer.def( "__deepcopy__", &__copy__);
-        PDB2_exposer.def( "clone", &__copy__);
+        PDB2_exposer.def( "__copy__", &__copy__<SireIO::PDB2>);
+        PDB2_exposer.def( "__deepcopy__", &__copy__<SireIO::PDB2>);
+        PDB2_exposer.def( "clone", &__copy__<SireIO::PDB2>);
         PDB2_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::PDB2 >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         PDB2_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::PDB2 >,
diff --git a/wrapper/IO/PDBParameters.pypp.cpp b/wrapper/IO/PDBParameters.pypp.cpp
index e359aa973..5108f9487 100644
--- a/wrapper/IO/PDBParameters.pypp.cpp
+++ b/wrapper/IO/PDBParameters.pypp.cpp
@@ -85,6 +85,8 @@ namespace bp = boost::python;
 
 SireIO::PDBParameters __copy__(const SireIO::PDBParameters &other){ return SireIO::PDBParameters(other); }
 
+#include "Helpers/copy.hpp"
+
 const char* pvt_get_name(const SireIO::PDBParameters&){ return "SireIO::PDBParameters";}
 
 #include "Helpers/release_gil_policy.hpp"
@@ -263,9 +265,9 @@ void register_PDBParameters_class(){
                 , "The function used to process segment names. Must be a StringMangler()\n\nsource  == segment-name-mangler\ndefault == TrimString()\n" );
         
         }
-        PDBParameters_exposer.def( "__copy__", &__copy__);
-        PDBParameters_exposer.def( "__deepcopy__", &__copy__);
-        PDBParameters_exposer.def( "clone", &__copy__);
+        PDBParameters_exposer.def( "__copy__", &__copy__<SireIO::PDBParameters>);
+        PDBParameters_exposer.def( "__deepcopy__", &__copy__<SireIO::PDBParameters>);
+        PDBParameters_exposer.def( "clone", &__copy__<SireIO::PDBParameters>);
         PDBParameters_exposer.def( "__str__", &pvt_get_name);
         PDBParameters_exposer.def( "__repr__", &pvt_get_name);
     }
diff --git a/wrapper/IO/PDBx.pypp.cpp b/wrapper/IO/PDBx.pypp.cpp
index 75c67ae48..127d66035 100644
--- a/wrapper/IO/PDBx.pypp.cpp
+++ b/wrapper/IO/PDBx.pypp.cpp
@@ -41,10 +41,14 @@ namespace bp = boost::python;
 
 #include "pdbx.h"
 
+#include <iostream>
+
 #include "pdbx.h"
 
 SireIO::PDBx __copy__(const SireIO::PDBx &other){ return SireIO::PDBx(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -261,9 +265,9 @@ void register_PDBx_class(){
         
         }
         PDBx_exposer.staticmethod( "typeName" );
-        PDBx_exposer.def( "__copy__", &__copy__);
-        PDBx_exposer.def( "__deepcopy__", &__copy__);
-        PDBx_exposer.def( "clone", &__copy__);
+        PDBx_exposer.def( "__copy__", &__copy__<SireIO::PDBx>);
+        PDBx_exposer.def( "__deepcopy__", &__copy__<SireIO::PDBx>);
+        PDBx_exposer.def( "clone", &__copy__<SireIO::PDBx>);
         PDBx_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::PDBx >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         PDBx_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::PDBx >,
diff --git a/wrapper/IO/PerturbationsLibrary.pypp.cpp b/wrapper/IO/PerturbationsLibrary.pypp.cpp
index 93e2ba601..dc44f0c9d 100644
--- a/wrapper/IO/PerturbationsLibrary.pypp.cpp
+++ b/wrapper/IO/PerturbationsLibrary.pypp.cpp
@@ -75,6 +75,8 @@ namespace bp = boost::python;
 
 SireIO::PerturbationsLibrary __copy__(const SireIO::PerturbationsLibrary &other){ return SireIO::PerturbationsLibrary(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -183,9 +185,9 @@ void register_PerturbationsLibrary_class(){
         
