├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── pull_request_template.md └── workflows │ ├── choose_branch.yaml │ ├── devel.yaml │ ├── main.yaml │ └── pr.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── INSTALL.rst ├── LICENSE ├── README.rst ├── SECURITY.md ├── actions ├── collect_failed.py ├── parse_requirements.py ├── test_requirements.py ├── update_recipe.py └── upload_package.py ├── corelib ├── CMakeLists.txt ├── build │ ├── INSTALL │ ├── README │ ├── addfile.pl │ ├── applyheader.pl │ ├── autowrap.py │ ├── beautify.py │ ├── cmake │ │ ├── CheckAndFixLTOLibrary.cmake │ │ ├── DownloadAndCheckMD5.cmake │ │ ├── FindGSL.cmake │ │ ├── FindNetCDF.cmake │ │ ├── FindOpenMM.cmake │ │ ├── FindSire.cmake │ │ ├── FindVector.cmake │ │ ├── GetGitVersion.cmake │ │ ├── GetSvnVersion.cmake │ │ ├── LogVariables.cmake │ │ ├── cmake_strip.in │ │ ├── cmake_uninstall.cmake.in │ │ ├── sire_config.h.in │ │ └── sire_version_template.h │ ├── create_uid.py │ ├── download_compile_sire.py │ ├── find_missing_seh.py │ ├── finddiff.pl │ ├── get_needed_libc_cxx.py │ ├── listfiles.pl │ ├── makedocs.py │ ├── python-config │ ├── removetilde.py │ ├── split.pl │ ├── static_headers.h │ ├── svnmvall.py │ ├── templates │ │ └── header │ └── test_compiler │ │ ├── CMakeLists.txt │ │ ├── test_error_packing │ │ ├── CMakeLists.txt │ │ └── main.cpp │ │ ├── test_mpi │ │ ├── CMakeLists.txt │ │ ├── README │ │ └── test_mpi.cpp │ │ ├── test_openmp │ │ ├── CMakeLists.txt │ │ ├── main.cpp │ │ └── test.cpp │ │ ├── test_qhash_lookup │ │ ├── CMakeLists.txt │ │ └── main.cpp │ │ ├── test_stream │ │ ├── CMakeLists.txt │ │ └── main.cpp │ │ └── test_template_rtti │ │ ├── CMakeLists.txt │ │ ├── libbar.cpp │ │ ├── libbar.h │ │ ├── libfoo.cpp │ │ ├── libfoo.h │ │ └── main.cpp ├── parameters │ └── amber.zmatrices ├── share │ └── build │ │ ├── install_sire.sh │ │ ├── makeself-header.sh │ │ ├── makeself.sh │ │ ├── remove_path.py │ │ └── restore_path.py ├── src │ ├── apps │ │ ├── CMakeLists.txt │ │ ├── sire │ │ │ ├── CMakeLists.txt │ │ │ ├── main.cpp │ │ │ └── sire.qrc │ │ ├── test_system │ │ │ ├── CMakeLists.txt │ │ │ ├── get_glibc_version.c │ │ │ └── get_uname.c │ │ └── testmulti │ │ │ ├── CMakeLists.txt │ │ │ ├── main.cpp │ │ │ ├── speedtest.cpp │ │ │ ├── speedtest_results │ │ │ ├── sqrttest.cpp │ │ │ └── vectest.cpp │ └── libs │ │ ├── CMakeLists.txt │ │ ├── SireAnalysis │ │ ├── CMakeLists.txt │ │ ├── bennetts.cpp │ │ ├── bennetts.h │ │ ├── fep.cpp │ │ ├── fep.h │ │ ├── register_sireanalysis.cpp │ │ ├── third_party │ │ │ ├── regress.cpp │ │ │ └── regress.h │ │ ├── ti.cpp │ │ ├── ti.h │ │ ├── ticomponents.cpp │ │ └── ticomponents.h │ │ ├── SireBase │ │ ├── CMakeLists.txt │ │ ├── array2d.cpp │ │ ├── array2d.h │ │ ├── array2d.hpp │ │ ├── arrayproperty.cpp │ │ ├── arrayproperty.hpp │ │ ├── atexit.cpp │ │ ├── atexit.h │ │ ├── booleanproperty.cpp │ │ ├── booleanproperty.h │ │ ├── chunkedhash.cpp │ │ ├── chunkedhash.hpp │ │ ├── chunkedvector.cpp │ │ ├── chunkedvector.hpp │ │ ├── combineproperties.cpp │ │ ├── combineproperties.h │ │ ├── console.cpp │ │ ├── console.h │ │ ├── convert_property.hpp │ │ ├── countflops.cpp │ │ ├── countflops.h │ │ ├── cpuid.cpp │ │ ├── cpuid.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── findexe.cpp │ │ ├── findexe.h │ │ ├── generalunitproperty.cpp │ │ ├── generalunitproperty.h │ │ ├── getinstalldir.cpp │ │ ├── getinstalldir.h │ │ ├── globalsharedpointer.cpp │ │ ├── globalsharedpointer.hpp │ │ ├── increment.h │ │ ├── incremint.h │ │ ├── lazyevaluator.cpp │ │ ├── lazyevaluator.h │ │ ├── lengthproperty.cpp │ │ ├── lengthproperty.h │ │ ├── linktoproperty.cpp │ │ ├── linktoproperty.h │ │ ├── majorminorversion.cpp │ │ ├── majorminorversion.h │ │ ├── meminfo.cpp │ │ ├── meminfo.h │ │ ├── nullproperty.hpp │ │ ├── numberproperty.cpp │ │ ├── numberproperty.h │ │ ├── packedarray2d.cpp │ │ ├── packedarray2d.h │ │ ├── packedarray2d.hpp │ │ ├── packedarrays.h │ │ ├── pagecache.cpp │ │ ├── pagecache.h │ │ ├── pairmatrix.hpp │ │ ├── parallel.cpp │ │ ├── parallel.h │ │ ├── podproperty.hpp │ │ ├── process.cpp │ │ ├── progressbar.cpp │ │ ├── progressbar.h │ │ ├── properties.cpp │ │ ├── properties.h │ │ ├── property.cpp │ │ ├── property.h │ │ ├── propertylist.cpp │ │ ├── propertylist.h │ │ ├── propertymap.cpp │ │ ├── propertymap.h │ │ ├── quickcopy.hpp │ │ ├── qvariant_metatype.h │ │ ├── range.cpp │ │ ├── range.h │ │ ├── ranges.cpp │ │ ├── ranges.h │ │ ├── refcountdata.cpp │ │ ├── refcountdata.h │ │ ├── register_sirebase.cpp │ │ ├── releasegil.cpp │ │ ├── releasegil.h │ │ ├── savestate.cpp │ │ ├── savestate.h │ │ ├── shareddatapointer.hpp │ │ ├── sharedpolypointer.cpp │ │ ├── sharedpolypointer.hpp │ │ ├── sharedpolypointer_cast.hpp │ │ ├── sire_process.h │ │ ├── slice.cpp │ │ ├── slice.h │ │ ├── sparsematrix.cpp │ │ ├── sparsematrix.hpp │ │ ├── stringmangler.cpp │ │ ├── stringmangler.h │ │ ├── stringproperty.cpp │ │ ├── stringproperty.h │ │ ├── tempdir.cpp │ │ ├── tempdir.h │ │ ├── test_sharedptr.cpp │ │ ├── timeproperty.cpp │ │ ├── timeproperty.h │ │ ├── trigarray2d.cpp │ │ ├── trigarray2d.h │ │ ├── trigarray2d.hpp │ │ ├── unittest.cpp │ │ ├── unittest.h │ │ ├── variantproperty.cpp │ │ └── variantproperty.h │ │ ├── SireCAS │ │ ├── CMakeLists.txt │ │ ├── abs.cpp │ │ ├── abs.h │ │ ├── complexvalues.cpp │ │ ├── complexvalues.h │ │ ├── conditional.cpp │ │ ├── conditional.h │ │ ├── constant.cpp │ │ ├── constant.h │ │ ├── doublefunc.cpp │ │ ├── doublefunc.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── exbase.cpp │ │ ├── exbase.h │ │ ├── exp.cpp │ │ ├── exp.h │ │ ├── expression.cpp │ │ ├── expression.h │ │ ├── expressionbase.cpp │ │ ├── expressionbase.h │ │ ├── expressionproperty.cpp │ │ ├── expressionproperty.h │ │ ├── expressions.cpp │ │ ├── expressions.h │ │ ├── function.cpp │ │ ├── function.h │ │ ├── functions.cpp │ │ ├── functions.h │ │ ├── functionsignature.cpp │ │ ├── functionsignature.h │ │ ├── hyperbolicfuncs.cpp │ │ ├── hyperbolicfuncs.h │ │ ├── i.cpp │ │ ├── i.h │ │ ├── identities.cpp │ │ ├── identities.h │ │ ├── integrationconstant.cpp │ │ ├── integrationconstant.h │ │ ├── invhyperbolicfuncs.cpp │ │ ├── invhyperbolicfuncs.h │ │ ├── invtrigfuncs.cpp │ │ ├── invtrigfuncs.h │ │ ├── lambdaschedule.cpp │ │ ├── lambdaschedule.h │ │ ├── minmax.cpp │ │ ├── minmax.h │ │ ├── power.cpp │ │ ├── power.h │ │ ├── powerconstant.cpp │ │ ├── powerconstant.h │ │ ├── product.cpp │ │ ├── product.h │ │ ├── register_sirecas.cpp │ │ ├── singlefunc.cpp │ │ ├── singlefunc.h │ │ ├── sum.cpp │ │ ├── sum.h │ │ ├── symbol.cpp │ │ ├── symbol.h │ │ ├── symbolcomplex.h │ │ ├── symbolexpression.cpp │ │ ├── symbolexpression.h │ │ ├── symbols.h │ │ ├── symbolvalue.h │ │ ├── trigfuncs.cpp │ │ ├── trigfuncs.h │ │ ├── values.cpp │ │ └── values.h │ │ ├── SireCluster │ │ ├── CMakeLists.txt │ │ ├── backend.cpp │ │ ├── backend.h │ │ ├── cluster.cpp │ │ ├── cluster.h │ │ ├── frontend.cpp │ │ ├── frontend.h │ │ ├── mpi │ │ │ ├── messages.cpp │ │ │ ├── messages.h │ │ │ ├── mpicluster.cpp │ │ │ ├── mpicluster.h │ │ │ ├── mpifrontend.cpp │ │ │ ├── mpifrontend.h │ │ │ ├── p2pcomm.cpp │ │ │ ├── p2pcomm.h │ │ │ ├── receivequeue.cpp │ │ │ ├── receivequeue.h │ │ │ ├── reply.cpp │ │ │ ├── reply.h │ │ │ ├── reservationmanager.cpp │ │ │ ├── reservationmanager.h │ │ │ ├── sendqueue.cpp │ │ │ └── sendqueue.h │ │ ├── node.cpp │ │ ├── node.h │ │ ├── nodes.cpp │ │ ├── nodes.h │ │ ├── promise.cpp │ │ ├── promise.h │ │ ├── register_sirecluster.cpp │ │ ├── workpacket.cpp │ │ └── workpacket.h │ │ ├── SireError │ │ ├── CMakeLists.txt │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── exception.cpp │ │ ├── exception.h │ │ ├── getbacktrace.cpp │ │ ├── getbacktrace.h │ │ ├── printerror.cpp │ │ ├── printerror.h │ │ └── version_error.h │ │ ├── SireFF │ │ ├── CMakeLists.txt │ │ ├── atomicffparameters.hpp │ │ ├── detail │ │ │ ├── atomiccoords3d.cpp │ │ │ ├── atomiccoords3d.h │ │ │ ├── atomicparameters.hpp │ │ │ ├── atomicparameters3d.hpp │ │ │ ├── ffmolecules.cpp │ │ │ ├── ffmolecules.h │ │ │ ├── ffmolecules3d.cpp │ │ │ └── ffmolecules3d.h │ │ ├── energytable.cpp │ │ ├── energytable.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── ff.cpp │ │ ├── ff.h │ │ ├── ff3d.cpp │ │ ├── ff3d.h │ │ ├── ffcomponent.cpp │ │ ├── ffcomponent.h │ │ ├── ffdetail.cpp │ │ ├── ffdetail.h │ │ ├── ffid.cpp │ │ ├── ffid.h │ │ ├── ffidentifier.cpp │ │ ├── ffidentifier.h │ │ ├── ffidx.h │ │ ├── ffmolgroup.cpp │ │ ├── ffmolgroup.h │ │ ├── ffname.h │ │ ├── ffparameters.cpp │ │ ├── ffparameters.h │ │ ├── fieldtable.cpp │ │ ├── fieldtable.h │ │ ├── forcefield.cpp │ │ ├── forcefield.h │ │ ├── forcefields.cpp │ │ ├── forcefields.h │ │ ├── forcetable.cpp │ │ ├── forcetable.h │ │ ├── g1ff.cpp │ │ ├── g1ff.h │ │ ├── g2ff.cpp │ │ ├── g2ff.h │ │ ├── inter2b2g3dff.hpp │ │ ├── inter2b2gff.hpp │ │ ├── inter2b3dff.hpp │ │ ├── inter2bff.hpp │ │ ├── intra2b2g3dff.hpp │ │ ├── intra2b2gff.hpp │ │ ├── intra2b3dff.hpp │ │ ├── intra2bff.hpp │ │ ├── patch.cpp │ │ ├── patch.h │ │ ├── patches.cpp │ │ ├── patches.h │ │ ├── point.cpp │ │ ├── point.h │ │ ├── potentialtable.cpp │ │ ├── potentialtable.h │ │ ├── probe.cpp │ │ ├── probe.h │ │ └── register_sireff.cpp │ │ ├── SireID │ │ ├── CMakeLists.txt │ │ ├── id.cpp │ │ ├── id.h │ │ ├── idandset.hpp │ │ ├── identifier.cpp │ │ ├── identifier.h │ │ ├── idorset.hpp │ │ ├── index.cpp │ │ ├── index.h │ │ ├── invertmatch.hpp │ │ ├── matchall.hpp │ │ ├── name.h │ │ ├── number.h │ │ ├── register_sireid.cpp │ │ └── specify.hpp │ │ ├── SireIO │ │ ├── CMakeLists.txt │ │ ├── README_Parsers.md │ │ ├── amber.cpp │ │ ├── amber.h │ │ ├── amberformat.cpp │ │ ├── amberformat.h │ │ ├── amberprm.cpp │ │ ├── amberprm.h │ │ ├── amberrst.cpp │ │ ├── amberrst.h │ │ ├── amberrst7.cpp │ │ ├── amberrst7.h │ │ ├── ambertraj.cpp │ │ ├── ambertraj.h │ │ ├── biosimspace.cpp │ │ ├── biosimspace.h │ │ ├── charmmpsf.cpp │ │ ├── charmmpsf.h │ │ ├── cube.cpp │ │ ├── cube.h │ │ ├── dcd.cpp │ │ ├── dcd.