Merge pull request #220 from OpenBioSim/fix_213_215_219

Fix issues 213, 215, and 219

corelib/src/libs/SireIO/amber.cpp

@@ -2151,7 +2151,7 @@ tuple<MoleculeGroup, SpacePtr> Amber::readCrdTop(const QString &crdfile, const Q
     // Now the box information
     SpacePtr spce;
 
-    if (pointers[IFBOX] == 1)
+    if (pointers[IFBOX] == 1 or pointers[IFBOX] == 2 or pointers[IFBOX] == 3)
     {
         /** Rectangular box, dimensions read from the crd file */
         Vector dimensions(crd_box[0], crd_box[1], crd_box[2]);
@@ -2173,12 +2173,6 @@ tuple<MoleculeGroup, SpacePtr> Amber::readCrdTop(const QString &crdfile, const Q
         // spce = PeriodicBox( Vector ( crdBox[0], crdBox[1], crdBox[2] ) ).asA<Space>() ;
         // qDebug() << " periodic box " << spce.toString() ;
     }
-    else if (pointers[IFBOX] == 2)
-    {
-        /** Truncated Octahedral box*/
-        throw SireError::incompatible_error(QObject::tr("Sire does not yet support a truncated octahedral box"),
-                                            CODELOC);
-    }
     else
     {
         /** Default is a non periodic system */

corelib/src/libs/SireIO/amberprm.cpp

@@ -2181,7 +2181,16 @@ QStringList toLines(const QVector<AmberParams> &params, const Space &space, int
 
     if (has_periodic_box)
     {
-        pointers[27] = 1;
+        // Orthorhombic box.
+        if (space.isA<PeriodicBox>())
+        {
+            pointers[27] = 1;
+        }
+        // General triclinic box.
+        else if (space.isA<TriclinicBox>())
+        {
+            pointers[27] = 3;
+        }
     }
 
     // here is the number of solvent molecules, and the index of the last

doc/source/changelog.rst

@@ -19,6 +19,10 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Print residue indices of perturbed water molecules to SOMD1 log.
 * Add support for creating Na+ and Cl- ions.
 * Fix ``sire.morph.merge`` function when one molecule is a monatomic ion.
+* Remove ``sire.move.OpenMMPMEFEP`` wrappers from build when OpenMM is not available.
+* Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser.
+* Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule.
+
 
 `2024.2.0 <https://github.com/openbiosim/sire/compare/2024.1.0...2024.2.0>`__ - June 2024
 -----------------------------------------------------------------------------------------

requirements_bss.txt

@@ -32,8 +32,6 @@ py3dmol
 pydot
 pygtail
 pyyaml
-rdkit >=2023.0.0
-gemmi >=0.6.4
 
 # The below are packages that aren't available on all
 # platforms/OSs and so need to be conditionally included

requirements_build.txt

@@ -11,11 +11,6 @@ make ; sys_platform == "linux"
 libtool ; sys_platform == "linux"
 sysroot_linux-64==2.17 ; sys_platform == "linux"
 
-# These packages are needed to compile
-# the SireRDKit plugin
-rdkit >=2023.0.0
-rdkit-dev >=2023.0.0
-
 # These packages are needed to compile
 # the SireGemmi plugin
 gemmi >=0.6.4

requirements_host.txt

@@ -5,14 +5,14 @@ gsl
 lazy_import
 libcblas
 libnetcdf
+librdkit-dev
 openmm
 pandas
 python
 qt-main
 rich
 tbb
 tbb-devel
-rdkit >=2023.0.0
 gemmi >=0.6.4
 
 # kartograf on Windows pulls in an openfe that has an old / incompatble

wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp

@@ -1576,14 +1576,29 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system,
     // between from_ghosts and to_ghosts
     for (const auto &from_ghost_idx : from_ghost_idxs)
     {
+        // work out the molecule index for the from ghost atom
+        int mol_from = 0;
+        while (start_indexes[mol_from] <= from_ghost_idx)
+            mol_from++;
+
         for (const auto &to_ghost_idx : to_ghost_idxs)
         {
+            // work out the molecule index for the to ghost atom
+            int mol_to = 0;
+            while (start_indexes[mol_to] <= to_ghost_idx)
+                mol_to++;
+
             if (not excluded_ghost_pairs.contains(IndexPair(from_ghost_idx, to_ghost_idx)))
             {
-                ghost_ghostff->addExclusion(from_ghost_idx, to_ghost_idx);
-                ghost_nonghostff->addExclusion(from_ghost_idx, to_ghost_idx);
-                cljff->addException(from_ghost_idx, to_ghost_idx,
-                                    0.0, 1e-9, 1e-9, true);
+                // only exclude if we haven't already excluded this pair
+                // and if the two atoms are in the same molecule
+                if (mol_from == mol_to)
+                {
+                    ghost_ghostff->addExclusion(from_ghost_idx, to_ghost_idx);
+                    ghost_nonghostff->addExclusion(from_ghost_idx, to_ghost_idx);
+                    cljff->addException(from_ghost_idx, to_ghost_idx,
+                                        0.0, 1e-9, 1e-9, true);
+                }
             }
         }
     }

wrapper/Move/CMakeNoOpenMM.txt

@@ -3,4 +3,5 @@ set ( SIRE_OPENMM_WRAPPERS
     NoOpenMM/OpenMMFrEnergyST.pypp.cpp
     NoOpenMM/OpenMMFrEnergyDT.pypp.cpp
     NoOpenMM/OpenMMMDIntegrator.pypp.cpp
+    NoOpenMM/OpenMMPMEFEP.pypp.cpp
     )