         }
         PerturbationsLibrary_exposer.staticmethod( "typeName" );
-        PerturbationsLibrary_exposer.def( "__copy__", &__copy__);
-        PerturbationsLibrary_exposer.def( "__deepcopy__", &__copy__);
-        PerturbationsLibrary_exposer.def( "clone", &__copy__);
+        PerturbationsLibrary_exposer.def( "__copy__", &__copy__<SireIO::PerturbationsLibrary>);
+        PerturbationsLibrary_exposer.def( "__deepcopy__", &__copy__<SireIO::PerturbationsLibrary>);
+        PerturbationsLibrary_exposer.def( "clone", &__copy__<SireIO::PerturbationsLibrary>);
         PerturbationsLibrary_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::PerturbationsLibrary >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         PerturbationsLibrary_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::PerturbationsLibrary >,
diff --git a/wrapper/IO/PerturbationsTemplate.pypp.cpp b/wrapper/IO/PerturbationsTemplate.pypp.cpp
index fc1f0e0f0..af5d80467 100644
--- a/wrapper/IO/PerturbationsTemplate.pypp.cpp
+++ b/wrapper/IO/PerturbationsTemplate.pypp.cpp
@@ -75,6 +75,8 @@ namespace bp = boost::python;
 
 SireIO::PerturbationsTemplate __copy__(const SireIO::PerturbationsTemplate &other){ return SireIO::PerturbationsTemplate(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 const char* pvt_get_name(const SireIO::PerturbationsTemplate&){ return "SireIO::PerturbationsTemplate";}
@@ -645,9 +647,9 @@ void register_PerturbationsTemplate_class(){
         
         }
         PerturbationsTemplate_exposer.staticmethod( "typeName" );
-        PerturbationsTemplate_exposer.def( "__copy__", &__copy__);
-        PerturbationsTemplate_exposer.def( "__deepcopy__", &__copy__);
-        PerturbationsTemplate_exposer.def( "clone", &__copy__);
+        PerturbationsTemplate_exposer.def( "__copy__", &__copy__<SireIO::PerturbationsTemplate>);
+        PerturbationsTemplate_exposer.def( "__deepcopy__", &__copy__<SireIO::PerturbationsTemplate>);
+        PerturbationsTemplate_exposer.def( "clone", &__copy__<SireIO::PerturbationsTemplate>);
         PerturbationsTemplate_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::PerturbationsTemplate >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         PerturbationsTemplate_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::PerturbationsTemplate >,
diff --git a/wrapper/IO/ProtoMS.pypp.cpp b/wrapper/IO/ProtoMS.pypp.cpp
index 9474db973..5d0e236ec 100644
--- a/wrapper/IO/ProtoMS.pypp.cpp
+++ b/wrapper/IO/ProtoMS.pypp.cpp
@@ -91,6 +91,8 @@ namespace bp = boost::python;
 
 SireIO::ProtoMS __copy__(const SireIO::ProtoMS &other){ return SireIO::ProtoMS(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 const char* pvt_get_name(const SireIO::ProtoMS&){ return "SireIO::ProtoMS";}
@@ -220,9 +222,9 @@ void register_ProtoMS_class(){
         }
         ProtoMS_exposer.staticmethod( "parameters" );
         ProtoMS_exposer.staticmethod( "typeName" );
-        ProtoMS_exposer.def( "__copy__", &__copy__);
-        ProtoMS_exposer.def( "__deepcopy__", &__copy__);
-        ProtoMS_exposer.def( "clone", &__copy__);
+        ProtoMS_exposer.def( "__copy__", &__copy__<SireIO::ProtoMS>);
+        ProtoMS_exposer.def( "__deepcopy__", &__copy__<SireIO::ProtoMS>);
+        ProtoMS_exposer.def( "clone", &__copy__<SireIO::ProtoMS>);
         ProtoMS_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::ProtoMS >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         ProtoMS_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::ProtoMS >,
diff --git a/wrapper/IO/ProtoMSParameters.pypp.cpp b/wrapper/IO/ProtoMSParameters.pypp.cpp
index 480fc0204..ad2d7bc93 100644
--- a/wrapper/IO/ProtoMSParameters.pypp.cpp
+++ b/wrapper/IO/ProtoMSParameters.pypp.cpp
@@ -91,6 +91,8 @@ namespace bp = boost::python;
 