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── filetrajectory.cpp │ │ ├── filetrajectory.h │ │ ├── filetrajectoryparser.cpp │ │ ├── filetrajectoryparser.h │ │ ├── flexibilitylibrary.cpp │ │ ├── flexibilitylibrary.h │ │ ├── fortranfile.cpp │ │ ├── fortranfile.h │ │ ├── getcoordsarray.cpp │ │ ├── getcoordsarray.h │ │ ├── gro87.cpp │ │ ├── gro87.h │ │ ├── grotop.cpp │ │ ├── grotop.h │ │ ├── iobase.cpp │ │ ├── iobase.h │ │ ├── mol2.cpp │ │ ├── mol2.h │ │ ├── moleculeparser.cpp │ │ ├── moleculeparser.h │ │ ├── netcdffile.cpp │ │ ├── netcdffile.h │ │ ├── pdb.cpp │ │ ├── pdb.h │ │ ├── pdb2.cpp │ │ ├── pdb2.h │ │ ├── pdbx.cpp │ │ ├── pdbx.h │ │ ├── perturbationslibrary.cpp │ │ ├── perturbationslibrary.h │ │ ├── protoms.cpp │ │ ├── protoms.h │ │ ├── register_sireio.cpp │ │ ├── sdf.cpp │ │ ├── sdf.h │ │ ├── supplementary.cpp │ │ ├── supplementary.h │ │ ├── textfile.cpp │ │ ├── textfile.h │ │ ├── third_party │ │ │ ├── xdrfile.c │ │ │ ├── xdrfile.h │ │ │ ├── xdrfile_trr.c │ │ │ ├── xdrfile_trr.h │ │ │ ├── xdrfile_xtc.c │ │ │ ├── xdrfile_xtc.h │ │ │ ├── xtc_seek.c │ │ │ └── xtc_seek.h │ │ ├── tinker.cpp │ │ ├── tinker.h │ │ ├── trajectorymonitor.cpp │ │ ├── trajectorymonitor.h │ │ ├── trr.cpp │ │ ├── trr.h │ │ ├── xdrfile.cpp │ │ ├── xdrfile.h │ │ ├── xtc.cpp │ │ ├── xtc.h │ │ ├── zmatrixmaker.cpp │ │ └── zmatrixmaker.h │ │ ├── SireMM │ │ ├── CMakeLists.txt │ │ ├── amberparams.cpp │ │ ├── amberparams.h │ │ ├── angle.cpp │ │ ├── angle.h │ │ ├── anglerestraints.cpp │ │ ├── anglerestraints.h │ │ ├── atomfunctions.cpp │ │ ├── atomfunctions.h │ │ ├── atomljs.cpp │ │ ├── atomljs.h │ │ ├── atompairs.hpp │ │ ├── bond.cpp │ │ ├── bond.h │ │ ├── bondrestraints.cpp │ │ ├── bondrestraints.h │ │ ├── boreschrestraints.cpp │ │ ├── boreschrestraints.h │ │ ├── clj14group.cpp │ │ ├── clj14group.h │ │ ├── cljatoms.cpp │ │ ├── cljatoms.h │ │ ├── cljboxes.cpp │ │ ├── cljboxes.h │ │ ├── cljcalculator.cpp │ │ ├── cljcalculator.h │ │ ├── cljcomponent.cpp │ │ ├── cljcomponent.h │ │ ├── cljdelta.cpp │ │ ├── cljdelta.h │ │ ├── cljextractor.cpp │ │ ├── cljextractor.h │ │ ├── cljfunction.cpp │ │ ├── cljfunction.h │ │ ├── cljgrid.cpp │ │ ├── cljgrid.h │ │ ├── cljgroup.cpp │ │ ├── cljgroup.h │ │ ├── cljnbpairs.cpp │ │ ├── cljnbpairs.h │ │ ├── cljparam.cpp │ │ ├── cljparam.h │ │ ├── cljpotential.cpp │ │ ├── cljpotential.h │ │ ├── cljprobe.cpp │ │ ├── cljprobe.h │ │ ├── cljrffunction.cpp │ │ ├── cljrffunction.h │ │ ├── cljshiftfunction.cpp │ │ ├── cljshiftfunction.h │ │ ├── cljworkspace.cpp │ │ ├── cljworkspace.h │ │ ├── cmapfunctions.cpp │ │ ├── cmapfunctions.h │ │ ├── cmapparameter.cpp │ │ ├── cmapparameter.h │ │ ├── coulombpotential.cpp │ │ ├── coulombpotential.h │ │ ├── detail │ │ │ └── intrascaledatomicparameters.hpp │ │ ├── dihedral.cpp │ │ ├── dihedral.h │ │ ├── dihedralrestraints.cpp │ │ ├── dihedralrestraints.h │ │ ├── distancerestraint.cpp │ │ ├── distancerestraint.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── excludedpairs.cpp │ │ ├── excludedpairs.h │ │ ├── fouratomfunctions.cpp │ │ ├── fouratomfunctions.h │ │ ├── gridff.cpp │ │ ├── gridff.h │ │ ├── gridff2.cpp │ │ ├── gridff2.h │ │ ├── gromacsparams.cpp │ │ ├── gromacsparams.h │ │ ├── improper.cpp │ │ ├── improper.h │ │ ├── intercljff.cpp │ │ ├── intercljff.h │ │ ├── intercoulombff.cpp │ │ ├── intercoulombff.h │ │ ├── interff.cpp │ │ ├── interff.h │ │ ├── intergroupff.cpp │ │ ├── intergroupff.h │ │ ├── interljff.cpp │ │ ├── interljff.h │ │ ├── internalcomponent.cpp │ │ ├── internalcomponent.h │ │ ├── internalff.cpp │ │ ├── internalff.h │ │ ├── internalgroupff.cpp │ │ ├── internalgroupff.h │ │ ├── internalparameters.cpp │ │ ├── internalparameters.h │ │ ├── internalperturbation.cpp │ │ ├── internalperturbation.h │ │ ├── intersoftcljff.cpp │ │ ├── intersoftcljff.h │ │ ├── intracljff.cpp │ │ ├── intracljff.h │ │ ├── intracoulombff.cpp │ │ ├── intracoulombff.h │ │ ├── intraff.cpp │ │ ├── intraff.h │ │ ├── intragroupff.cpp │ │ ├── intragroupff.h │ │ ├── intraljff.cpp │ │ ├── intraljff.h │ │ ├── intrasoftcljff.cpp │ │ ├── intrasoftcljff.h │ │ ├── inversebondrestraints.cpp │ │ ├── inversebondrestraints.h │ │ ├── lj1264parameter.cpp │ │ ├── lj1264parameter.h │ │ ├── ljfunction.h │ │ ├── ljpair.cpp │ │ ├── ljpair.h │ │ ├── ljparameter.cpp │ │ ├── ljparameter.h │ │ ├── ljparameterdb.cpp │ │ ├── ljparameterdb.h │ │ ├── ljperturbation.cpp │ │ ├── ljperturbation.h │ │ ├── ljpotential.cpp │ │ ├── ljpotential.h │ │ ├── mmdetail.cpp │ │ ├── mmdetail.h │ │ ├── morsepotentialrestraints.cpp │ │ ├── morsepotentialrestraints.h │ │ ├── multicljcomponent.cpp │ │ ├── multicljcomponent.h │ │ ├── positionalrestraints.cpp │ │ ├── positionalrestraints.h │ │ ├── register_siremm.cpp │ │ ├── restraint.cpp │ │ ├── restraint.h │ │ ├── restraintcomponent.cpp │ │ ├── restraintcomponent.h │ │ ├── restraintff.cpp │ │ ├── restraintff.h │ │ ├── restraints.cpp │ │ ├── restraints.h │ │ ├── rmsdrestraints.cpp │ │ ├── rmsdrestraints.h │ │ ├── selectorangle.cpp │ │ ├── selectorangle.h │ │ ├── selectorbond.cpp │ │ ├── selectorbond.h │ │ ├── selectordihedral.cpp │ │ ├── selectordihedral.h │ │ ├── selectorimproper.cpp │ │ ├── selectorimproper.h │ │ ├── selectormangle.cpp │ │ ├── selectormangle.h │ │ ├── selectormbond.cpp │ │ ├── selectormbond.h │ │ ├── selectormdihedral.cpp │ │ ├── selectormdihedral.h │ │ ├── selectormimproper.cpp │ │ ├── selectormimproper.h │ │ ├── softcljcomponent.cpp │ │ ├── softcljcomponent.h │ │ ├── softcljpotential.cpp │ │ ├── softcljpotential.h │ │ ├── switchingfunction.cpp │ │ ├── switchingfunction.h │ │ ├── testff.cpp │ │ ├── testff.h │ │ ├── threeatomfunctions.cpp │ │ ├── threeatomfunctions.h │ │ ├── twoatomfunctions.cpp │ │ └── twoatomfunctions.h │ │ ├── SireMaths │ │ ├── CMakeLists.txt │ │ ├── ThirdParty │ │ │ ├── MersenneTwister.h │ │ │ ├── avx_mathfun.h │ │ │ ├── neon_mathfun.h │ │ │ ├── sse2neon.h │ │ │ └── sse_mathfun.h │ │ ├── accumulator.cpp │ │ ├── accumulator.h │ │ ├── align.cpp │ │ ├── align.h │ │ ├── axisset.cpp │ │ ├── axisset.h │ │ ├── boys.cpp │ │ ├── boys.h │ │ ├── complex.cpp │ │ ├── complex.h │ │ ├── constants.h │ │ ├── distvector.cpp │ │ ├── distvector.h │ │ ├── energytrajectory.cpp │ │ ├── energytrajectory.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── freeenergyaverage.cpp │ │ ├── freeenergyaverage.h │ │ ├── gamma.cpp │ │ ├── gamma.h │ │ ├── histogram.cpp │ │ ├── histogram.h │ │ ├── line.cpp │ │ ├── line.h │ │ ├── linearap.cpp │ │ ├── linearap.h │ │ ├── make_tvalues.py │ │ ├── maths.h │ │ ├── matrix.cpp │ │ ├── matrix.h │ │ ├── multidouble.cpp │ │ ├── multidouble.h │ │ ├── multifixed.cpp │ │ ├── multifixed.h │ │ ├── multifloat.cpp │ │ ├── multifloat.h │ │ ├── multiint.cpp │ │ ├── multiint.h │ │ ├── multiquaternion.cpp │ │ ├── multiquaternion.h │ │ ├── multiuint.cpp │ │ ├── multiuint.h │ │ ├── multivector.cpp │ │ ├── multivector.h │ │ ├── n4matrix.cpp │ │ ├── n4matrix.h │ │ ├── nmatrix.cpp │ │ ├── nmatrix.h │ │ ├── nvector.cpp │ │ ├── nvector.h │ │ ├── plane.cpp │ │ ├── plane.h │ │ ├── quaternion.cpp │ │ ├── quaternion.h │ │ ├── rangenerator.cpp │ │ ├── rangenerator.h │ │ ├── rational.cpp │ │ ├── rational.h │ │ ├── register_siremaths.cpp │ │ ├── rotate.h │ │ ├── sincos.cpp │ │ ├── sincos.h │ │ ├── sire_blaspack.f │ │ ├── sire_lapack.cpp │ │ ├── sire_lapack.h │ │ ├── sire_linpack.cpp │ │ ├── sire_linpack.h │ │ ├── sphere.cpp │ │ ├── sphere.h │ │ ├── sphereproperty.cpp │ │ ├── sphereproperty.h │ │ ├── t_values │ │ ├── third_party │ │ │ └── eig3 │ │ │ │ ├── eig3.cpp │ │ │ │ ├── eig3.h │ │ │ │ └── readme.txt │ │ ├── torsion.cpp │ │ ├── torsion.h │ │ ├── triangle.cpp │ │ ├── triangle.h │ │ ├── trigmatrix.cpp │ │ ├── trigmatrix.h │ │ ├── vector.cpp │ │ ├── vector.h │ │ ├── vector3d.hpp │ │ ├── vectorproperty.cpp │ │ └── vectorproperty.h │ │ ├── SireMol │ │ ├── CMakeLists.txt │ │ ├── amberparameters.cpp │ │ ├── amberparameters.h │ │ ├── angleid.cpp │ │ ├── angleid.h │ │ ├── atom.cpp │ │ ├── atom.h │ │ ├── atombeads.h │ │ ├── atomcharges.h │ │ ├── atomcoords.cpp │ │ ├── atomcoords.h │ │ ├── atomcutting.cpp │ │ ├── atomcutting.h │ │ ├── atomeditor.cpp │ │ ├── atomeditor.h │ │ ├── atomelements.h │ │ ├── atomenergies.h │ │ ├── atomforces.h │ │ ├── atomid.cpp │ │ ├── atomid.h │ │ ├── atomidcombos.h │ │ ├── atomidentifier.cpp │ │ ├── atomidentifier.h │ │ ├── atomidx.h │ │ ├── atomidxmapping.cpp │ │ ├── atomidxmapping.h │ │ ├── atommapping.cpp │ │ ├── atommapping.h │ │ ├── atommasses.h │ │ ├── atommatch.cpp │ │ ├── atommatch.h │ │ ├── atommatcher.cpp │ │ ├── atommatcher.h │ │ ├── atommatchers.cpp │ │ ├── atommatchers.h │ │ ├── atomname.h │ │ ├── atomnum.h │ │ ├── atompolarisabilities.h │ │ ├── atomproperty.cpp │ │ ├── atomproperty.hpp │ │ ├── atompropertylist.h │ │ ├── atomradicals.h │ │ ├── atomradii.h │ │ ├── atomselection.cpp │ │ ├── atomselection.h │ │ ├── atomsin.hpp │ │ ├── atomvelocities.h │ │ ├── bead.cpp │ │ ├── bead.h │ │ ├── beadeditor.cpp │ │ ├── beadeditor.h │ │ ├── beadid.cpp │ │ ├── beadid.h │ │ ├── beadidx.h │ │ ├── beading.cpp │ │ ├── beading.h │ │ ├── beadnum.h │ │ ├── beadproperty.cpp │ │ ├── beadproperty.hpp │ │ ├── beads.cpp │ │ ├── beads.h │ │ ├── bondhunter.cpp │ │ ├── bondhunter.h │ │ ├── bondid.cpp │ │ ├── bondid.h │ │ ├── bondorder.cpp │ │ ├── bondorder.h │ │ ├── calculateaxes.hpp │ │ ├── cgatomidx.cpp │ │ ├── cgatomidx.h │ │ ├── cgeditor.cpp │ │ ├── cgeditor.h │ │ ├── cgid.cpp │ │ ├── cgid.h │ │ ├── cgidentifier.cpp │ │ ├── cgidentifier.h │ │ ├── cgidx.h │ │ ├── cgname.h │ │ ├── cgproperty.cpp │ │ ├── cgproperty.hpp │ │ ├── chain.cpp │ │ ├── chain.h │ │ ├── chaineditor.cpp │ │ ├── chaineditor.h │ │ ├── chainid.cpp │ │ ├── chainid.h │ │ ├── chainidentifier.cpp │ │ ├── chainidentifier.h │ │ ├── chainidx.h │ │ ├── chainname.h │ │ ├── chainproperty.cpp │ │ ├── chainproperty.hpp │ │ ├── chainresid.cpp │ │ ├── chainresid.h │ │ ├── chargeperturbation.cpp │ │ ├── chargeperturbation.h │ │ ├── chirality.cpp │ │ ├── chirality.h │ │ ├── cmapid.cpp │ │ ├── cmapid.h │ │ ├── connectivity.cpp │ │ ├── connectivity.h │ │ ├── core.h │ │ ├── cutgroup.cpp │ │ ├── cutgroup.h │ │ ├── cuttingfunction.cpp │ │ ├── cuttingfunction.h │ │ ├── dihedralid.cpp │ │ ├── dihedralid.h │ │ ├── editor.hpp │ │ ├── element-data.h │ │ ├── element.h │ │ ├── elementdb.cpp │ │ ├── elementdb.