wrapper/Move/CMakeNoOpenMMFile.txt

@@ -3,6 +3,7 @@ set ( PYPP_OPENMM_SOURCES
     NoOpenMM/OpenMMFrEnergyST.pypp.cpp
     NoOpenMM/OpenMMFrEnergyDT.pypp.cpp
     NoOpenMM/OpenMMMDIntegrator.pypp.cpp
+    NoOpenMM/OpenMMPMEFEP.pypp.cpp
     )
 
 set( SIRE_OPENMM_LIBRARIES "" )

wrapper/Move/CMakeOpenMM.txt

@@ -3,4 +3,5 @@ set ( SIRE_OPENMM_WRAPPERS
     OpenMMFrEnergyST.pypp.cpp
     OpenMMFrEnergyDT.pypp.cpp
     OpenMMMDIntegrator.pypp.cpp
+    OpenMMPMEFEP.pypp.cpp
     )

wrapper/Move/CMakeOpenMMFile.txt

@@ -3,4 +3,5 @@ set ( PYPP_OPENMM_SOURCES
        OpenMMMDIntegrator.pypp.cpp
        OpenMMFrEnergyDT.pypp.cpp
        OpenMMFrEnergyST.pypp.cpp
+       OpenMMPMEFEP.pypp.cpp
     )

wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp

@@ -0,0 +1,108 @@
+// This file has been generated by Py++.
+
+// (C) Christopher Woods, GPL >= 3 License
+
+#include "boost/python.hpp"
+#include "OpenMMPMEFEP.pypp.hpp"
+
+namespace bp = boost::python;
+
+#include "SireFF/forcetable.h"
+
+#include "SireIO/amber.h"
+
+#include "SireMM/atomljs.h"
+
+#include "SireMM/internalff.h"
+
+#include "SireMM/internalperturbation.h"
+
+#include "SireMaths/constants.h"
+
+#include "SireMaths/rangenerator.h"
+
+#include "SireMaths/vector.h"
+
+#include "SireMol/amberparameters.h"
+
+#include "SireMol/atomcharges.h"
+
+#include "SireMol/atomcoords.h"
+
+#include "SireMol/atommasses.h"
+
+#include "SireMol/bondid.h"
+
+#include "SireMol/connectivity.h"
+
+#include "SireMol/mgname.h"
+
+#include "SireMol/molecule.h"
+
+#include "SireMol/core.h"
+
+#include "SireMol/moleculegroup.h"
+
+#include "SireMol/moleditor.h"
+
+#include "SireMol/partialmolecule.h"
+
+#include "SireMol/perturbation.h"
+
+#include "SireMove/flexibility.h"
+
+#include "SireStream/datastream.h"
+
+#include "SireStream/shareddatastream.h"
+
+#include "SireSystem/system.h"
+
+#include "SireUnits/convert.h"
+
+#include "SireUnits/temperature.h"
+
+#include "SireUnits/units.h"
+
+#include "SireVol/periodicbox.h"
+
+#include "ensemble.h"
+
+#include "openmmfrenergyst.h"
+
+#include <QDebug>
+
+#include <QTime>
+
+#include <iostream>
+
+#include "openmmfrenergyst.h"
+
+SireMove::OpenMMPMEFEP __copy__(const SireMove::OpenMMPMEFEP &other){ return SireMove::OpenMMPMEFEP(other); }
+
+const char* pvt_get_name(const SireMove::OpenMMPMEFEP&){ return "SireMove::OpenMMPMEFEP";}
+
+void register_OpenMMPMEFEP_class(){
+
+    { //::SireMove::OpenMMPMEFEP
+        typedef bp::class_< SireMove::OpenMMPMEFEP > OpenMMPMEFEP_exposer_t;
+        OpenMMPMEFEP_exposer_t OpenMMPMEFEP_exposer = OpenMMPMEFEP_exposer_t( "OpenMMPMEFEP", bp::init< >() );
+        bp::scope OpenMMPMEFEP_scope( OpenMMPMEFEP_exposer );
+        { //::SireMove::OpenMMPMEFEP::typeName
+
+            typedef char const * ( *typeName_function_type )(  );
+            typeName_function_type typeName_function_value( &::SireMove::OpenMMPMEFEP::typeName );
+
+            OpenMMPMEFEP_exposer.def(
+                "typeName"
+                , typeName_function_value );
+
+        }
+        OpenMMPMEFEP_exposer.staticmethod( "typeName" );
+        OpenMMPMEFEP_exposer.def( "__copy__", &__copy__);
+        OpenMMPMEFEP_exposer.def( "__deepcopy__", &__copy__);
+        OpenMMPMEFEP_exposer.def( "clone", &__copy__);
+        OpenMMPMEFEP_exposer.def( "__str__", &pvt_get_name);
+        OpenMMPMEFEP_exposer.def( "__repr__", &pvt_get_name);
+    }
+
+}

wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp

@@ -0,0 +1,10 @@
+// This file has been generated by Py++.
+
+// (C) Christopher Woods, GPL >= 3 License
+
+#ifndef OpenMMPMEFEP_hpp__pyplusplus_wrapper
+#define OpenMMPMEFEP_hpp__pyplusplus_wrapper
+
+void register_OpenMMPMEFEP_class();
+
+#endif//OpenMMPMEFEP_hpp__pyplusplus_wrapper