 SireIO::ProtoMSParameters __copy__(const SireIO::ProtoMSParameters &other){ return SireIO::ProtoMSParameters(other); }
 
+#include "Helpers/copy.hpp"
+
 const char* pvt_get_name(const SireIO::ProtoMSParameters&){ return "SireIO::ProtoMSParameters";}
 
 #include "Helpers/release_gil_policy.hpp"
@@ -281,9 +283,9 @@ void register_ProtoMSParameters_class(){
                 , "Return the name of the property that will contain the\nz-matrix\n\ndefault == zmatrix\n" );
         
         }
-        ProtoMSParameters_exposer.def( "__copy__", &__copy__);
-        ProtoMSParameters_exposer.def( "__deepcopy__", &__copy__);
-        ProtoMSParameters_exposer.def( "clone", &__copy__);
+        ProtoMSParameters_exposer.def( "__copy__", &__copy__<SireIO::ProtoMSParameters>);
+        ProtoMSParameters_exposer.def( "__deepcopy__", &__copy__<SireIO::ProtoMSParameters>);
+        ProtoMSParameters_exposer.def( "clone", &__copy__<SireIO::ProtoMSParameters>);
         ProtoMSParameters_exposer.def( "__str__", &pvt_get_name);
         ProtoMSParameters_exposer.def( "__repr__", &pvt_get_name);
     }
diff --git a/wrapper/IO/SDF.pypp.cpp b/wrapper/IO/SDF.pypp.cpp
index 63806c302..4811d1dde 100644
--- a/wrapper/IO/SDF.pypp.cpp
+++ b/wrapper/IO/SDF.pypp.cpp
@@ -71,6 +71,8 @@ namespace bp = boost::python;
 
 SireIO::SDF __copy__(const SireIO::SDF &other){ return SireIO::SDF(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -312,9 +314,9 @@ void register_SDF_class(){
         
         }
         SDF_exposer.staticmethod( "typeName" );
-        SDF_exposer.def( "__copy__", &__copy__);
-        SDF_exposer.def( "__deepcopy__", &__copy__);
-        SDF_exposer.def( "clone", &__copy__);
+        SDF_exposer.def( "__copy__", &__copy__<SireIO::SDF>);
+        SDF_exposer.def( "__deepcopy__", &__copy__<SireIO::SDF>);
+        SDF_exposer.def( "clone", &__copy__<SireIO::SDF>);
         SDF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::SDF >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         SDF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::SDF >,
diff --git a/wrapper/IO/SireIO_containers.cpp b/wrapper/IO/SireIO_containers.cpp
index 2136feffc..138c5c47a 100644
--- a/wrapper/IO/SireIO_containers.cpp
+++ b/wrapper/IO/SireIO_containers.cpp
@@ -52,6 +52,7 @@ using boost::python::register_tuple;
 
 void register_SireIO_containers()
 {
+    register_list< QVector<QVector<float>> >();
     register_list< QList<MoleculeParserPtr> >();
 
     register_list< QVector<GroMolType> >();
diff --git a/wrapper/IO/SireIO_properties.cpp b/wrapper/IO/SireIO_properties.cpp
index 9f26f536d..9315b796c 100644
--- a/wrapper/IO/SireIO_properties.cpp
+++ b/wrapper/IO/SireIO_properties.cpp
@@ -4,16 +4,6 @@
 #include "Base/convertproperty.hpp"
 #include "SireIO_properties.h"
 