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── evaluator.cpp │ │ ├── evaluator.h │ │ ├── evaluatorm.cpp │ │ ├── evaluatorm.h │ │ ├── findmcs.cpp │ │ ├── geometryperturbation.cpp │ │ ├── geometryperturbation.h │ │ ├── getghostparam.hpp │ │ ├── getrmsd.cpp │ │ ├── getrmsd.h │ │ ├── groupatomids.cpp │ │ ├── groupatomids.h │ │ ├── groupgroupids.cpp │ │ ├── groupgroupids.h │ │ ├── hybridization.cpp │ │ ├── hybridization.h │ │ ├── improperid.cpp │ │ ├── improperid.h │ │ ├── iswater.cpp │ │ ├── iswater.h │ │ ├── mgid.cpp │ │ ├── mgid.h │ │ ├── mgidentifier.cpp │ │ ├── mgidentifier.h │ │ ├── mgidsandmaps.cpp │ │ ├── mgidsandmaps.h │ │ ├── mgidx.h │ │ ├── mgname.h │ │ ├── mgnum.h │ │ ├── molatomid.cpp │ │ ├── molatomid.h │ │ ├── molecule.cpp │ │ ├── molecule.h │ │ ├── moleculecutting.cpp │ │ ├── moleculecutting.h │ │ ├── moleculedata.cpp │ │ ├── moleculedata.h │ │ ├── moleculegroup.cpp │ │ ├── moleculegroup.h │ │ ├── moleculegroups.cpp │ │ ├── moleculegroups.h │ │ ├── moleculeinfo.cpp │ │ ├── moleculeinfo.h │ │ ├── moleculeinfodata.cpp │ │ ├── moleculeinfodata.h │ │ ├── moleculeinfodataeditor.cpp │ │ ├── molecules.cpp │ │ ├── molecules.h │ │ ├── moleculeview.cpp │ │ ├── moleculeview.h │ │ ├── moleditor.cpp │ │ ├── moleditor.h │ │ ├── molgroupworkspace.cpp │ │ ├── molgroupworkspace.h │ │ ├── molid.cpp │ │ ├── molid.h │ │ ├── molidentifier.cpp │ │ ├── molidentifier.h │ │ ├── molidx.h │ │ ├── molinfo.h │ │ ├── molname.h │ │ ├── molnum.h │ │ ├── molresid.cpp │ │ ├── molresid.h │ │ ├── molviewproperty.cpp │ │ ├── molviewproperty.h │ │ ├── molwithresid.cpp │ │ ├── molwithresid.h │ │ ├── mover.cpp │ │ ├── mover.h │ │ ├── mover.hpp │ │ ├── mover_metaid.h │ │ ├── parser.cpp │ │ ├── parser.h │ │ ├── partialmolecule.cpp │ │ ├── partialmolecule.h │ │ ├── perturbation.cpp │ │ ├── perturbation.h │ │ ├── radical.cpp │ │ ├── radical.h │ │ ├── register_siremol.cpp │ │ ├── reseditor.cpp │ │ ├── reseditor.h │ │ ├── resid.cpp │ │ ├── resid.h │ │ ├── residentifier.cpp │ │ ├── residentifier.h │ │ ├── residue.cpp │ │ ├── residue.h │ │ ├── residuecutting.cpp │ │ ├── residuecutting.h │ │ ├── residx.h │ │ ├── resin.hpp │ │ ├── resname.h │ │ ├── resnum.h │ │ ├── resproperty.cpp │ │ ├── resproperty.hpp │ │ ├── segeditor.cpp │ │ ├── segeditor.h │ │ ├── segid.cpp │ │ ├── segid.h │ │ ├── segidentifier.cpp │ │ ├── segidentifier.h │ │ ├── segidx.h │ │ ├── segment.cpp │ │ ├── segment.h │ │ ├── segname.h │ │ ├── segproperty.cpp │ │ ├── segproperty.hpp │ │ ├── select.cpp │ │ ├── select.h │ │ ├── selector.hpp │ │ ├── selectorm.hpp │ │ ├── selectormol.cpp │ │ ├── selectormol.h │ │ ├── specifymol.cpp │ │ ├── specifymol.h │ │ ├── stereochemistry.cpp │ │ ├── stereochemistry.h │ │ ├── structureeditor.cpp │ │ ├── structureeditor.h │ │ ├── trajectory.cpp │ │ ├── trajectory.h │ │ ├── trajectoryaligner.cpp │ │ ├── trajectoryaligner.h │ │ ├── viewsofmol.cpp │ │ ├── viewsofmol.h │ │ ├── volumemap.cpp │ │ ├── volumemap.h │ │ ├── weightfunction.cpp │ │ ├── weightfunction.h │ │ ├── withatoms.cpp │ │ ├── withatoms.h │ │ ├── within.cpp │ │ ├── within.h │ │ ├── withres.cpp │ │ └── withres.h │ │ ├── SireMove │ │ ├── CMakeLists.txt │ │ ├── dlmrigidbody.cpp │ │ ├── dlmrigidbody.h │ │ ├── dynamics.cpp │ │ ├── dynamics.h │ │ ├── ensemble.cpp │ │ ├── ensemble.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── flexibility.cpp │ │ ├── flexibility.h │ │ ├── getpoint.cpp │ │ ├── getpoint.h │ │ ├── gibbsmove.cpp │ │ ├── gibbsmove.h │ │ ├── hybridmc.cpp │ │ ├── hybridmc.h │ │ ├── integrator.cpp │ │ ├── integrator.h │ │ ├── integratorworkspace.cpp │ │ ├── integratorworkspace.h │ │ ├── integratorworkspacejm.cpp │ │ ├── integratorworkspacejm.h │ │ ├── internalmove.cpp │ │ ├── internalmove.h │ │ ├── internalmovesingle.cpp │ │ ├── internalmovesingle.h │ │ ├── moldeleter.cpp │ │ ├── moldeleter.h │ │ ├── moleculardynamics.cpp │ │ ├── moleculardynamics.h │ │ ├── molinserter.cpp │ │ ├── molinserter.h │ │ ├── montecarlo.cpp │ │ ├── montecarlo.h │ │ ├── move.cpp │ │ ├── move.h │ │ ├── moves.cpp │ │ ├── moves.h │ │ ├── mtsmc.cpp │ │ ├── mtsmc.h │ │ ├── openmmfrenergydt.cpp │ │ ├── openmmfrenergydt.h │ │ ├── openmmfrenergyst.cpp │ │ ├── openmmfrenergyst.h │ │ ├── openmmmdintegrator.cpp │ │ ├── openmmmdintegrator.h │ │ ├── openmmpmefep.cpp │ │ ├── openmmpmefep.h │ │ ├── posvel.h │ │ ├── prefsampler.cpp │ │ ├── prefsampler.h │ │ ├── rbworkspace.cpp │ │ ├── rbworkspace.h │ │ ├── rbworkspacejm.cpp │ │ ├── rbworkspacejm.h │ │ ├── register_siremove.cpp │ │ ├── repexmove.cpp │ │ ├── repexmove.h │ │ ├── repexmove2.cpp │ │ ├── repexmove2.h │ │ ├── replica.cpp │ │ ├── replica.h │ │ ├── replicas.cpp │ │ ├── replicas.h │ │ ├── rigidbodymc.cpp │ │ ├── rigidbodymc.h │ │ ├── sampler.cpp │ │ ├── sampler.h │ │ ├── simpacket.cpp │ │ ├── simpacket.h │ │ ├── simstore.cpp │ │ ├── simstore.h │ │ ├── simulation.cpp │ │ ├── simulation.h │ │ ├── supramove.cpp │ │ ├── supramove.h │ │ ├── supramoves.cpp │ │ ├── supramoves.h │ │ ├── suprasim.cpp │ │ ├── suprasim.h │ │ ├── suprasimpacket.cpp │ │ ├── suprasimpacket.h │ │ ├── suprasubmove.cpp │ │ ├── suprasubmove.h │ │ ├── suprasubmoves.cpp │ │ ├── suprasubmoves.h │ │ ├── suprasubsim.cpp │ │ ├── suprasubsim.h │ │ ├── suprasubsimpacket.cpp │ │ ├── suprasubsimpacket.h │ │ ├── suprasubsystem.cpp │ │ ├── suprasubsystem.h │ │ ├── suprasystem.cpp │ │ ├── suprasystem.h │ │ ├── titrationmove.cpp │ │ ├── titrationmove.h │ │ ├── titrator.cpp │ │ ├── titrator.h │ │ ├── uniformsampler.cpp │ │ ├── uniformsampler.h │ │ ├── velocitygenerator.cpp │ │ ├── velocitygenerator.h │ │ ├── velocityverlet.cpp │ │ ├── velocityverlet.h │ │ ├── volumechanger.cpp │ │ ├── volumechanger.h │ │ ├── volumemove.cpp │ │ ├── volumemove.h │ │ ├── weightedmoves.cpp │ │ ├── weightedmoves.h │ │ ├── zmatmove.cpp │ │ ├── zmatmove.h │ │ ├── zmatrix.cpp │ │ └── zmatrix.h │ │ ├── SireSearch │ │ ├── CMakeLists.txt │ │ ├── approx_equal.cpp │ │ ├── approx_equal.h │ │ ├── ast.cpp │ │ ├── ast.h │ │ ├── grammar.h │ │ ├── helper_funcs.cpp │ │ ├── helper_funcs.h │ │ ├── idengine.cpp │ │ ├── idengine.h │ │ ├── parser.cpp │ │ ├── parser.h │ │ └── register_siresearch.cpp │ │ ├── SireStream │ │ ├── CMakeLists.txt │ │ ├── ThirdParty │ │ │ ├── md5.c │ │ │ └── md5.h │ │ ├── datastream.cpp │ │ ├── datastream.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── getmagic.cpp │ │ ├── magic_error.cpp │ │ ├── magic_error.h │ │ ├── md5sum.cpp │ │ ├── md5sum.h │ │ ├── metatype.cpp │ │ ├── metatype.h │ │ ├── registeralternativename.h │ │ ├── shareddatastream.cpp │ │ ├── shareddatastream.h │ │ ├── sharestrings.cpp │ │ ├── sharestrings.h │ │ ├── streamdata.cpp │ │ ├── streamdata.hpp │ │ ├── streampolypointer.hpp │ │ ├── version_error.h │ │ └── versionid.h │ │ ├── SireSystem │ │ ├── CMakeLists.txt │ │ ├── anglecomponent.cpp │ │ ├── anglecomponent.h │ │ ├── calculate_energy.cpp │ │ ├── calculate_energy.h │ │ ├── chargeconstraint.cpp │ │ ├── chargeconstraint.h │ │ ├── checkpoint.cpp │ │ ├── checkpoint.h │ │ ├── closemols.cpp │ │ ├── closemols.h │ │ ├── constraint.cpp │ │ ├── constraint.h │ │ ├── constraints.cpp │ │ ├── constraints.h │ │ ├── create_test_molecule.cpp │ │ ├── create_test_molecule.h │ │ ├── delta.cpp │ │ ├── delta.h │ │ ├── dihedralcomponent.cpp │ │ ├── dihedralcomponent.h │ │ ├── distancecomponent.cpp │ │ ├── distancecomponent.h │ │ ├── energymonitor.cpp │ │ ├── energymonitor.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── forcefieldinfo.cpp │ │ ├── forcefieldinfo.h │ │ ├── freeenergymonitor.cpp │ │ ├── freeenergymonitor.h │ │ ├── geometrycomponent.cpp │ │ ├── geometrycomponent.h │ │ ├── idassigner.cpp │ │ ├── idassigner.h │ │ ├── identityconstraint.cpp │ │ ├── identityconstraint.h │ │ ├── merge.cpp │ │ ├── merge.h │ │ ├── moleculeconstraint.cpp │ │ ├── moleculeconstraint.h │ │ ├── monitorcomponent.cpp │ │ ├── monitorcomponent.h │ │ ├── monitorcomponents.cpp │ │ ├── monitorcomponents.h │ │ ├── monitorid.cpp │ │ ├── monitorid.h │ │ ├── monitoridentifier.cpp │ │ ├── monitoridentifier.h │ │ ├── monitoridx.h │ │ ├── monitormonitor.cpp │ │ ├── monitormonitor.h │ │ ├── monitorname.h │ │ ├── monitorproperty.cpp │ │ ├── monitorproperty.h │ │ ├── perturbationconstraint.cpp │ │ ├── perturbationconstraint.h │ │ ├── polarisecharges.cpp │ │ ├── polarisecharges.h │ │ ├── register_siresystem.cpp │ │ ├── spacewrapper.cpp │ │ ├── spacewrapper.h │ │ ├── sysid.cpp │ │ ├── sysid.h │ │ ├── sysidentifier.cpp │ │ ├── sysidentifier.h │ │ ├── sysidx.h │ │ ├── sysname.h │ │ ├── system.cpp │ │ ├── system.h │ │ ├── systemmonitor.cpp │ │ ├── systemmonitor.h │ │ ├── systemmonitors.cpp │ │ ├── systemmonitors.h │ │ ├── systemtrajectory.cpp │ │ ├── systemtrajectory.h │ │ ├── volmapmonitor.cpp │ │ └── volmapmonitor.h │ │ ├── SireUnits │ │ ├── CMakeLists.txt │ │ ├── angle.cpp │ │ ├── angle.h │ │ ├── ast.cpp │ │ ├── ast.h │ │ ├── convert.cpp │ │ ├── convert.h │ │ ├── dimensions.cpp │ │ ├── dimensions.h │ │ ├── generalunit.cpp │ │ ├── generalunit.h │ │ ├── grammar.h │ │ ├── parser.cpp │ │ ├── register_sireunits.cpp │ │ ├── temperature.cpp │ │ ├── temperature.h │ │ └── units.h │ │ ├── SireVol │ │ ├── CMakeLists.txt │ │ ├── aabox.cpp │ │ ├── aabox.h │ │ ├── cartesian.cpp │ │ ├── cartesian.h │ │ ├── combinedspace.cpp │ │ ├── combinedspace.h │ │ ├── combinespaces.cpp │ │ ├── combinespaces.h │ │ ├── coordgroup.cpp │ │ ├── coordgroup.h │ │ ├── errors.cpp │ │ ├── errors.h │ │ ├── grid.cpp │ │ ├── grid.h │ │ ├── gridinfo.cpp │ │ ├── gridinfo.h │ │ ├── patching.cpp │ │ ├── patching.h │ │ ├── periodicbox.cpp │ │ ├── periodicbox.h │ │ ├── register_sirevol.cpp │ │ ├── space.cpp │ │ ├── space.h │ │ ├── transformedspace.cpp │ │ ├── transformedspace.h │ │ ├── triclinicbox.cpp │ │ └── triclinicbox.h │ │ ├── Squire │ │ ├── CMakeLists.txt │ │ ├── am1bcc.cpp │ │ ├── am1bcc.h │ │ ├── gto.cpp │ │ ├── gto.h │ │ ├── hf.cpp │ │ ├── hf.h │ │ ├── latticecharges.cpp │ │ ├── latticecharges.h │ │ ├── molpro.cpp │ │ ├── molpro.h │ │ ├── mopac.cpp │ │ ├── mopac.h │ │ ├── orbital.cpp │ │ ├── orbital.h │ │ ├── orca.cpp │ │ ├── orca.h │ │ ├── pgto.cpp │ │ ├── pgto.h │ │ ├── pointcharge.cpp │ │ ├── pointcharge.h │ │ ├── pointdipole.cpp │ │ ├── pointdipole.h │ │ ├── qmchargecalculator.cpp │ │ ├── qmchargecalculator.h │ │ ├── qmchargeconstraint.cpp │ │ ├── qmchargeconstraint.h │ │ ├── qmff.cpp │ │ ├── qmff.h │ │ ├── qmmmelecembedpotential.cpp │ │ ├── qmmmelecembedpotential.h │ │ ├── qmmmff.cpp │ │ ├── qmmmff.h │ │ ├── qmmmpotential.cpp │ │ ├── qmmmpotential.h │ │ ├── qmpotential.cpp │ │ ├── qmpotential.h │ │ ├── qmprogram.cpp │ │ ├── qmprogram.h │ │ ├── register_squire.cpp │ │ ├── sgto.cpp │ │ ├── sgto.h │ │ ├── sqm.cpp │ │ └── sqm.h │ │ ├── sireglobal.h │ │ └── tostring.h └── templates │ ├── ions │ ├── cl_tip3p.prm7 │ ├── cl_tip4p.prm7 │ ├── na_tip3p.prm7 │ └── na_tip4p.prm7 │ └── water │ ├── opc.gro87 │ ├── opc.grotop │ ├── opc.itp │ ├── opc.prm7 │ ├── opc.rst7 │ ├── opc_solvate.gro │ ├── spc.gro87 │ ├── spc.grotop │ ├── spce.gro87 │ ├── spce.grotop │ ├── spce.prm7 │ ├── spce.rst7 │ ├── tip3p.gro87 │ ├── tip3p.grotop │ ├── tip3p.prm7 │ ├── tip3p.rst7 │ ├── tip4p.gro87 │ ├── tip4p.grotop │ ├── tip4p.prm7 │ ├── tip4p.rst7 │ ├── tip5p.gro87 │ ├── tip5p.grotop │ ├── tip5p.prm7 │ └── tip5p.rst7 ├── doc ├── Makefile ├── requirements.txt ├── source │ ├── _static │ │ ├── css │ │ │ ├── custom_fonts.css │ │ │ ├── custom_pygments.css │ │ │ └── custom_style.css │ │ └── js │ │ │ └── custom.js │ ├── _templates │ │ └── sidebar │ │ │ └── search.html │ ├── acknowledgements.rst │ ├── api │ │ ├── base.rst │ │ ├── cas.rst │ │ ├── convert.rst │ │ ├── index.rst │ │ ├── index_base.rst │ │ ├── index_cas.rst │ │ ├── index_convert.rst │ │ ├── index_io.rst │ │ ├── index_maths.rst │ │ ├── index_mm.rst │ │ ├── index_mol.rst │ │ ├── index_morph.rst │ │ ├── index_restraints.rst │ │ ├── index_search.rst │ │ ├── index_stream.rst │ │ ├── index_system.rst │ │ ├── index_units.rst │ │ ├── index_utils.rst │ │ ├── index_vol.rst │ │ ├── io.rst │ │ ├── io_parser.rst │ │ ├── maths.rst │ │ ├── mm.rst │ │ ├── mol.rst │ │ ├── morph.rst │ │ ├── restraints.rst │ │ ├── search.rst │ │ ├── sire.rst │ │ ├── sire_modules.rst │ │ ├── stream.rst │ │ ├── system.rst │ │ ├── units.rst │ │ ├── utils.rst │ │ └── vol.rst │ ├── blogposts.rst │ ├── changelog.rst │ ├── cheatsheet │ │ ├── images │ │ │ ├── view_01.png │ │ │ ├── view_02.png │ │ │ ├── view_03.png │ │ │ ├── view_04.png │ │ │ ├── view_05.png │ │ │ ├── view_06.jpg │ │ │ ├── view_07.jpg │ │ │ ├── view_08.jpg │ │ │ ├── view_09.jpg │ │ │ ├── view_10.jpg │ │ │ ├── view_11.jpg │ │ │ ├── view_12.jpg │ │ │ ├── view_13.jpg │ │ │ ├── view_14.jpg │ │ │ ├── view_15.jpg │ │ │ ├── view_16.jpg │ │ │ ├── view_17.jpg │ │ │ ├── view_18.jpg │ │ │ ├── view_19.jpg │ │ │ └── view_20.jpg │ │ ├── index.rst │ │ ├── openmm.rst │ │ ├── search.rst │ │ ├── trajectory.rst │ │ ├── units.rst │ │ └── view.rst │ ├── code_of_conduct.rst │ ├── conf.py │ ├── contributing │ │ ├── codestyle.rst │ │ ├── development.rst │ │ ├── index.rst │ │ ├── packaging.rst │ │ └── roadmap.rst │ ├── contributors.rst │ ├── features.rst │ ├── images │ │ ├── favicon.png │ │ └── logo.svg │ ├── index.rst │ ├── install.rst │ ├── quickstart │ │ ├── images │ │ │ ├── qs01.jpg │ │ │ ├── qs02.jpg │ │ │ ├── qs03.jpg │ │ │ ├── qs04.jpg │ │ │ ├── qs05.jpg │ │ │ └── qs06.jpg │ │ └── index.rst │ ├── support.rst │ └── tutorial │ │ ├── index.rst │ │ ├── index_part01.rst │ │ ├── index_part02.rst │ │ ├── index_part03.rst │ │ ├── index_part04.rst │ │ ├── index_part05.rst │ │ ├── index_part06.rst │ │ ├── index_part07.rst │ │ ├── index_part08.rst │ │ ├── part01 │ │ ├── 01_importing_sire.rst │ │ ├── 02_loading_a_molecule.rst │ │ ├── 03_simple_indexing.rst │ │ ├── 04_saving_a_molecule.rst │ │ ├── 05_loading_from_multiple_files.rst │ │ ├── 06_trajectories.rst │ │ ├── 07_supported_file_formats.rst │ │ └── images │ │ │ ├── 3NSS.jpg │ │ │ ├── A0A538R8Y3.jpg │ │ │ ├── cholesterol.jpg │ │ │ └── cholesterol_2d.png │ │ ├── part02 │ │ ├── 01_indexing_atoms.rst │ │ ├── 02_indexing_residues.rst │ │ ├── 03_indexing_chains.rst │ │ ├── 04_indexing_segments.rst │ │ ├── 05_indexing_molecules.rst │ │ ├── 06_indexing_bonds.rst │ │ ├── 07_indexing_angles.rst │ │ ├── 08_indexing_dihedrals.rst │ │ ├── 09_indexing_impropers.rst │ │ ├── 10_searching.rst │ │ └── images │ │ │ └── 7SA1.jpg │ │ ├── part03 │ │ ├── 01_atom_properties.rst │ │ ├── 02_cursors.rst │ │ ├── 03_residue_properties.rst │ │ ├── 04_molecule_properties.rst │ │ ├── 05_bond_properties.rst │ │ ├── 06_angle_properties.rst │ │ ├── 07_dihedral_properties.rst │ │ └── 08_improper_properties.rst │ │ ├── part04 │ │ ├── 01_measure.rst │ │ ├── 02_trajectory.rst │ │ ├── 03_energies.rst │ │ ├── 04_energy_trajectories.rst │ │ ├── 05_movement.rst │ │ ├── 06_move_internals.rst │ │ └── images │ │ │ ├── 04_02_01.jpg │ │ │ ├── 04_02_02.jpg │ │ │ ├── 04_02_03.jpg │ │ │ ├── 04_02_04.jpg │ │ │ ├── 04_02_05.jpg │ │ │ ├── 04_02_06.jpg │ │ │ ├── 04_02_07.jpg │ │ │ ├── 04_04_01.jpg │ │ │ ├── 04_04_02.jpg │ │ │ ├── 04_04_03.jpg │ │ │ ├── 04_05_01.jpg │ │ │ ├── 04_06_01.jpg │ │ │ ├── 04_06_02.jpg │ │ │ ├── 04_06_03.jpg │ │ │ └── 04_06_04.jpg │ │ ├── part05 │ │ ├── 01_convert.rst │ │ ├── 02_view.rst │ │ ├── 03_smiles.rst │ │ ├── 04_smarts.rst │ │ ├── 05_dynamics.rst │ │ └── images │ │ │ ├── 05_02_01.png │ │ │ ├── 05_02_02.png │ │ │ ├── 05_02_03.png │ │ │ ├── 05_02_04.png │ │ │ ├── 05_03_01.jpg │ │ │ ├── 05_05_01.jpg │ │ │ ├── 05_05_02.jpg │ │ │ └── 05_05_03.jpg │ │ ├── part06 │ │ ├── 01_merge.rst │ │ ├── 02_alchemical_dynamics.rst │ │ ├── 03_restraints.rst │ │ ├── 04_alchemical_restraints.rst │ │ ├── 05_free_energy_perturbation.rst │ │ ├── 06_faster_fep.rst │ │ ├── images │ │ │ ├── 06_01_01.jpg │ │ │ ├── 06_01_02.jpg │ │ │ ├── 06_02_01.jpg │ │ │ ├── 06_02_02.jpg │ │ │ ├── 06_02_03.jpg │ │ │ ├── 06_02_04.jpg │ │ │ ├── 06_04_01.jpg │ │ │ ├── 06_04_02.jpg │ │ │ ├── 06_05_01.jpg │ │ │ ├── 06_06_01.jpg │ │ │ └── 06_06_02.jpg │ │ └── scripts │ │ │ └── run_md.py │ │ ├── part07 │ │ ├── 01_perturbation.rst │ │ ├── 02_levers.rst │ │ ├── 03_ghosts.rst │ │ ├── 04_merge.rst │ │ ├── 05_pertfile.rst │ │ ├── 06_decouple.rst │ │ ├── 07_residue.rst │ │ └── images │ │ │ ├── 07_01_01.jpg │ │ │ ├── 07_02_01.jpg │ │ │ ├── 07_02_02.jpg │ │ │ ├── 07_03_01.jpg │ │ │ ├── 07_04_01.jpg │ │ │ ├── 07_04_02.jpg │ │ │ ├── 07_04_03.jpg │ │ │ └── 07_06_01.jpg │ │ └── part08 │ │ ├── 01_intro.rst │ │ ├── 02_emle.rst │ │ ├── 03_adp_pmf.rst │ │ ├── 04_diels_alder.rst │ │ ├── images │ │ ├── abyu.png │ │ ├── ala.png │ │ ├── pmf_abyu.png │ │ └── pmf_adp.png │ │ └── sire_emle.ipynb └── winbuild.bat ├── docker ├── README.md └── sire-generate-wrappers │ ├── Dockerfile_arm64 │ ├── Dockerfile_x86 │ ├── README.md │ ├── bashrc │ ├── create_includes_tarball │ ├── generate_wrappers │ ├── push_wrappers │ ├── scanner.py │ └── unpack_headers ├── recipes └── sire │ ├── LICENSE │ ├── bld.bat │ ├── build.sh │ ├── conda_build_config.yaml │ └── template.yaml ├── requirements_bss.txt ├── requirements_build.txt ├── requirements_emle.txt ├── requirements_host.txt ├── requirements_run.txt ├── requirements_test.txt ├── setup.py ├── src └── sire │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _colname.py │ ├── _load.py │ ├── _match.py │ ├── _measure.py │ ├── _parallel.py │ ├── _pythonize.py │ ├── analysis │ ├── CMakeLists.txt │ └── __init__.py │ ├── base │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _pagecache.py │ └── _progressbar.py │ ├── build │ └── cmake │ │ ├── cmake_uninstall.cmake.in │ │ └── install_python.cmake │ ├── cas │ ├── CMakeLists.txt │ └── __init__.py │ ├── cluster │ ├── CMakeLists.txt │ └── __init__.py │ ├── config │ ├── CMakeLists.txt │ └── __init__.py │ ├── convert │ ├── CMakeLists.txt │ ├── __init__.py │ └── openmm │ │ ├── CMakeLists.txt │ │ └── __init__.py │ ├── error │ ├── CMakeLists.txt │ └── __init__.py │ ├── ff │ ├── CMakeLists.txt │ └── __init__.py │ ├── id │ ├── CMakeLists.txt │ └── __init__.py │ ├── io │ ├── CMakeLists.txt │ ├── __init__.py │ └── parser │ │ ├── CMakeLists.txt │ │ └── __init__.py │ ├── maths │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _sphere.py │ └── _vector.py │ ├── mm │ ├── CMakeLists.txt │ └── __init__.py │ ├── mol │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _cursor.py │ ├── _dynamics.py │ ├── _element.py │ ├── _minimisation.py │ ├── _smiles.py │ ├── _trajectory.py │ └── _view.py │ ├── morph │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _alchemy.py │ ├── _decouple.py │ ├── _ghost_atoms.py │ ├── _hmr.py │ ├── _merge.py │ ├── _mutate.py │ ├── _pertfile.py │ ├── _perturbation.py │ ├── _repex.py │ └── _xml.py │ ├── move │ ├── CMakeLists.txt │ └── __init__.py │ ├── options │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _dynamics_options.py │ └── _option.py │ ├── qm │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _emle.py │ └── _utils.py │ ├── qt │ ├── CMakeLists.txt │ └── __init__.py │ ├── restraints │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _restraints.py │ └── _standard_state_correction.py │ ├── search │ ├── CMakeLists.txt │ └── __init__.py │ ├── squire │ ├── CMakeLists.txt │ └── __init__.py │ ├── stream │ ├── CMakeLists.txt │ └── __init__.py │ ├── system │ ├── CMakeLists.txt │ ├── __init__.py │ └── _system.py │ ├── units │ ├── CMakeLists.txt │ └── __init__.py │ ├── utils │ ├── CMakeLists.txt │ ├── __init__.py │ ├── _console.py │ ├── _profiler.py │ ├── _simple.py │ ├── _spring_flowers.py │ └── _try_import.py │ └── vol │ ├── CMakeLists.txt │ └── __init__.py ├── tests ├── base │ ├── test_pagecache.py │ ├── test_propertymap.py │ └── test_wrap.py ├── biosimspace │ ├── test_select.py │ └── test_set_coordinates.py ├── cas │ └── test_lambdaschedule.py ├── conftest.py ├── convert │ ├── test_gemmi.py │ ├── test_openmm.py │ ├── test_openmm_constraints.py │ ├── test_openmm_dynamic_constraints.py │ ├── test_openmm_lambda.py │ ├── test_openmm_minimise.py │ ├── test_openmm_rest2.py │ ├── test_openmm_restraints.py │ ├── test_openmm_trajectory.py │ ├── test_rdkit.py │ └── test_smarts.py ├── io │ ├── test_ambercmap.py │ ├── test_ambertraj.py │ ├── test_ambervels.py │ ├── test_ambrst.py │ ├── test_ambrst7.py │ ├── test_dcd.py │ ├── test_gro87.py │ ├── test_grotop.py │ ├── test_nolabel.py │ ├── test_pdb2.py │ ├── test_pdbx.py │ ├── test_prmtop.py │ ├── test_sdf.py │ ├── test_string_save.py │ ├── test_trajectories.py │ └── test_velocities.py ├── maths │ └── test_alignment.py ├── mm │ ├── test_angles.py │ ├── test_bonds.py │ ├── test_cljfunction.py │ ├── test_cljpairs.py │ ├── test_dihedrals.py │ ├── test_energy.py │ ├── test_excluded.py │ ├── test_impropers.py │ ├── test_index_bonds.py │ ├── test_index_internals.py │ ├── test_measure.py │ ├── test_nullangles.py │ └── test_nullbonds.py ├── mol │ ├── test_atomprops.py │ ├── test_complex_indexing.py │ ├── test_cursor.py │ ├── test_dynamics.py │ ├── test_element.py │ ├── test_extract.py │ ├── test_find.py │ ├── test_join.py │ ├── test_make_whole.py │ ├── test_mapping.py │ ├── test_matcher.py │ ├── test_move.py │ ├── test_reorder.py │ ├── test_rmsd.py │ └── test_trajectory.py ├── morph │ ├── input │ │ └── neopentane_methane.pert │ ├── test_decouple.py │ ├── test_hmr.py │ ├── test_match.py │ ├── test_merge.py │ └── test_pert.py ├── move │ └── test_ensemble.py ├── options │ └── test_options.py ├── qm │ └── test_qm.py ├── restraints │ ├── test_angle_dihedral_restraints.py │ ├── test_boresch.py │ ├── test_morse_potential_restraints.py │ ├── test_rmsd_restraints.py │ └── test_standard_state_correction.py ├── search │ ├── test_property_search.py │ ├── test_search_closest.py │ └── test_search_order.py ├── somd │ ├── test_boresch_corr.py │ ├── test_somd.py │ └── test_standardstatecorrection.py ├── stream │ ├── test_partial_selection.py │ ├── test_stream_header.py │ └── test_stream_lever.py ├── system │ ├── test_add_atoms.py │ ├── test_forcefieldinfo.py │ └── test_shared_properties.py ├── units │ ├── test_generalunit.py │ ├── test_parse_unit.py │ ├── test_parse_vector.py │ ├── test_pickling.py │ └── test_temperature.py └── vol │ └── test_triclinic.py ├── version.txt └── wrapper ├── Analysis ├── Bennetts.pypp.cpp ├── Bennetts.pypp.hpp ├── BennettsRatios.pypp.cpp ├── BennettsRatios.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ComponentGradients.pypp.cpp ├── ComponentGradients.pypp.hpp ├── DataPoint.pypp.cpp ├── DataPoint.pypp.hpp ├── FEP.pypp.cpp ├── FEP.pypp.hpp ├── FEPDeltas.pypp.cpp ├── FEPDeltas.pypp.hpp ├── Gradients.pypp.cpp ├── Gradients.pypp.hpp ├── PMF.pypp.cpp ├── PMF.pypp.hpp ├── SireAnalysis_containers.cpp ├── SireAnalysis_containers.h ├── SireAnalysis_registrars.cpp ├── SireAnalysis_registrars.h ├── TI.pypp.cpp ├── TI.pypp.hpp ├── TIComponents.pypp.cpp ├── TIComponents.pypp.hpp ├── TIPMF.pypp.cpp ├── TIPMF.pypp.hpp ├── _Analysis.main.cpp ├── __init__.py └── active_headers.h ├── AutoGenerate ├── README ├── create_wrappers.py ├── doxygen.py ├── restore.py └── scanheaders.py ├── Base ├── Array2DBase.pypp.cpp ├── Array2DBase.pypp.hpp ├── Array2D_double_.pypp.cpp ├── Array2D_double_.pypp.hpp ├── ArrayProperty_QString_.pypp.cpp ├── ArrayProperty_QString_.pypp.hpp ├── ArrayProperty_double_.pypp.cpp ├── ArrayProperty_double_.pypp.hpp ├── ArrayProperty_int_.pypp.cpp ├── ArrayProperty_int_.pypp.hpp ├── BooleanProperty.pypp.cpp ├── BooleanProperty.