-#include "SireError/errors.h"
-#include "SireMol/cuttingfunction.h"
-#include "SireMol/molecule.h"
-#include "SireMol/molidx.h"
-#include "SireMol/mover.hpp"
-#include "SireStream/datastream.h"
-#include "iobase.h"
-#include <QDebug>
-#include <QFile>
-#include "iobase.h"
 #include "SireBase/booleanproperty.h"
 #include "SireBase/parallel.h"
 #include "SireBase/progressbar.h"
@@ -49,8 +39,18 @@
 #include <QMutex>
 #include <QTextStream>
 #include "moleculeparser.h"
+#include "SireError/errors.h"
+#include "SireMol/cuttingfunction.h"
+#include "SireMol/molecule.h"
+#include "SireMol/molidx.h"
+#include "SireMol/mover.hpp"
+#include "SireStream/datastream.h"
+#include "iobase.h"
+#include <QDebug>
+#include <QFile>
+#include "iobase.h"
 void register_SireIO_properties()
 {
-    register_property_container< SireIO::IOPtr, SireIO::IOBase >();
     register_property_container< SireIO::MoleculeParserPtr, SireIO::MoleculeParser >();
+    register_property_container< SireIO::IOPtr, SireIO::IOBase >();
 }
diff --git a/wrapper/IO/SireIO_registrars.cpp b/wrapper/IO/SireIO_registrars.cpp
index 4e90f4026..b7e1662ae 100644
--- a/wrapper/IO/SireIO_registrars.cpp
+++ b/wrapper/IO/SireIO_registrars.cpp
@@ -3,79 +3,79 @@
 
 #include "SireIO_registrars.h"
 
-#include "iobase.h"
-#include "amber.h"
-#include "filetrajectoryparser.h"
-#include "flexibilitylibrary.h"
-#include "trr.h"
 #include "grotop.h"
-#include "amberrst7.h"
-#include "mol2.h"
 #include "protoms.h"
-#include "pdb2.h"
+#include "filetrajectory.h"
+#include "amberrst7.h"
 #include "moleculeparser.h"
-#include "amberrst.h"
-#include "trajectorymonitor.h"
+#include "iobase.h"
 #include "supplementary.h"
-#include "xtc.h"
-#include "filetrajectory.h"
-#include "gro87.h"
-#include "charmmpsf.h"
-#include "perturbationslibrary.h"
-#include "dcd.h"
-#include "amberprm.h"
-#include "tinker.h"
 #include "zmatrixmaker.h"
+#include "tinker.h"
+#include "amberprm.h"
+#include "dcd.h"
+#include "charmmpsf.h"
 #include "ambertraj.h"
-#include "sdf.h"
+#include "xtc.h"
+#include "pdb2.h"
+#include "trr.h"
+#include "filetrajectoryparser.h"
 #include "pdb.h"
+#include "mol2.h"
+#include "trajectorymonitor.h"
+#include "gro87.h"
+#include "flexibilitylibrary.h"
 #include "pdbx.h"
+#include "amberrst.h"
+#include "amber.h"
+#include "perturbationslibrary.h"
+#include "sdf.h"
 
 #include "Helpers/objectregistry.hpp"
 