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── CPUID.pypp.cpp ├── CPUID.pypp.hpp ├── ChunkedVector_double_.pypp.cpp ├── ChunkedVector_double_.pypp.hpp ├── CombineProperties.pypp.cpp ├── CombineProperties.pypp.hpp ├── DoubleArrayProperty.pypp.cpp ├── DoubleArrayProperty.pypp.hpp ├── FlopsMark.pypp.cpp ├── FlopsMark.pypp.hpp ├── GeneralUnitArrayProperty.pypp.cpp ├── GeneralUnitArrayProperty.pypp.hpp ├── GeneralUnitProperty.pypp.cpp ├── GeneralUnitProperty.pypp.hpp ├── Incremint.pypp.cpp ├── Incremint.pypp.hpp ├── IntegerArrayProperty.pypp.cpp ├── IntegerArrayProperty.pypp.hpp ├── LazyEvaluator.pypp.cpp ├── LazyEvaluator.pypp.hpp ├── LengthProperty.pypp.cpp ├── LengthProperty.pypp.hpp ├── LinkToProperty.pypp.cpp ├── LinkToProperty.pypp.hpp ├── LowerCaseString.pypp.cpp ├── LowerCaseString.pypp.hpp ├── MajorMinorVersion.pypp.cpp ├── MajorMinorVersion.pypp.hpp ├── MemInfo.pypp.cpp ├── MemInfo.pypp.hpp ├── NoMangling.pypp.cpp ├── NoMangling.pypp.hpp ├── NullProperty.pypp.cpp ├── NullProperty.pypp.hpp ├── NumberProperty.pypp.cpp ├── NumberProperty.pypp.hpp ├── PackedArray2D_DoubleArrayProperty.pypp.cpp ├── PackedArray2D_DoubleArrayProperty.pypp.hpp ├── PackedArray2D_DoubleArrayProperty_Array.pypp.cpp ├── PackedArray2D_DoubleArrayProperty_Array.pypp.hpp ├── PackedArray2D_IntegerArrayProperty.pypp.cpp ├── PackedArray2D_IntegerArrayProperty.pypp.hpp ├── PackedArray2D_IntegerArrayProperty_Array.pypp.cpp ├── PackedArray2D_IntegerArrayProperty_Array.pypp.hpp ├── PackedArray2D_PropertyList.pypp.cpp ├── PackedArray2D_PropertyList.pypp.hpp ├── PackedArray2D_PropertyList_Array.pypp.cpp ├── PackedArray2D_PropertyList_Array.pypp.hpp ├── PackedArray2D_QString_.pypp.cpp ├── PackedArray2D_QString_.pypp.hpp ├── PackedArray2D_QString_Array.pypp.cpp ├── PackedArray2D_QString_Array.pypp.hpp ├── PackedArray2D_QVariant_.pypp.cpp ├── PackedArray2D_QVariant_.pypp.hpp ├── PackedArray2D_QVariant_Array.pypp.cpp ├── PackedArray2D_QVariant_Array.pypp.hpp ├── PackedArray2D_StringArrayProperty.pypp.cpp ├── PackedArray2D_StringArrayProperty.pypp.hpp ├── PackedArray2D_StringArrayProperty_Array.pypp.cpp ├── PackedArray2D_StringArrayProperty_Array.pypp.hpp ├── PackedArray2D_double_.pypp.cpp ├── PackedArray2D_double_.pypp.hpp ├── PackedArray2D_double_Array.pypp.cpp ├── PackedArray2D_double_Array.pypp.hpp ├── PackedArray2D_int_.pypp.cpp ├── PackedArray2D_int_.pypp.hpp ├── PackedArray2D_int_Array.pypp.cpp ├── PackedArray2D_int_Array.pypp.hpp ├── PageCache.pypp.cpp ├── PageCache.pypp.hpp ├── Process.pypp.cpp ├── Process.pypp.hpp ├── ProgressBar.pypp.cpp ├── ProgressBar.pypp.hpp ├── Properties.pypp.cpp ├── Properties.pypp.hpp ├── Property.pypp.cpp ├── Property.pypp.hpp ├── PropertyList.pypp.cpp ├── PropertyList.pypp.hpp ├── PropertyMap.pypp.cpp ├── PropertyMap.pypp.hpp ├── PropertyName.pypp.cpp ├── PropertyName.pypp.hpp ├── Range.pypp.cpp ├── Range.pypp.hpp ├── SimpleRange.pypp.cpp ├── SimpleRange.pypp.hpp ├── SireBase_containers.cpp ├── SireBase_containers.h ├── SireBase_properties.cpp ├── SireBase_properties.h ├── SireBase_registrars.cpp ├── SireBase_registrars.h ├── StringArrayProperty.pypp.cpp ├── StringArrayProperty.pypp.hpp ├── StringMangler.pypp.cpp ├── StringMangler.pypp.hpp ├── StringProperty.pypp.cpp ├── StringProperty.pypp.hpp ├── TempDir.pypp.cpp ├── TempDir.pypp.hpp ├── TimeProperty.pypp.cpp ├── TimeProperty.pypp.hpp ├── TrigArray2DBase.pypp.cpp ├── TrigArray2DBase.pypp.hpp ├── TrigArray2D_double_.pypp.cpp ├── TrigArray2D_double_.pypp.hpp ├── TrimString.pypp.cpp ├── TrimString.pypp.hpp ├── UnitTest.pypp.cpp ├── UnitTest.pypp.hpp ├── UpperCaseString.pypp.cpp ├── UpperCaseString.pypp.hpp ├── VariantProperty.pypp.cpp ├── VariantProperty.pypp.hpp ├── Version.pypp.cpp ├── Version.pypp.hpp ├── _Base.main.cpp ├── _Base_free_functions.pypp.cpp ├── _Base_free_functions.pypp.hpp ├── __init__.py ├── active_headers.h ├── autoconvert_Slice.cpp ├── convertpackedarray.hpp ├── convertproperty.hpp ├── releasegil_impl.cpp ├── releasegil_impl.h ├── special_code.py ├── vector_less__double__greater_.pypp.cpp └── vector_less__double__greater_.pypp.hpp ├── CAS ├── Abs.pypp.cpp ├── Abs.pypp.hpp ├── AlwaysFalse.pypp.cpp ├── AlwaysFalse.pypp.hpp ├── AlwaysTrue.pypp.cpp ├── AlwaysTrue.pypp.hpp ├── ArcCos.pypp.cpp ├── ArcCos.pypp.hpp ├── ArcCosh.pypp.cpp ├── ArcCosh.pypp.hpp ├── ArcCot.pypp.cpp ├── ArcCot.pypp.hpp ├── ArcCoth.pypp.cpp ├── ArcCoth.pypp.hpp ├── ArcCsc.pypp.cpp ├── ArcCsc.pypp.hpp ├── ArcCsch.pypp.cpp ├── ArcCsch.pypp.hpp ├── ArcSec.pypp.cpp ├── ArcSec.pypp.hpp ├── ArcSech.pypp.cpp ├── ArcSech.pypp.hpp ├── ArcSin.pypp.cpp ├── ArcSin.pypp.hpp ├── ArcSinh.pypp.cpp ├── ArcSinh.pypp.hpp ├── ArcTan.pypp.cpp ├── ArcTan.pypp.hpp ├── ArcTanh.pypp.cpp ├── ArcTanh.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ComplexPower.pypp.cpp ├── ComplexPower.pypp.hpp ├── ComplexValues.pypp.cpp ├── ComplexValues.pypp.hpp ├── Condition.pypp.cpp ├── Condition.pypp.hpp ├── Conditional.pypp.cpp ├── Conditional.pypp.hpp ├── Constant.pypp.cpp ├── Constant.pypp.hpp ├── Cos.pypp.cpp ├── Cos.pypp.hpp ├── Cosh.pypp.cpp ├── Cosh.pypp.hpp ├── Cot.pypp.cpp ├── Cot.pypp.hpp ├── Coth.pypp.cpp ├── Coth.pypp.hpp ├── Csc.pypp.cpp ├── Csc.pypp.hpp ├── Csch.pypp.cpp ├── Csch.pypp.hpp ├── DoubleFunc.pypp.cpp ├── DoubleFunc.pypp.hpp ├── EqualTo.pypp.cpp ├── EqualTo.pypp.hpp ├── ExBase.pypp.cpp ├── ExBase.pypp.hpp ├── Exp.pypp.cpp ├── Exp.pypp.hpp ├── Expression.pypp.cpp ├── Expression.pypp.hpp ├── ExpressionBase.pypp.cpp ├── ExpressionBase.pypp.hpp ├── ExpressionProperty.pypp.cpp ├── ExpressionProperty.pypp.hpp ├── Factor.pypp.cpp ├── Factor.pypp.hpp ├── GreaterOrEqualThan.pypp.cpp ├── GreaterOrEqualThan.pypp.hpp ├── GreaterThan.pypp.cpp ├── GreaterThan.pypp.hpp ├── I.pypp.cpp ├── I.pypp.hpp ├── Identities.pypp.cpp ├── Identities.pypp.hpp ├── IntegerPower.pypp.cpp ├── IntegerPower.pypp.hpp ├── IntegrationConstant.pypp.cpp ├── IntegrationConstant.pypp.hpp ├── LambdaSchedule.pypp.cpp ├── LambdaSchedule.pypp.hpp ├── LessOrEqualThan.pypp.cpp ├── LessOrEqualThan.pypp.hpp ├── LessThan.pypp.cpp ├── LessThan.pypp.hpp ├── Ln.pypp.cpp ├── Ln.pypp.hpp ├── Max.pypp.cpp ├── Max.pypp.hpp ├── Min.pypp.cpp ├── Min.pypp.hpp ├── NotEqualTo.pypp.cpp ├── NotEqualTo.pypp.hpp ├── Power.pypp.cpp ├── Power.pypp.hpp ├── PowerConstant.pypp.cpp ├── PowerConstant.pypp.hpp ├── PowerFunction.pypp.cpp ├── PowerFunction.pypp.hpp ├── Product.pypp.cpp ├── Product.pypp.hpp ├── RationalPower.pypp.cpp ├── RationalPower.pypp.hpp ├── RealPower.pypp.cpp ├── RealPower.pypp.hpp ├── Sec.pypp.cpp ├── Sec.pypp.hpp ├── Sech.pypp.cpp ├── Sech.pypp.hpp ├── Sin.pypp.cpp ├── Sin.pypp.hpp ├── SingleFunc.pypp.cpp ├── SingleFunc.pypp.hpp ├── Sinh.pypp.cpp ├── Sinh.pypp.hpp ├── SireCAS_containers.cpp ├── SireCAS_containers.h ├── SireCAS_registrars.cpp ├── SireCAS_registrars.h ├── Sum.pypp.cpp ├── Sum.pypp.hpp ├── Symbol.pypp.cpp ├── Symbol.pypp.hpp ├── SymbolComplex.pypp.cpp ├── SymbolComplex.pypp.hpp ├── SymbolExpression.pypp.cpp ├── SymbolExpression.pypp.hpp ├── SymbolValue.pypp.cpp ├── SymbolValue.pypp.hpp ├── Tan.pypp.cpp ├── Tan.pypp.hpp ├── Tanh.pypp.cpp ├── Tanh.pypp.hpp ├── Values.pypp.cpp ├── Values.pypp.hpp ├── _CAS.main.cpp ├── _CAS_free_functions.pypp.cpp ├── _CAS_free_functions.pypp.hpp ├── __init__.py ├── active_headers.h └── special_code.py ├── CMakeLists.txt ├── Cluster ├── AbortPacket.pypp.cpp ├── AbortPacket.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Cluster.pypp.cpp ├── Cluster.pypp.hpp ├── ErrorPacket.pypp.cpp ├── ErrorPacket.pypp.hpp ├── Node.pypp.cpp ├── Node.pypp.hpp ├── Nodes.pypp.cpp ├── Nodes.pypp.hpp ├── Promise.pypp.cpp ├── Promise.pypp.hpp ├── SireCluster_containers.cpp ├── SireCluster_containers.h ├── SireCluster_registrars.cpp ├── SireCluster_registrars.h ├── ThisThread.pypp.cpp ├── ThisThread.pypp.hpp ├── WorkPacket.pypp.cpp ├── WorkPacket.pypp.hpp ├── WorkPacketBase.pypp.cpp ├── WorkPacketBase.pypp.hpp ├── WorkTest.pypp.cpp ├── WorkTest.pypp.hpp ├── _Cluster.main.cpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Convert ├── CMakeLists.txt ├── SireGemmi │ ├── CMakeLists.txt │ ├── _SireGemmi.main.cpp │ ├── sire_gemmi.cpp │ └── sire_gemmi.h ├── SireOpenMM │ ├── CMakeAutogenFile.txt │ ├── CMakeLists.txt │ ├── LambdaLever.pypp.cpp │ ├── LambdaLever.pypp.hpp │ ├── NullQMEngine.pypp.cpp │ ├── NullQMEngine.pypp.hpp │ ├── OpenMMMetaData.pypp.cpp │ ├── OpenMMMetaData.pypp.hpp │ ├── PerturbableOpenMMMolecule.pypp.cpp │ ├── PerturbableOpenMMMolecule.pypp.hpp │ ├── PyQMCallback.pypp.cpp │ ├── PyQMCallback.pypp.hpp │ ├── PyQMEngine.pypp.cpp │ ├── PyQMEngine.pypp.hpp │ ├── PyQMForce.pypp.cpp │ ├── PyQMForce.pypp.hpp │ ├── QMEngine.pypp.cpp │ ├── QMEngine.pypp.hpp │ ├── QMForce.pypp.cpp │ ├── QMForce.pypp.hpp │ ├── README_WRAPPERS.txt │ ├── SireOpenMM_properties.cpp │ ├── SireOpenMM_properties.h │ ├── SireOpenMM_registrars.cpp │ ├── SireOpenMM_registrars.h │ ├── TorchQMEngine.pypp.cpp │ ├── TorchQMEngine.pypp.hpp │ ├── TorchQMForce.pypp.cpp │ ├── TorchQMForce.pypp.hpp │ ├── _SireOpenMM.main.cpp │ ├── _SireOpenMM_free_functions.pypp.cpp │ ├── _SireOpenMM_free_functions.pypp.hpp │ ├── _perturbablemol.py │ ├── _sommcontext.py │ ├── active_headers.h │ ├── lambdalever.cpp │ ├── lambdalever.h │ ├── lbgfs │ │ ├── arithmetic_ansi.h │ │ ├── arithmetic_optimised.h │ │ ├── arithmetic_sse_double.h │ │ ├── arithmetic_sse_float.h │ │ ├── lbfgs.cpp │ │ └── lbfgs.h │ ├── openmmminimise.cpp │ ├── openmmminimise.h │ ├── openmmmolecule.cpp │ ├── openmmmolecule.h │ ├── pyqm.cpp │ ├── pyqm.h │ ├── qmmm.cpp │ ├── qmmm.h │ ├── register_extras.cpp │ ├── register_extras.h │ ├── scanheaders.py │ ├── sire_openmm.cpp │ ├── sire_openmm.h │ ├── sire_to_openmm_system.cpp │ ├── special_code.py │ ├── torchqm.cpp │ ├── torchqm.h │ ├── vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp │ └── vector_less__OpenMM_scope_Vec3__greater_.pypp.hpp ├── SireRDKit │ ├── CMakeLists.txt │ ├── _SireRDKit.main.cpp │ ├── sire_rdkit.cpp │ └── sire_rdkit.h └── __init__.py ├── Error ├── CMakeLists.txt ├── __init__.py ├── wrap_SireError.cpp ├── wrap_SireError.h └── wrap_exceptions.cpp ├── FF ├── AtomPoint.pypp.cpp ├── AtomPoint.