 void register_SireIO_objects()
 {
 
-    ObjectRegistry::registerConverterFor< SireIO::NullIO >();
-    ObjectRegistry::registerConverterFor< SireIO::Amber >();
-    ObjectRegistry::registerConverterFor< SireIO::FileTrajectoryParser >();
-    ObjectRegistry::registerConverterFor< SireIO::FlexibilityLibrary >();
-    ObjectRegistry::registerConverterFor< SireIO::FlexibilityTemplate >();
-    ObjectRegistry::registerConverterFor< SireIO::TRR >();
     ObjectRegistry::registerConverterFor< SireIO::GroTop >();
     ObjectRegistry::registerConverterFor< SireIO::GroMolType >();
     ObjectRegistry::registerConverterFor< SireIO::GroAtom >();
     ObjectRegistry::registerConverterFor< SireIO::GroSystem >();
+    ObjectRegistry::registerConverterFor< SireIO::ProtoMS >();
+    ObjectRegistry::registerConverterFor< SireIO::FileTrajectory >();
     ObjectRegistry::registerConverterFor< SireIO::AmberRst7 >();
+    ObjectRegistry::registerConverterFor< SireIO::NullParser >();
+    ObjectRegistry::registerConverterFor< SireIO::BrokenParser >();
+    ObjectRegistry::registerConverterFor< SireIO::NullIO >();
+    ObjectRegistry::registerConverterFor< SireIO::Supplementary >();
+    ObjectRegistry::registerConverterFor< SireIO::ZmatrixMaker >();
+    ObjectRegistry::registerConverterFor< SireIO::Tinker >();
+    ObjectRegistry::registerConverterFor< SireIO::AmberPrm >();
+    ObjectRegistry::registerConverterFor< SireIO::DCD >();
+    ObjectRegistry::registerConverterFor< SireIO::PSFAtom >();
+    ObjectRegistry::registerConverterFor< SireIO::CharmmParam >();
+    ObjectRegistry::registerConverterFor< SireIO::CharmmPSF >();
+    ObjectRegistry::registerConverterFor< SireIO::AmberTraj >();
+    ObjectRegistry::registerConverterFor< SireIO::XTC >();
+    ObjectRegistry::registerConverterFor< SireIO::PDBAtom >();
+    ObjectRegistry::registerConverterFor< SireIO::PDB2 >();
+    ObjectRegistry::registerConverterFor< SireIO::TRR >();
+    ObjectRegistry::registerConverterFor< SireIO::FileTrajectoryParser >();
+    ObjectRegistry::registerConverterFor< SireIO::PDB >();
     ObjectRegistry::registerConverterFor< SireIO::Mol2Atom >();
     ObjectRegistry::registerConverterFor< SireIO::Mol2Bond >();
     ObjectRegistry::registerConverterFor< SireIO::Mol2Molecule >();
     ObjectRegistry::registerConverterFor< SireIO::Mol2Substructure >();
     ObjectRegistry::registerConverterFor< SireIO::Mol2 >();
-    ObjectRegistry::registerConverterFor< SireIO::ProtoMS >();
-    ObjectRegistry::registerConverterFor< SireIO::PDBAtom >();
-    ObjectRegistry::registerConverterFor< SireIO::PDB2 >();
-    ObjectRegistry::registerConverterFor< SireIO::NullParser >();
-    ObjectRegistry::registerConverterFor< SireIO::BrokenParser >();
-    ObjectRegistry::registerConverterFor< SireIO::AmberRst >();
     ObjectRegistry::registerConverterFor< SireIO::TrajectoryMonitor >();
-    ObjectRegistry::registerConverterFor< SireIO::Supplementary >();
-    ObjectRegistry::registerConverterFor< SireIO::XTC >();
-    ObjectRegistry::registerConverterFor< SireIO::FileTrajectory >();
     ObjectRegistry::registerConverterFor< SireIO::Gro87 >();
-    ObjectRegistry::registerConverterFor< SireIO::PSFAtom >();
-    ObjectRegistry::registerConverterFor< SireIO::CharmmParam >();
-    ObjectRegistry::registerConverterFor< SireIO::CharmmPSF >();
+    ObjectRegistry::registerConverterFor< SireIO::FlexibilityLibrary >();
+    ObjectRegistry::registerConverterFor< SireIO::FlexibilityTemplate >();
+    ObjectRegistry::registerConverterFor< SireIO::PDBx >();
+    ObjectRegistry::registerConverterFor< SireIO::AmberRst >();
+    ObjectRegistry::registerConverterFor< SireIO::Amber >();
     ObjectRegistry::registerConverterFor< SireIO::PerturbationsLibrary >();
     ObjectRegistry::registerConverterFor< SireIO::PerturbationsTemplate >();
-    ObjectRegistry::registerConverterFor< SireIO::DCD >();
-    ObjectRegistry::registerConverterFor< SireIO::AmberPrm >();
-    ObjectRegistry::registerConverterFor< SireIO::Tinker >();
-    ObjectRegistry::registerConverterFor< SireIO::ZmatrixMaker >();
-    ObjectRegistry::registerConverterFor< SireIO::AmberTraj >();
     ObjectRegistry::registerConverterFor< SireIO::SDF >();
-    ObjectRegistry::registerConverterFor< SireIO::PDB >();
-    ObjectRegistry::registerConverterFor< SireIO::PDBx >();
 
 }
 
diff --git a/wrapper/IO/Supplementary.pypp.cpp b/wrapper/IO/Supplementary.pypp.cpp
index 4f42dfea4..5a935d445 100644
--- a/wrapper/IO/Supplementary.pypp.cpp
+++ b/wrapper/IO/Supplementary.pypp.cpp
@@ -23,6 +23,8 @@ namespace bp = boost::python;
 
 SireIO::Supplementary __copy__(const SireIO::Supplementary &other){ return SireIO::Supplementary(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -189,9 +191,9 @@ void register_Supplementary_class(){
         
         }
         Supplementary_exposer.staticmethod( "typeName" );
-        Supplementary_exposer.def( "__copy__", &__copy__);
-        Supplementary_exposer.def( "__deepcopy__", &__copy__);
-        Supplementary_exposer.def( "clone", &__copy__);
+        Supplementary_exposer.def( "__copy__", &__copy__<SireIO::Supplementary>);
+        Supplementary_exposer.def( "__deepcopy__", &__copy__<SireIO::Supplementary>);
+        Supplementary_exposer.def( "clone", &__copy__<SireIO::Supplementary>);
         Supplementary_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::Supplementary >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         Supplementary_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::Supplementary >,
diff --git a/wrapper/IO/TRR.pypp.cpp b/wrapper/IO/TRR.pypp.cpp
index afcec861a..17609ea33 100644
--- a/wrapper/IO/TRR.pypp.cpp
+++ b/wrapper/IO/TRR.pypp.cpp
@@ -65,6 +65,8 @@ namespace bp = boost::python;
 
 SireIO::TRR __copy__(const SireIO::TRR &other){ return SireIO::TRR(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -334,9 +336,9 @@ void register_TRR_class(){
         }
         TRR_exposer.staticmethod( "parse" );
         TRR_exposer.staticmethod( "typeName" );
-        TRR_exposer.def( "__copy__", &__copy__);
-        TRR_exposer.def( "__deepcopy__", &__copy__);
-        TRR_exposer.def( "clone", &__copy__);
+        TRR_exposer.def( "__copy__", &__copy__<SireIO::TRR>);
+        TRR_exposer.def( "__deepcopy__", &__copy__<SireIO::TRR>);
+        TRR_exposer.def( "clone", &__copy__<SireIO::TRR>);
         TRR_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::TRR >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         TRR_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::TRR >,
diff --git a/wrapper/IO/Tinker.pypp.cpp b/wrapper/IO/Tinker.pypp.cpp
index 2ebc0a381..480f5c7da 100644
--- a/wrapper/IO/Tinker.pypp.cpp
+++ b/wrapper/IO/Tinker.pypp.cpp
@@ -39,6 +39,8 @@ namespace bp = boost::python;
 
 SireIO::Tinker __copy__(const SireIO::Tinker &other){ return SireIO::Tinker(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -106,9 +108,9 @@ void register_Tinker_class(){
         }
         Tinker_exposer.staticmethod( "parameters" );
         Tinker_exposer.staticmethod( "typeName" );
-        Tinker_exposer.def( "__copy__", &__copy__);
-        Tinker_exposer.def( "__deepcopy__", &__copy__);
-        Tinker_exposer.def( "clone", &__copy__);
+        Tinker_exposer.def( "__copy__", &__copy__<SireIO::Tinker>);
+        Tinker_exposer.def( "__deepcopy__", &__copy__<SireIO::Tinker>);
+        Tinker_exposer.def( "clone", &__copy__<SireIO::Tinker>);
         Tinker_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::Tinker >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         Tinker_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::Tinker >,
diff --git a/wrapper/IO/TinkerParameters.pypp.cpp b/wrapper/IO/TinkerParameters.pypp.cpp
index fdf3b0e0a..56945f334 100644
--- a/wrapper/IO/TinkerParameters.pypp.cpp
+++ b/wrapper/IO/TinkerParameters.pypp.cpp
@@ -39,6 +39,8 @@ namespace bp = boost::python;
 
 SireIO::TinkerParameters __copy__(const SireIO::TinkerParameters &other){ return SireIO::TinkerParameters(other); }
 
+#include "Helpers/copy.hpp"
+
 const char* pvt_get_name(const SireIO::TinkerParameters&){ return "SireIO::TinkerParameters";}
 
 #include "Helpers/release_gil_policy.hpp"
@@ -49,9 +51,9 @@ void register_TinkerParameters_class(){
         typedef bp::class_< SireIO::TinkerParameters, bp::bases< SireIO::IOParametersBase > > TinkerParameters_exposer_t;
         TinkerParameters_exposer_t TinkerParameters_exposer = TinkerParameters_exposer_t( "TinkerParameters", "This class holds all of the sources and default values of the\nproperties and parameters used by the Tinker readerwriter\n\nAuthor: Christopher Woods\n", bp::init< >("Constructor") );
         bp::scope TinkerParameters_scope( TinkerParameters_exposer );
-        TinkerParameters_exposer.def( "__copy__", &__copy__);
-        TinkerParameters_exposer.def( "__deepcopy__", &__copy__);
-        TinkerParameters_exposer.def( "clone", &__copy__);
+        TinkerParameters_exposer.def( "__copy__", &__copy__<SireIO::TinkerParameters>);
+        TinkerParameters_exposer.def( "__deepcopy__", &__copy__<SireIO::TinkerParameters>);
+        TinkerParameters_exposer.def( "clone", &__copy__<SireIO::TinkerParameters>);
         TinkerParameters_exposer.def( "__str__", &pvt_get_name);
         TinkerParameters_exposer.def( "__repr__", &pvt_get_name);
     }
diff --git a/wrapper/IO/TrajectoryMonitor.pypp.cpp b/wrapper/IO/TrajectoryMonitor.pypp.cpp
index cf2a88a72..980b65828 100644
--- a/wrapper/IO/TrajectoryMonitor.pypp.cpp
+++ b/wrapper/IO/TrajectoryMonitor.pypp.cpp
@@ -37,6 +37,8 @@ namespace bp = boost::python;
 
 SireIO::TrajectoryMonitor __copy__(const SireIO::TrajectoryMonitor &other){ return SireIO::TrajectoryMonitor(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -133,9 +135,9 @@ void register_TrajectoryMonitor_class(){
         
         }
         TrajectoryMonitor_exposer.staticmethod( "typeName" );
-        TrajectoryMonitor_exposer.def( "__copy__", &__copy__);
-        TrajectoryMonitor_exposer.def( "__deepcopy__", &__copy__);
-        TrajectoryMonitor_exposer.def( "clone", &__copy__);
+        TrajectoryMonitor_exposer.def( "__copy__", &__copy__<SireIO::TrajectoryMonitor>);
+        TrajectoryMonitor_exposer.def( "__deepcopy__", &__copy__<SireIO::TrajectoryMonitor>);
+        TrajectoryMonitor_exposer.def( "clone", &__copy__<SireIO::TrajectoryMonitor>);
         TrajectoryMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::TrajectoryMonitor >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         TrajectoryMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::TrajectoryMonitor >,
diff --git a/wrapper/IO/XTC.pypp.cpp b/wrapper/IO/XTC.pypp.cpp
index aa386ebd3..472bc26a5 100644
--- a/wrapper/IO/XTC.pypp.cpp
+++ b/wrapper/IO/XTC.pypp.cpp
@@ -65,6 +65,8 @@ namespace bp = boost::python;
 
 SireIO::XTC __copy__(const SireIO::XTC &other){ return SireIO::XTC(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 #include "Helpers/str.hpp"
@@ -334,9 +336,9 @@ void register_XTC_class(){
         }
         XTC_exposer.staticmethod( "parse" );
         XTC_exposer.staticmethod( "typeName" );
-        XTC_exposer.def( "__copy__", &__copy__);
-        XTC_exposer.def( "__deepcopy__", &__copy__);
-        XTC_exposer.def( "clone", &__copy__);
+        XTC_exposer.def( "__copy__", &__copy__<SireIO::XTC>);
+        XTC_exposer.def( "__deepcopy__", &__copy__<SireIO::XTC>);
+        XTC_exposer.def( "clone", &__copy__<SireIO::XTC>);
         XTC_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::XTC >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         XTC_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::XTC >,
diff --git a/wrapper/IO/ZmatrixMaker.pypp.cpp b/wrapper/IO/ZmatrixMaker.pypp.cpp
index b6c95c6ac..c2f0a31d3 100644
--- a/wrapper/IO/ZmatrixMaker.pypp.cpp
+++ b/wrapper/IO/ZmatrixMaker.pypp.cpp
@@ -49,6 +49,8 @@ namespace bp = boost::python;
 
 SireIO::ZmatrixMaker __copy__(const SireIO::ZmatrixMaker &other){ return SireIO::ZmatrixMaker(other); }
 
+#include "Helpers/copy.hpp"
+
 #include "Qt/qdatastream.hpp"
 
 const char* pvt_get_name(const SireIO::ZmatrixMaker&){ return "SireIO::ZmatrixMaker";}
@@ -112,9 +114,9 @@ void register_ZmatrixMaker_class(){
         
         }
         ZmatrixMaker_exposer.staticmethod( "typeName" );
-        ZmatrixMaker_exposer.def( "__copy__", &__copy__);
-        ZmatrixMaker_exposer.def( "__deepcopy__", &__copy__);
-        ZmatrixMaker_exposer.def( "clone", &__copy__);
+        ZmatrixMaker_exposer.def( "__copy__", &__copy__<SireIO::ZmatrixMaker>);
+        ZmatrixMaker_exposer.def( "__deepcopy__", &__copy__<SireIO::ZmatrixMaker>);
+        ZmatrixMaker_exposer.def( "clone", &__copy__<SireIO::ZmatrixMaker>);
         ZmatrixMaker_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireIO::ZmatrixMaker >,
                             bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() );
         ZmatrixMaker_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireIO::ZmatrixMaker >,
diff --git a/wrapper/IO/_IO_free_functions.pypp.cpp b/wrapper/IO/_IO_free_functions.pypp.cpp
index fa5466500..4a5b57a62 100644
--- a/wrapper/IO/_IO_free_functions.pypp.cpp
+++ b/wrapper/IO/_IO_free_functions.pypp.cpp
@@ -9,6 +9,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -41,6 +43,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -109,6 +113,42 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
+#include "SireError/errors.h"
+
+#include "SireMol/atomelements.h"
+
+#include "SireMol/atommasses.h"
+
+#include "SireMol/connectivity.h"
+
+#include "SireMol/core.h"
+
+#include "SireMol/mgname.h"
+
+#include "SireMol/moleditor.h"
+
+#include "SireMol/molidx.h"
+
+#include "SireSystem/system.h"
+
+#include "SireUnits/units.h"
+
+#include "SireVol/periodicbox.h"
+
+#include "SireVol/triclinicbox.h"
+
+#include "biosimspace.h"
+
+#include "moleculeparser.h"
+
+#include "biosimspace.h"
+
+#include "SireBase/getinstalldir.h"
+
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -141,6 +181,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -173,6 +215,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -205,6 +249,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -237,6 +283,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -269,6 +317,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -301,6 +351,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -333,6 +385,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -365,6 +419,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -397,6 +453,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -429,6 +487,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -461,6 +521,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -493,6 +555,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -525,6 +589,8 @@ namespace bp = boost::python;
 
 #include "SireBase/getinstalldir.h"
 
+#include "SireBase/parallel.h"
+
 #include "SireError/errors.h"
 
 #include "SireMol/atomelements.h"
@@ -739,6 +805,19 @@ void register_free_functions(){
     
     }
 
+    { //::SireIO::setCoordinates
+    
+        typedef ::SireSystem::System ( *setCoordinates_function_type )( ::SireSystem::System &,::QVector<QVector<float>> const &,bool const,::SireBase::PropertyMap const & );
+        setCoordinates_function_type setCoordinates_function_value( &::SireIO::setCoordinates );
+        
+        bp::def( 
+            "setCoordinates"
+            , setCoordinates_function_value
+            , ( bp::arg("system"), bp::arg("coordinates"), bp::arg("is_lambda1")=(bool const)(false), bp::arg("map")=SireBase::PropertyMap() )
+            , "Set the coordinates of the entire system.\nPar:am system\nThe molecular system of interest.\n\nPar:am coordinates\nThe new coordinates for the system.\n\nPar:am map\nA dictionary of user-defined molecular property names.\n\nRetval: system\nThe system with updated coordinates.\n" );
+    
+    }
+
     { //::SireIO::setGromacsWater
     
         typedef ::SireSystem::System ( *setGromacsWater_function_type )( ::SireSystem::System const &,::QString const &,::SireBase::PropertyMap const &,bool );