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Center.pypp.cpp ├── Center.pypp.hpp ├── CenterOfGeometry.pypp.cpp ├── CenterOfGeometry.pypp.hpp ├── CenterOfMass.pypp.cpp ├── CenterOfMass.pypp.hpp ├── EnergyTable.pypp.cpp ├── EnergyTable.pypp.hpp ├── FF.pypp.cpp ├── FF.pypp.hpp ├── FF3D.pypp.cpp ├── FF3D.pypp.hpp ├── FFComponent.pypp.cpp ├── FFComponent.pypp.hpp ├── FFDetail.pypp.cpp ├── FFDetail.pypp.hpp ├── FFID.pypp.cpp ├── FFID.pypp.hpp ├── FFIdx.pypp.cpp ├── FFIdx.pypp.hpp ├── FFMolGroup.pypp.cpp ├── FFMolGroup.pypp.hpp ├── FFName.pypp.cpp ├── FFName.pypp.hpp ├── FieldTable.pypp.cpp ├── FieldTable.pypp.hpp ├── ForceFields.pypp.cpp ├── ForceFields.pypp.hpp ├── ForceTable.pypp.cpp ├── ForceTable.pypp.hpp ├── G1FF.pypp.cpp ├── G1FF.pypp.hpp ├── G2FF.pypp.cpp ├── G2FF.pypp.hpp ├── GridFieldTable.pypp.cpp ├── GridFieldTable.pypp.hpp ├── GridPotentialTable.pypp.cpp ├── GridPotentialTable.pypp.hpp ├── IDAndSet_FFID_.pypp.cpp ├── IDAndSet_FFID_.pypp.hpp ├── IDOrSet_FFID_.pypp.cpp ├── IDOrSet_FFID_.pypp.hpp ├── MolEnergyTable.pypp.cpp ├── MolEnergyTable.pypp.hpp ├── MolFieldTable.pypp.cpp ├── MolFieldTable.pypp.hpp ├── MolForceTable.pypp.cpp ├── MolForceTable.pypp.hpp ├── MolPotentialTable.pypp.cpp ├── MolPotentialTable.pypp.hpp ├── NullFF.pypp.cpp ├── NullFF.pypp.hpp ├── NullProbe.pypp.cpp ├── NullProbe.pypp.hpp ├── Point.pypp.cpp ├── Point.pypp.hpp ├── PointRef.pypp.cpp ├── PointRef.pypp.hpp ├── PotentialTable.pypp.cpp ├── PotentialTable.pypp.hpp ├── Probe.pypp.cpp ├── Probe.pypp.hpp ├── SingleComponent.pypp.cpp ├── SingleComponent.pypp.hpp ├── SireFF_containers.cpp ├── SireFF_containers.h ├── SireFF_properties.cpp ├── SireFF_properties.h ├── SireFF_registrars.cpp ├── SireFF_registrars.h ├── Specify_FFID_.pypp.cpp ├── Specify_FFID_.pypp.hpp ├── VectorPoint.pypp.cpp ├── VectorPoint.pypp.hpp ├── _FF.main.cpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Helpers ├── CMakeLists.txt ├── clone_const_reference.hpp ├── convertdict.hpp ├── convertlist.hpp ├── convertset.hpp ├── convertsharedpointer.hpp ├── copy.hpp ├── len.hpp ├── objectregistry.cpp ├── objectregistry.hpp ├── pair.hpp ├── pyboost11.hpp ├── pycontainer.hpp ├── release_gil_policy.cpp ├── release_gil_policy.hpp ├── str.hpp └── tuples.hpp ├── ID ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ID.pypp.cpp ├── ID.pypp.hpp ├── Index.pypp.cpp ├── Index.pypp.hpp ├── IndexBase.pypp.cpp ├── IndexBase.pypp.hpp ├── Name.pypp.cpp ├── Name.pypp.hpp ├── Number.pypp.cpp ├── Number.pypp.hpp ├── SireID_registrars.cpp ├── SireID_registrars.h ├── _ID.main.cpp ├── _ID_enumerations.pypp.cpp ├── _ID_enumerations.pypp.hpp ├── __init__.py ├── active_headers.h └── special_code.py ├── IO ├── Amber.pypp.cpp ├── Amber.pypp.hpp ├── AmberPrm.pypp.cpp ├── AmberPrm.pypp.hpp ├── AmberRst.pypp.cpp ├── AmberRst.pypp.hpp ├── AmberRst7.pypp.cpp ├── AmberRst7.pypp.hpp ├── AmberTraj.pypp.cpp ├── AmberTraj.pypp.hpp ├── BrokenParser.pypp.cpp ├── BrokenParser.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── CharmmPSF.pypp.cpp ├── CharmmPSF.pypp.hpp ├── Cube.pypp.cpp ├── Cube.pypp.hpp ├── DCD.pypp.cpp ├── DCD.pypp.hpp ├── FileTrajectoryParser.pypp.cpp ├── FileTrajectoryParser.pypp.hpp ├── FlexibilityLibrary.pypp.cpp ├── FlexibilityLibrary.pypp.hpp ├── FlexibilityTemplate.pypp.cpp ├── FlexibilityTemplate.pypp.hpp ├── Gro87.pypp.cpp ├── Gro87.pypp.hpp ├── GroAtom.pypp.cpp ├── GroAtom.pypp.hpp ├── GroMolType.pypp.cpp ├── GroMolType.pypp.hpp ├── GroSystem.pypp.cpp ├── GroSystem.pypp.hpp ├── GroTop.pypp.cpp ├── GroTop.pypp.hpp ├── IOBase.pypp.cpp ├── IOBase.pypp.hpp ├── IOParametersBase.pypp.cpp ├── IOParametersBase.pypp.hpp ├── Mol2.pypp.cpp ├── Mol2.pypp.hpp ├── MoleculeParser.pypp.cpp ├── MoleculeParser.pypp.hpp ├── NullIO.pypp.cpp ├── NullIO.pypp.hpp ├── NullParser.pypp.cpp ├── NullParser.pypp.hpp ├── PDB.pypp.cpp ├── PDB.pypp.hpp ├── PDB2.pypp.cpp ├── PDB2.pypp.hpp ├── PDBParameters.pypp.cpp ├── PDBParameters.pypp.hpp ├── PDBx.pypp.cpp ├── PDBx.pypp.hpp ├── PerturbationsLibrary.pypp.cpp ├── PerturbationsLibrary.pypp.hpp ├── PerturbationsTemplate.pypp.cpp ├── PerturbationsTemplate.pypp.hpp ├── ProtoMS.pypp.cpp ├── ProtoMS.pypp.hpp ├── ProtoMSParameters.pypp.cpp ├── ProtoMSParameters.pypp.hpp ├── SDF.pypp.cpp ├── SDF.pypp.hpp ├── SireIO_containers.cpp ├── SireIO_containers.h ├── SireIO_properties.cpp ├── SireIO_properties.h ├── SireIO_registrars.cpp ├── SireIO_registrars.h ├── Supplementary.pypp.cpp ├── Supplementary.pypp.hpp ├── TRR.pypp.cpp ├── TRR.pypp.hpp ├── Tinker.pypp.cpp ├── Tinker.pypp.hpp ├── TinkerParameters.pypp.cpp ├── TinkerParameters.pypp.hpp ├── TrajectoryMonitor.pypp.cpp ├── TrajectoryMonitor.pypp.hpp ├── XTC.pypp.cpp ├── XTC.pypp.hpp ├── ZmatrixMaker.pypp.cpp ├── ZmatrixMaker.pypp.hpp ├── _IO.main.cpp ├── _IO_free_functions.pypp.cpp ├── _IO_free_functions.pypp.hpp ├── _IO_load.cpp ├── _IO_load.h ├── __init__.py ├── active_headers.h └── special_code.py ├── MM ├── AmberAngle.pypp.cpp ├── AmberAngle.pypp.hpp ├── AmberBond.pypp.cpp ├── AmberBond.pypp.hpp ├── AmberDihPart.pypp.cpp ├── AmberDihPart.pypp.hpp ├── AmberDihedral.pypp.cpp ├── AmberDihedral.pypp.hpp ├── AmberNB14.pypp.cpp ├── AmberNB14.pypp.hpp ├── AmberParams.pypp.cpp ├── AmberParams.pypp.hpp ├── Angle.pypp.cpp ├── Angle.pypp.hpp ├── AngleComponent.pypp.cpp ├── AngleComponent.pypp.hpp ├── AngleParameterName.pypp.cpp ├── AngleParameterName.pypp.hpp ├── AngleRestraint.pypp.cpp ├── AngleRestraint.pypp.hpp ├── AngleRestraints.pypp.cpp ├── AngleRestraints.pypp.hpp ├── AngleSymbols.pypp.cpp ├── AngleSymbols.pypp.hpp ├── AtomFunction.pypp.cpp ├── AtomFunction.pypp.hpp ├── AtomFunctions.pypp.cpp ├── AtomFunctions.pypp.hpp ├── AtomLJs.pypp.cpp ├── AtomLJs.pypp.hpp ├── AtomPairs_CLJScaleFactor_.pypp.cpp ├── AtomPairs_CLJScaleFactor_.pypp.hpp ├── AtomPairs_CoulombScaleFactor_.pypp.cpp ├── AtomPairs_CoulombScaleFactor_.pypp.hpp ├── AtomPairs_LJScaleFactor_.pypp.cpp ├── AtomPairs_LJScaleFactor_.pypp.hpp ├── BendBendComponent.pypp.cpp ├── BendBendComponent.pypp.hpp ├── BendBendParameterName.pypp.cpp ├── BendBendParameterName.pypp.hpp ├── BendBendSymbols.pypp.cpp ├── BendBendSymbols.pypp.hpp ├── Bond.pypp.cpp ├── Bond.pypp.hpp ├── BondComponent.pypp.cpp ├── BondComponent.pypp.hpp ├── BondParameterName.pypp.cpp ├── BondParameterName.pypp.hpp ├── BondRestraint.pypp.cpp ├── BondRestraint.pypp.hpp ├── BondRestraints.pypp.cpp ├── BondRestraints.pypp.hpp ├── BondSymbols.pypp.cpp ├── BondSymbols.pypp.hpp ├── BoreschRestraint.pypp.cpp ├── BoreschRestraint.pypp.hpp ├── BoreschRestraints.pypp.cpp ├── BoreschRestraints.pypp.hpp ├── CHARMMSwitchingFunction.pypp.cpp ├── CHARMMSwitchingFunction.pypp.hpp ├── CLJ14Group.pypp.cpp ├── CLJ14Group.pypp.hpp ├── CLJAtom.pypp.cpp ├── CLJAtom.pypp.hpp ├── CLJAtoms.pypp.cpp ├── CLJAtoms.pypp.hpp ├── CLJBox.pypp.cpp ├── CLJBox.pypp.hpp ├── CLJBoxDistance.pypp.cpp ├── CLJBoxDistance.pypp.hpp ├── CLJBoxIndex.pypp.cpp ├── CLJBoxIndex.pypp.hpp ├── CLJBoxes.pypp.cpp ├── CLJBoxes.pypp.hpp ├── CLJCalculator.pypp.cpp ├── CLJCalculator.pypp.hpp ├── CLJComponent.pypp.cpp ├── CLJComponent.pypp.hpp ├── CLJCutoffFunction.pypp.cpp ├── CLJCutoffFunction.pypp.hpp ├── CLJDelta.pypp.cpp ├── CLJDelta.pypp.hpp ├── CLJExtractor.pypp.cpp ├── CLJExtractor.pypp.hpp ├── CLJFunction.pypp.cpp ├── CLJFunction.pypp.hpp ├── CLJGrid.pypp.cpp ├── CLJGrid.pypp.hpp ├── CLJGroup.pypp.cpp ├── CLJGroup.pypp.hpp ├── CLJIntraFunction.pypp.cpp ├── CLJIntraFunction.pypp.hpp ├── CLJIntraRFFunction.pypp.cpp ├── CLJIntraRFFunction.pypp.hpp ├── CLJIntraShiftFunction.pypp.cpp ├── CLJIntraShiftFunction.pypp.hpp ├── CLJNBPairs.pypp.cpp ├── CLJNBPairs.pypp.hpp ├── CLJParameterNames.pypp.cpp ├── CLJParameterNames.pypp.hpp ├── CLJParameterNames3D.pypp.cpp ├── CLJParameterNames3D.pypp.hpp ├── CLJPotentialInterface_InterCLJPotential_.pypp.cpp ├── CLJPotentialInterface_InterCLJPotential_.pypp.hpp ├── CLJPotentialInterface_InterSoftCLJPotential_.pypp.cpp ├── CLJPotentialInterface_InterSoftCLJPotential_.pypp.hpp ├── CLJPotentialInterface_IntraCLJPotential_.pypp.cpp ├── CLJPotentialInterface_IntraCLJPotential_.pypp.hpp ├── CLJPotentialInterface_IntraSoftCLJPotential_.pypp.cpp ├── CLJPotentialInterface_IntraSoftCLJPotential_.pypp.hpp ├── CLJProbe.pypp.cpp ├── CLJProbe.pypp.hpp ├── CLJRFFunction.pypp.cpp ├── CLJRFFunction.pypp.hpp ├── CLJScaleFactor.pypp.cpp ├── CLJScaleFactor.pypp.hpp ├── CLJShiftFunction.pypp.cpp ├── CLJShiftFunction.pypp.hpp ├── CLJSoftFunction.pypp.cpp ├── CLJSoftFunction.pypp.hpp ├── CLJSoftIntraFunction.pypp.cpp ├── CLJSoftIntraFunction.pypp.hpp ├── CLJSoftIntraRFFunction.pypp.cpp ├── CLJSoftIntraRFFunction.pypp.hpp ├── CLJSoftIntraShiftFunction.pypp.cpp ├── CLJSoftIntraShiftFunction.pypp.hpp ├── CLJSoftRFFunction.pypp.cpp ├── CLJSoftRFFunction.pypp.hpp ├── CLJSoftShiftFunction.pypp.cpp ├── CLJSoftShiftFunction.pypp.hpp ├── CLJWorkspace.pypp.cpp ├── CLJWorkspace.pypp.hpp ├── CMAPFunction.pypp.cpp ├── CMAPFunction.pypp.hpp ├── CMAPFunctions.pypp.cpp ├── CMAPFunctions.pypp.hpp ├── CMAPParameter.pypp.cpp ├── CMAPParameter.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ChargeParameterName.pypp.cpp ├── ChargeParameterName.pypp.hpp ├── ChargeParameterName3D.pypp.cpp ├── ChargeParameterName3D.pypp.hpp ├── CoulombComponent.pypp.cpp ├── CoulombComponent.pypp.hpp ├── CoulombNBPairs.pypp.cpp ├── CoulombNBPairs.pypp.hpp ├── CoulombPotentialInterface_InterCoulombPotential_.pypp.cpp ├── CoulombPotentialInterface_InterCoulombPotential_.pypp.hpp ├── CoulombPotentialInterface_IntraCoulombPotential_.pypp.cpp ├── CoulombPotentialInterface_IntraCoulombPotential_.pypp.hpp ├── CoulombProbe.pypp.cpp ├── CoulombProbe.pypp.hpp ├── CoulombScaleFactor.pypp.cpp ├── CoulombScaleFactor.pypp.hpp ├── Dihedral.pypp.cpp ├── Dihedral.pypp.hpp ├── DihedralComponent.pypp.cpp ├── DihedralComponent.pypp.hpp ├── DihedralParameterName.pypp.cpp ├── DihedralParameterName.pypp.hpp ├── DihedralRestraint.pypp.cpp ├── DihedralRestraint.pypp.hpp ├── DihedralRestraints.pypp.cpp ├── DihedralRestraints.pypp.hpp ├── DihedralSymbols.pypp.cpp ├── DihedralSymbols.pypp.hpp ├── DistanceRestraint.pypp.cpp ├── DistanceRestraint.pypp.hpp ├── DoubleDistanceRestraint.pypp.cpp ├── DoubleDistanceRestraint.pypp.hpp ├── ExcludedPairs.pypp.cpp ├── ExcludedPairs.pypp.hpp ├── FourAtomFunction.pypp.cpp ├── FourAtomFunction.pypp.hpp ├── FourAtomFunctions.pypp.cpp ├── FourAtomFunctions.pypp.hpp ├── FourAtomPerturbation.pypp.cpp ├── FourAtomPerturbation.pypp.hpp ├── GridFF.pypp.cpp ├── GridFF.pypp.hpp ├── GridFF2.pypp.cpp ├── GridFF2.pypp.hpp ├── GromacsAngle.pypp.cpp ├── GromacsAngle.pypp.hpp ├── GromacsAtomType.pypp.cpp ├── GromacsAtomType.pypp.hpp ├── GromacsBond.pypp.cpp ├── GromacsBond.pypp.hpp ├── GromacsDihedral.pypp.cpp ├── GromacsDihedral.pypp.hpp ├── GroupInternalParameters.pypp.cpp ├── GroupInternalParameters.pypp.hpp ├── HarmonicSwitchingFunction.pypp.cpp ├── HarmonicSwitchingFunction.pypp.hpp ├── Improper.pypp.cpp ├── Improper.pypp.hpp ├── ImproperComponent.pypp.cpp ├── ImproperComponent.pypp.hpp ├── ImproperParameterName.pypp.cpp ├── ImproperParameterName.pypp.hpp ├── ImproperSymbols.pypp.cpp ├── ImproperSymbols.pypp.hpp ├── InterCLJFF.pypp.cpp ├── InterCLJFF.pypp.hpp ├── InterCLJFFBase.pypp.cpp ├── InterCLJFFBase.pypp.hpp ├── InterCoulombFF.pypp.cpp ├── InterCoulombFF.pypp.hpp ├── InterCoulombFFBase.pypp.cpp ├── InterCoulombFFBase.pypp.hpp ├── InterFF.pypp.cpp ├── InterFF.pypp.hpp ├── InterGroupCLJFF.pypp.cpp ├── InterGroupCLJFF.pypp.hpp ├── InterGroupCLJFFBase.pypp.cpp ├── InterGroupCLJFFBase.pypp.hpp ├── InterGroupCoulombFF.pypp.cpp ├── InterGroupCoulombFF.pypp.hpp ├── InterGroupCoulombFFBase.pypp.cpp ├── InterGroupCoulombFFBase.pypp.hpp ├── InterGroupFF.pypp.cpp ├── InterGroupFF.pypp.hpp ├── InterGroupLJFF.pypp.cpp ├── InterGroupLJFF.pypp.hpp ├── InterGroupLJFFBase.pypp.cpp ├── InterGroupLJFFBase.pypp.hpp ├── InterGroupSoftCLJFF.pypp.cpp ├── InterGroupSoftCLJFF.pypp.hpp ├── InterGroupSoftCLJFFBase.pypp.cpp ├── InterGroupSoftCLJFFBase.pypp.hpp ├── InterLJFF.pypp.cpp ├── InterLJFF.pypp.hpp ├── InterLJFFBase.pypp.cpp ├── InterLJFFBase.pypp.hpp ├── InterSoftCLJFF.pypp.cpp ├── InterSoftCLJFF.pypp.hpp ├── InterSoftCLJFFBase.pypp.cpp ├── InterSoftCLJFFBase.pypp.hpp ├── InternalComponent.pypp.cpp ├── InternalComponent.pypp.hpp ├── InternalFF.pypp.cpp ├── InternalFF.pypp.hpp ├── InternalGroupFF.pypp.cpp ├── InternalGroupFF.pypp.hpp ├── InternalParameterNames.pypp.cpp ├── InternalParameterNames.pypp.hpp ├── InternalParameterNames3D.pypp.cpp ├── InternalParameterNames3D.pypp.hpp ├── InternalParameters.pypp.cpp ├── InternalParameters.pypp.hpp ├── InternalParameters3D.pypp.cpp ├── InternalParameters3D.pypp.hpp ├── InternalPerturbation.pypp.cpp ├── InternalPerturbation.pypp.hpp ├── InternalSymbols.pypp.cpp ├── InternalSymbols.pypp.hpp ├── InternalSymbolsBase.pypp.cpp ├── InternalSymbolsBase.pypp.hpp ├── Intra14Component.pypp.cpp ├── Intra14Component.pypp.hpp ├── Intra14CoulombComponent.pypp.cpp ├── Intra14CoulombComponent.pypp.hpp ├── Intra14LJComponent.pypp.cpp ├── Intra14LJComponent.pypp.hpp ├── IntraCLJFF.pypp.cpp ├── IntraCLJFF.pypp.hpp ├── IntraCLJFFBase.pypp.cpp ├── IntraCLJFFBase.pypp.hpp ├── IntraCoulombFF.pypp.cpp ├── IntraCoulombFF.pypp.hpp ├── IntraCoulombFFBase.pypp.cpp ├── IntraCoulombFFBase.pypp.hpp ├── IntraFF.pypp.cpp ├── IntraFF.pypp.hpp ├── IntraGroupCLJFF.pypp.cpp ├── IntraGroupCLJFF.pypp.hpp ├── IntraGroupCLJFFBase.pypp.cpp ├── IntraGroupCLJFFBase.pypp.hpp ├── IntraGroupCoulombFF.pypp.cpp ├── IntraGroupCoulombFF.pypp.hpp ├── IntraGroupCoulombFFBase.pypp.cpp ├── IntraGroupCoulombFFBase.pypp.hpp ├── IntraGroupFF.pypp.cpp ├── IntraGroupFF.pypp.hpp ├── IntraGroupLJFF.pypp.cpp ├── IntraGroupLJFF.pypp.hpp ├── IntraGroupLJFFBase.pypp.cpp ├── IntraGroupLJFFBase.pypp.hpp ├── IntraGroupSoftCLJFF.pypp.cpp ├── IntraGroupSoftCLJFF.pypp.hpp ├── IntraGroupSoftCLJFFBase.pypp.cpp ├── IntraGroupSoftCLJFFBase.pypp.hpp ├── IntraLJFF.pypp.cpp ├── IntraLJFF.pypp.hpp ├── IntraLJFFBase.pypp.cpp ├── IntraLJFFBase.pypp.hpp ├── IntraSoftCLJFF.pypp.cpp ├── IntraSoftCLJFF.pypp.hpp ├── IntraSoftCLJFFBase.pypp.cpp ├── IntraSoftCLJFFBase.pypp.hpp ├── InverseBondRestraint.pypp.cpp ├── InverseBondRestraint.pypp.hpp ├── InverseBondRestraints.pypp.cpp ├── InverseBondRestraints.pypp.hpp ├── LJ1264Parameter.pypp.cpp ├── LJ1264Parameter.pypp.hpp ├── LJComponent.pypp.cpp ├── LJComponent.pypp.hpp ├── LJException.pypp.cpp ├── LJException.pypp.hpp ├── LJExceptionID.pypp.cpp ├── LJExceptionID.pypp.hpp ├── LJNBPairs.pypp.cpp ├── LJNBPairs.pypp.hpp ├── LJParameter.pypp.cpp ├── LJParameter.pypp.hpp ├── LJParameterName.pypp.cpp ├── LJParameterName.pypp.hpp ├── LJParameterName3D.pypp.cpp ├── LJParameterName3D.pypp.hpp ├── LJPerturbation.pypp.cpp ├── LJPerturbation.pypp.hpp ├── LJPotentialInterface_InterLJPotential_.pypp.cpp ├── LJPotentialInterface_InterLJPotential_.pypp.hpp ├── LJPotentialInterface_IntraLJPotential_.pypp.cpp ├── LJPotentialInterface_IntraLJPotential_.pypp.hpp ├── LJProbe.pypp.cpp ├── LJProbe.pypp.hpp ├── LJScaleFactor.pypp.cpp ├── LJScaleFactor.pypp.hpp ├── MMDetail.pypp.cpp ├── MMDetail.pypp.hpp ├── MorsePotentialRestraint.pypp.cpp ├── MorsePotentialRestraint.pypp.hpp ├── MorsePotentialRestraints.pypp.cpp ├── MorsePotentialRestraints.pypp.hpp ├── Mover_Angle_.pypp.cpp ├── Mover_Angle_.pypp.hpp ├── Mover_Bond_.pypp.cpp ├── Mover_Bond_.pypp.hpp ├── Mover_Dihedral_.pypp.cpp ├── Mover_Dihedral_.pypp.hpp ├── Mover_Improper_.pypp.cpp ├── Mover_Improper_.pypp.hpp ├── Mover_SelectorAngle_.pypp.cpp ├── Mover_SelectorAngle_.pypp.hpp ├── Mover_SelectorBond_.pypp.cpp ├── Mover_SelectorBond_.pypp.hpp ├── Mover_SelectorDihedral_.pypp.cpp ├── Mover_SelectorDihedral_.pypp.hpp ├── Mover_SelectorImproper_.pypp.cpp ├── Mover_SelectorImproper_.pypp.hpp ├── MultiCLJComponent.pypp.cpp ├── MultiCLJComponent.pypp.hpp ├── NoCutoff.pypp.cpp ├── NoCutoff.pypp.hpp ├── NullCLJFunction.pypp.cpp ├── NullCLJFunction.pypp.hpp ├── NullRestraint.pypp.cpp ├── NullRestraint.pypp.hpp ├── PositionalRestraint.pypp.cpp ├── PositionalRestraint.pypp.hpp ├── PositionalRestraints.pypp.cpp ├── PositionalRestraints.pypp.hpp ├── RMSDRestraint.pypp.cpp ├── RMSDRestraint.pypp.hpp ├── RMSDRestraints.pypp.cpp ├── RMSDRestraints.pypp.hpp ├── Restraint.pypp.cpp ├── Restraint.pypp.hpp ├── Restraint3D.pypp.cpp ├── Restraint3D.pypp.hpp ├── RestraintComponent.pypp.cpp ├── RestraintComponent.pypp.hpp ├── RestraintFF.pypp.cpp ├── RestraintFF.pypp.hpp ├── Restraints.pypp.cpp ├── Restraints.pypp.hpp ├── ScaledCLJParameterNames3D.pypp.cpp ├── ScaledCLJParameterNames3D.pypp.hpp ├── ScaledChargeParameterNames3D.pypp.cpp ├── ScaledChargeParameterNames3D.pypp.hpp ├── ScaledLJParameterNames3D.pypp.cpp ├── ScaledLJParameterNames3D.pypp.hpp ├── SelectorAngle.pypp.cpp ├── SelectorAngle.pypp.hpp ├── SelectorBond.pypp.cpp ├── SelectorBond.pypp.hpp ├── SelectorDihedral.pypp.cpp ├── SelectorDihedral.pypp.hpp ├── SelectorImproper.pypp.cpp ├── SelectorImproper.pypp.hpp ├── SelectorMAngle.pypp.cpp ├── SelectorMAngle.pypp.hpp ├── SelectorMBond.pypp.cpp ├── SelectorMBond.pypp.hpp ├── SelectorMDihedral.pypp.cpp ├── SelectorMDihedral.pypp.hpp ├── SelectorMImproper.pypp.cpp ├── SelectorMImproper.pypp.hpp ├── SireMM_containers.cpp ├── SireMM_containers.h ├── SireMM_properties.cpp ├── SireMM_properties.h ├── SireMM_registrars.cpp ├── SireMM_registrars.h ├── SoftCLJComponent.pypp.cpp ├── SoftCLJComponent.pypp.hpp ├── SoftCLJPotentialInterface_InterSoftCLJPotential_.pypp.cpp ├── SoftCLJPotentialInterface_InterSoftCLJPotential_.pypp.hpp ├── SoftCLJPotentialInterface_IntraSoftCLJPotential_.pypp.cpp ├── SoftCLJPotentialInterface_IntraSoftCLJPotential_.pypp.hpp ├── StretchBendComponent.pypp.cpp ├── StretchBendComponent.pypp.hpp ├── StretchBendParameterName.pypp.cpp ├── StretchBendParameterName.pypp.hpp ├── StretchBendSymbols.pypp.cpp ├── StretchBendSymbols.pypp.hpp ├── StretchBendTorsionComponent.pypp.cpp ├── StretchBendTorsionComponent.pypp.hpp ├── StretchBendTorsionParameterName.pypp.cpp ├── StretchBendTorsionParameterName.pypp.hpp ├── StretchBendTorsionSymbols.pypp.cpp ├── StretchBendTorsionSymbols.pypp.hpp ├── StretchStretchComponent.pypp.cpp ├── StretchStretchComponent.pypp.hpp ├── StretchStretchParameterName.pypp.cpp ├── StretchStretchParameterName.pypp.hpp ├── StretchStretchSymbols.pypp.cpp ├── StretchStretchSymbols.pypp.hpp ├── SwitchingFunction.pypp.cpp ├── SwitchingFunction.pypp.hpp ├── TestFF.pypp.cpp ├── TestFF.pypp.hpp ├── ThreeAtomFunction.pypp.cpp ├── ThreeAtomFunction.pypp.hpp ├── ThreeAtomFunctions.pypp.cpp ├── ThreeAtomFunctions.pypp.hpp ├── ThreeAtomPerturbation.pypp.cpp ├── ThreeAtomPerturbation.pypp.hpp ├── TripleDistanceRestraint.pypp.cpp ├── TripleDistanceRestraint.pypp.hpp ├── TwoAtomFunction.pypp.cpp ├── TwoAtomFunction.pypp.hpp ├── TwoAtomFunctions.pypp.cpp ├── TwoAtomFunctions.pypp.hpp ├── TwoAtomPerturbation.pypp.cpp ├── TwoAtomPerturbation.pypp.hpp ├── UreyBradleyComponent.pypp.cpp ├── UreyBradleyComponent.pypp.hpp ├── UreyBradleyParameterName.pypp.cpp ├── UreyBradleyParameterName.pypp.hpp ├── _MM.main.cpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Maths ├── Accumulator.pypp.cpp ├── Accumulator.pypp.hpp ├── Array2D_Matrix_.pypp.cpp ├── Array2D_Matrix_.pypp.hpp ├── Array2D_NMatrix_.pypp.cpp ├── Array2D_NMatrix_.pypp.hpp ├── Array2D_SireMaths_AccumulatorPtr_.pypp.cpp ├── Array2D_SireMaths_AccumulatorPtr_.pypp.hpp ├── Array2D_Vector_.pypp.cpp ├── Array2D_Vector_.pypp.hpp ├── ArrayProperty_Vector_.pypp.cpp ├── ArrayProperty_Vector_.pypp.hpp ├── Average.pypp.cpp ├── Average.pypp.hpp ├── AverageAndStddev.pypp.cpp ├── AverageAndStddev.pypp.hpp ├── AxisSet.pypp.cpp ├── AxisSet.pypp.hpp ├── BennettsFreeEnergyAverage.pypp.cpp ├── BennettsFreeEnergyAverage.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Complex.pypp.cpp ├── Complex.pypp.hpp ├── DistVector.pypp.cpp ├── DistVector.pypp.hpp ├── EnergyTrajectory.pypp.cpp ├── EnergyTrajectory.pypp.hpp ├── ExpAverage.pypp.cpp ├── ExpAverage.pypp.hpp ├── FreeEnergyAverage.pypp.cpp ├── FreeEnergyAverage.pypp.hpp ├── Histogram.pypp.cpp ├── Histogram.pypp.hpp ├── HistogramBin.pypp.cpp ├── HistogramBin.pypp.hpp ├── HistogramValue.pypp.cpp ├── HistogramValue.pypp.hpp ├── Line.pypp.cpp ├── Line.pypp.hpp ├── Matrix.pypp.cpp ├── Matrix.pypp.hpp ├── Median.pypp.cpp ├── Median.pypp.hpp ├── MultiDouble.pypp.cpp ├── MultiDouble.pypp.hpp ├── MultiFixed.pypp.cpp ├── MultiFixed.pypp.hpp ├── MultiFloat.pypp.cpp ├── MultiFloat.pypp.hpp ├── MultiInt.pypp.cpp ├── MultiInt.pypp.hpp ├── MultiUInt.pypp.cpp ├── MultiUInt.pypp.hpp ├── MultiVector.pypp.cpp ├── MultiVector.pypp.hpp ├── N4Matrix.pypp.cpp ├── N4Matrix.pypp.hpp ├── NMatrix.pypp.cpp ├── NMatrix.pypp.hpp ├── NVector.pypp.cpp ├── NVector.pypp.hpp ├── NullAccumulator.pypp.cpp ├── NullAccumulator.pypp.hpp ├── Plane.pypp.cpp ├── Plane.pypp.hpp ├── Quaternion.pypp.cpp ├── Quaternion.pypp.hpp ├── RanGenerator.pypp.cpp ├── RanGenerator.pypp.hpp ├── Rational.pypp.cpp ├── Rational.pypp.hpp ├── RecordValues.pypp.cpp ├── RecordValues.pypp.hpp ├── SireMaths_containers.cpp ├── SireMaths_containers.h ├── SireMaths_properties.cpp ├── SireMaths_properties.h ├── SireMaths_registrars.cpp ├── SireMaths_registrars.h ├── Sphere.pypp.cpp ├── Sphere.pypp.hpp ├── SphereArrayProperty.pypp.cpp ├── SphereArrayProperty.pypp.hpp ├── SphereProperty.pypp.cpp ├── SphereProperty.pypp.hpp ├── Torsion.pypp.cpp ├── Torsion.pypp.hpp ├── Transform.pypp.cpp ├── Transform.pypp.hpp ├── Triangle.pypp.cpp ├── Triangle.pypp.hpp ├── TrigArray2D_Matrix_.pypp.cpp ├── TrigArray2D_Matrix_.pypp.hpp ├── TrigArray2D_Vector_.pypp.cpp ├── TrigArray2D_Vector_.pypp.hpp ├── TrigMatrix.pypp.cpp ├── TrigMatrix.pypp.hpp ├── Vector.pypp.cpp ├── Vector.pypp.hpp ├── VectorArrayProperty.pypp.cpp ├── VectorArrayProperty.pypp.hpp ├── VectorProperty.pypp.cpp ├── VectorProperty.pypp.hpp ├── _Maths.main.cpp ├── _Maths_free_functions.pypp.cpp ├── _Maths_free_functions.pypp.hpp ├── _Maths_global_variables.pyman.cpp ├── _Maths_global_variables.pyman.hpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Mol ├── AbsFromMass.pypp.cpp ├── AbsFromMass.pypp.hpp ├── AbsFromNumber.pypp.cpp ├── AbsFromNumber.pypp.hpp ├── AmberParameters.pypp.cpp ├── AmberParameters.pypp.hpp ├── AngleID.pypp.cpp ├── AngleID.pypp.hpp ├── AnglePerturbation.pypp.cpp ├── AnglePerturbation.pypp.hpp ├── Atom.pypp.cpp ├── Atom.pypp.hpp ├── AtomBeads.pypp.cpp ├── AtomBeads.pypp.hpp ├── AtomCharges.pypp.cpp ├── AtomCharges.pypp.hpp ├── AtomChiralities.pypp.cpp ├── AtomChiralities.pypp.hpp ├── AtomCoordMatcher.pypp.cpp ├── AtomCoordMatcher.pypp.hpp ├── AtomCoords.pypp.cpp ├── AtomCoords.pypp.hpp ├── AtomCutting.pypp.cpp ├── AtomCutting.pypp.hpp ├── AtomDoubleArrayProperty.pypp.cpp ├── AtomDoubleArrayProperty.pypp.hpp ├── AtomEditor.pypp.cpp ├── AtomEditor.pypp.hpp ├── AtomEditorBase.pypp.cpp ├── AtomEditorBase.pypp.hpp ├── AtomElements.pypp.cpp ├── AtomElements.pypp.hpp ├── AtomEnergies.pypp.cpp ├── AtomEnergies.pypp.hpp ├── AtomFloatProperty.pypp.cpp ├── AtomFloatProperty.pypp.hpp ├── AtomForces.pypp.cpp ├── AtomForces.pypp.hpp ├── AtomHybridizations.pypp.cpp ├── AtomHybridizations.pypp.hpp ├── AtomID.pypp.cpp ├── AtomID.pypp.hpp ├── AtomIDMatcher.pypp.cpp ├── AtomIDMatcher.pypp.hpp ├── AtomIdx.pypp.cpp ├── AtomIdx.pypp.hpp ├── AtomIdxMapping.pypp.cpp ├── AtomIdxMapping.pypp.hpp ├── AtomIdxMappingEntry.pypp.cpp ├── AtomIdxMappingEntry.pypp.hpp ├── AtomIdxMatcher.pypp.cpp ├── AtomIdxMatcher.pypp.hpp ├── AtomIntProperty.pypp.cpp ├── AtomIntProperty.pypp.hpp ├── AtomIntegerArrayProperty.pypp.cpp ├── AtomIntegerArrayProperty.pypp.hpp ├── AtomMCSMatcher.pypp.cpp ├── AtomMCSMatcher.pypp.hpp ├── AtomMapping.pypp.cpp ├── AtomMapping.pypp.hpp ├── AtomMasses.pypp.cpp ├── AtomMasses.pypp.hpp ├── AtomMatch.pypp.cpp ├── AtomMatch.pypp.hpp ├── AtomMatchInverter.pypp.cpp ├── AtomMatchInverter.pypp.hpp ├── AtomMatchM.pypp.cpp ├── AtomMatchM.pypp.hpp ├── AtomMatcher.pypp.cpp ├── AtomMatcher.pypp.hpp ├── AtomMultiMatcher.pypp.cpp ├── AtomMultiMatcher.pypp.hpp ├── AtomName.pypp.cpp ├── AtomName.pypp.hpp ├── AtomNameMatcher.pypp.cpp ├── AtomNameMatcher.pypp.hpp ├── AtomNum.pypp.cpp ├── AtomNum.pypp.hpp ├── AtomNumMatcher.pypp.cpp ├── AtomNumMatcher.pypp.hpp ├── AtomPolarisabilities.pypp.cpp ├── AtomPolarisabilities.pypp.hpp ├── AtomProp.pypp.cpp ├── AtomProp.pypp.hpp ├── AtomPropertyList.pypp.cpp ├── AtomPropertyList.pypp.hpp ├── AtomPropertyProperty.pypp.cpp ├── AtomPropertyProperty.pypp.hpp ├── AtomRadicals.pypp.cpp ├── AtomRadicals.pypp.hpp ├── AtomRadii.pypp.cpp ├── AtomRadii.pypp.hpp ├── AtomResultMatcher.pypp.cpp ├── AtomResultMatcher.pypp.hpp ├── AtomSelection.pypp.cpp ├── AtomSelection.pypp.hpp ├── AtomStringArrayProperty.pypp.cpp ├── AtomStringArrayProperty.pypp.hpp ├── AtomStringProperty.pypp.cpp ├── AtomStringProperty.pypp.hpp ├── AtomStructureEditor.pypp.cpp ├── AtomStructureEditor.pypp.hpp ├── AtomVariantProperty.pypp.cpp ├── AtomVariantProperty.pypp.hpp ├── AtomVelocities.pypp.cpp ├── AtomVelocities.pypp.hpp ├── AtomsIn_CGID_.pypp.cpp ├── AtomsIn_CGID_.pypp.hpp ├── AtomsIn_ChainID_.pypp.cpp ├── AtomsIn_ChainID_.pypp.hpp ├── AtomsIn_ResID_.pypp.cpp ├── AtomsIn_ResID_.pypp.hpp ├── AtomsIn_SegID_.pypp.cpp ├── AtomsIn_SegID_.pypp.hpp ├── Bead.pypp.cpp ├── Bead.pypp.hpp ├── BeadEditor.pypp.cpp ├── BeadEditor.pypp.hpp ├── BeadEditorBase.pypp.cpp ├── BeadEditorBase.pypp.hpp ├── BeadFloatProperty.pypp.cpp ├── BeadFloatProperty.pypp.hpp ├── BeadID.pypp.cpp ├── BeadID.pypp.hpp ├── BeadIdx.pypp.cpp ├── BeadIdx.pypp.hpp ├── BeadIntProperty.pypp.cpp ├── BeadIntProperty.pypp.hpp ├── BeadNum.pypp.cpp ├── BeadNum.pypp.hpp ├── BeadProp.pypp.cpp ├── BeadProp.pypp.hpp ├── BeadPropertyProperty.pypp.cpp ├── BeadPropertyProperty.pypp.hpp ├── BeadStringProperty.pypp.cpp ├── BeadStringProperty.pypp.hpp ├── BeadVariantProperty.pypp.cpp ├── BeadVariantProperty.pypp.hpp ├── Beading.pypp.cpp ├── Beading.pypp.hpp ├── Beads.pypp.cpp ├── Beads.pypp.hpp ├── BondHunter.pypp.cpp ├── BondHunter.pypp.hpp ├── BondID.pypp.cpp ├── BondID.pypp.hpp ├── BondOrder.pypp.cpp ├── BondOrder.pypp.hpp ├── BondPerturbation.pypp.cpp ├── BondPerturbation.pypp.hpp ├── CGAtomID.pypp.cpp ├── CGAtomID.pypp.hpp ├── CGAtomIdx.pypp.cpp ├── CGAtomIdx.pypp.hpp ├── CGChainID.pypp.cpp ├── CGChainID.pypp.hpp ├── CGEditor.pypp.cpp ├── CGEditor.pypp.hpp ├── CGEditorBase.pypp.cpp ├── CGEditorBase.pypp.hpp ├── CGFloatProperty.pypp.cpp ├── CGFloatProperty.pypp.hpp ├── CGID.pypp.cpp ├── CGID.pypp.hpp ├── CGIdx.pypp.cpp ├── CGIdx.pypp.hpp ├── CGIntProperty.pypp.cpp ├── CGIntProperty.pypp.hpp ├── CGName.pypp.cpp ├── CGName.pypp.hpp ├── CGProp.pypp.cpp ├── CGProp.pypp.hpp ├── CGPropertyProperty.pypp.cpp ├── CGPropertyProperty.pypp.hpp ├── CGResID.pypp.cpp ├── CGResID.pypp.hpp ├── CGStringProperty.pypp.cpp ├── CGStringProperty.pypp.hpp ├── CGStructureEditor.pypp.cpp ├── CGStructureEditor.pypp.hpp ├── CGVariantProperty.pypp.cpp ├── CGVariantProperty.pypp.hpp ├── CGsWithAtoms.pypp.cpp ├── CGsWithAtoms.pypp.hpp ├── CMAPID.pypp.cpp ├── CMAPID.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Chain.pypp.cpp ├── Chain.pypp.hpp ├── ChainAtomID.pypp.cpp ├── ChainAtomID.pypp.hpp ├── ChainEditor.pypp.cpp ├── ChainEditor.pypp.hpp ├── ChainEditorBase.pypp.cpp ├── ChainEditorBase.pypp.hpp ├── ChainFloatProperty.pypp.cpp ├── ChainFloatProperty.pypp.hpp ├── ChainID.pypp.cpp ├── ChainID.pypp.hpp ├── ChainIdx.pypp.cpp ├── ChainIdx.pypp.hpp ├── ChainIntProperty.pypp.cpp ├── ChainIntProperty.pypp.hpp ├── ChainName.pypp.cpp ├── ChainName.pypp.hpp ├── ChainProp.pypp.cpp ├── ChainProp.pypp.hpp ├── ChainPropertyProperty.pypp.cpp ├── ChainPropertyProperty.pypp.hpp ├── ChainResID.pypp.cpp ├── ChainResID.pypp.hpp ├── ChainStringProperty.pypp.cpp ├── ChainStringProperty.pypp.hpp ├── ChainStructureEditor.pypp.cpp ├── ChainStructureEditor.pypp.hpp ├── ChainVariantProperty.pypp.cpp ├── ChainVariantProperty.pypp.hpp ├── ChainsWithAtoms.pypp.cpp ├── ChainsWithAtoms.pypp.hpp ├── ChainsWithRes.pypp.cpp ├── ChainsWithRes.pypp.hpp ├── ChargePerturbation.pypp.cpp ├── ChargePerturbation.pypp.hpp ├── ChemicalBondHunter.pypp.cpp ├── ChemicalBondHunter.pypp.hpp ├── Chirality.pypp.cpp ├── Chirality.pypp.hpp ├── Connectivity.pypp.cpp ├── Connectivity.pypp.hpp ├── ConnectivityBase.pypp.cpp ├── ConnectivityBase.pypp.hpp ├── ConnectivityEditor.pypp.cpp ├── ConnectivityEditor.pypp.hpp ├── CovalentBondHunter.pypp.cpp ├── CovalentBondHunter.pypp.hpp ├── CovalentBondHunterParameters.pypp.cpp ├── CovalentBondHunterParameters.pypp.hpp ├── CutGroup.pypp.cpp ├── CutGroup.pypp.hpp ├── CuttingFunction.pypp.cpp ├── CuttingFunction.pypp.hpp ├── DihedralID.pypp.cpp ├── DihedralID.pypp.hpp ├── DihedralPerturbation.pypp.cpp ├── DihedralPerturbation.pypp.hpp ├── Element.pypp.cpp ├── Element.pypp.hpp ├── Evaluator.pypp.cpp ├── Evaluator.pypp.hpp ├── EvaluatorM.pypp.cpp ├── EvaluatorM.pypp.hpp ├── Force3D.pypp.cpp ├── Force3D.pypp.hpp ├── Frame.pypp.cpp ├── Frame.pypp.hpp ├── FrameTransform.pypp.cpp ├── FrameTransform.pypp.hpp ├── GeometryPerturbation.pypp.cpp ├── GeometryPerturbation.pypp.hpp ├── GeometryPerturbations.pypp.cpp ├── GeometryPerturbations.pypp.hpp ├── GroupAtomIDBase.pypp.cpp ├── GroupAtomIDBase.pypp.hpp ├── Hybridization.pypp.cpp ├── Hybridization.pypp.hpp ├── IDAndSet_AtomID_.pypp.cpp ├── IDAndSet_AtomID_.pypp.hpp ├── IDAndSet_CGID_.pypp.cpp ├── IDAndSet_CGID_.pypp.hpp ├── IDAndSet_ChainID_.pypp.cpp ├── IDAndSet_ChainID_.pypp.hpp ├── IDAndSet_MGID_.pypp.cpp ├── IDAndSet_MGID_.pypp.hpp ├── IDAndSet_MolID_.pypp.cpp ├── IDAndSet_MolID_.pypp.hpp ├── IDAndSet_ResID_.pypp.cpp ├── IDAndSet_ResID_.pypp.hpp ├── IDAndSet_SegID_.pypp.cpp ├── IDAndSet_SegID_.pypp.hpp ├── IDOrSet_AtomID_.pypp.cpp ├── IDOrSet_AtomID_.pypp.hpp ├── IDOrSet_CGID_.pypp.cpp ├── IDOrSet_CGID_.pypp.hpp ├── IDOrSet_ChainID_.pypp.cpp ├── IDOrSet_ChainID_.pypp.hpp ├── IDOrSet_MGID_.pypp.cpp ├── IDOrSet_MGID_.pypp.hpp ├── IDOrSet_MolID_.pypp.cpp ├── IDOrSet_MolID_.pypp.hpp ├── IDOrSet_ResID_.pypp.cpp ├── IDOrSet_ResID_.pypp.hpp ├── IDOrSet_SegID_.pypp.cpp ├── IDOrSet_SegID_.pypp.hpp ├── ImproperID.pypp.cpp ├── ImproperID.pypp.hpp ├── InvertMatch_AtomID_.pypp.cpp ├── InvertMatch_AtomID_.pypp.hpp ├── InvertMatch_CGID_.pypp.cpp ├── InvertMatch_CGID_.pypp.hpp ├── InvertMatch_ChainID_.pypp.cpp ├── InvertMatch_ChainID_.pypp.hpp ├── InvertMatch_ResID_.pypp.cpp ├── InvertMatch_ResID_.pypp.hpp ├── InvertMatch_SegID_.pypp.cpp ├── InvertMatch_SegID_.pypp.hpp ├── MGID.pypp.cpp ├── MGID.pypp.hpp ├── MGIDsAndMaps.pypp.cpp ├── MGIDsAndMaps.pypp.hpp ├── MGIdx.pypp.cpp ├── MGIdx.pypp.hpp ├── MGName.pypp.cpp ├── MGName.pypp.hpp ├── MGNum.pypp.cpp ├── MGNum.pypp.hpp ├── MatchAll_AtomID_.pypp.cpp ├── MatchAll_AtomID_.pypp.hpp ├── MatchAll_CGID_.pypp.cpp ├── MatchAll_CGID_.pypp.hpp ├── MatchAll_ChainID_.pypp.cpp ├── MatchAll_ChainID_.pypp.hpp ├── MatchAll_ResID_.pypp.cpp ├── MatchAll_ResID_.pypp.hpp ├── MatchAll_SegID_.pypp.cpp ├── MatchAll_SegID_.pypp.hpp ├── MolAtomID.pypp.cpp ├── MolAtomID.pypp.hpp ├── MolEditor.pypp.cpp ├── MolEditor.pypp.hpp ├── MolEditorBase.pypp.cpp ├── MolEditorBase.pypp.hpp ├── MolGroupsBase.pypp.cpp ├── MolGroupsBase.pypp.hpp ├── MolID.pypp.cpp ├── MolID.pypp.hpp ├── MolIdx.pypp.cpp ├── MolIdx.pypp.hpp ├── MolInfo.pypp.cpp ├── MolInfo.pypp.hpp ├── MolName.pypp.cpp ├── MolName.pypp.hpp ├── MolNum.pypp.cpp ├── MolNum.pypp.hpp ├── MolResID.pypp.cpp ├── MolResID.pypp.hpp ├── MolResNum.pypp.cpp ├── MolResNum.pypp.hpp ├── MolStructureEditor.pypp.cpp ├── MolStructureEditor.pypp.hpp ├── MolViewProperty.pypp.cpp ├── MolViewProperty.pypp.hpp ├── MolWithResID.pypp.cpp ├── MolWithResID.pypp.hpp ├── Molecule.pypp.cpp ├── Molecule.pypp.hpp ├── MoleculeBeading.pypp.cpp ├── MoleculeBeading.pypp.hpp ├── MoleculeGroup.pypp.cpp ├── MoleculeGroup.pypp.hpp ├── MoleculeGroups.pypp.cpp ├── MoleculeGroups.pypp.hpp ├── MoleculeInfo.pypp.cpp ├── MoleculeInfo.pypp.hpp ├── MoleculeProperty.pypp.cpp ├── MoleculeProperty.pypp.hpp ├── MoleculeView.pypp.cpp ├── MoleculeView.pypp.hpp ├── Molecules.pypp.cpp ├── Molecules.pypp.hpp ├── MoverBase.pypp.cpp ├── MoverBase.pypp.hpp ├── Mover_Atom_.pypp.cpp ├── Mover_Atom_.pypp.hpp ├── Mover_Bead_.pypp.cpp ├── Mover_Bead_.pypp.hpp ├── Mover_Beads_.pypp.cpp ├── Mover_Beads_.pypp.hpp ├── Mover_Chain_.pypp.cpp ├── Mover_Chain_.pypp.hpp ├── Mover_CutGroup_.pypp.cpp ├── Mover_CutGroup_.pypp.hpp ├── Mover_Molecule_.pypp.cpp ├── Mover_Molecule_.pypp.hpp ├── Mover_PartialMolecule_.pypp.cpp ├── Mover_PartialMolecule_.pypp.hpp ├── Mover_Residue_.pypp.cpp ├── Mover_Residue_.pypp.hpp ├── Mover_Segment_.pypp.cpp ├── Mover_Segment_.pypp.hpp ├── Mover_Selector_Atom_.pypp.cpp ├── Mover_Selector_Atom_.pypp.hpp ├── Mover_Selector_Chain_.pypp.cpp ├── Mover_Selector_Chain_.pypp.hpp ├── Mover_Selector_CutGroup_.pypp.cpp ├── Mover_Selector_CutGroup_.pypp.hpp ├── Mover_Selector_Residue_.pypp.cpp ├── Mover_Selector_Residue_.pypp.hpp ├── Mover_Selector_Segment_.pypp.cpp ├── Mover_Selector_Segment_.pypp.hpp ├── NullBeading.pypp.cpp ├── NullBeading.pypp.hpp ├── NullBondHunter.pypp.cpp ├── NullBondHunter.pypp.hpp ├── NullGeometryPerturbation.pypp.cpp ├── NullGeometryPerturbation.pypp.hpp ├── NullPerturbation.pypp.cpp ├── NullPerturbation.pypp.hpp ├── PartialMolecule.pypp.cpp ├── PartialMolecule.pypp.hpp ├── Perturbation.pypp.cpp ├── Perturbation.pypp.hpp ├── PerturbationSymbols.pypp.cpp ├── PerturbationSymbols.pypp.hpp ├── Perturbations.pypp.cpp ├── Perturbations.pypp.hpp ├── Radical.pypp.cpp ├── Radical.pypp.hpp ├── RelFromMass.pypp.cpp ├── RelFromMass.pypp.hpp ├── RelFromNumber.pypp.cpp ├── RelFromNumber.pypp.hpp ├── ResAtomID.pypp.cpp ├── ResAtomID.pypp.hpp ├── ResEditor.pypp.cpp ├── ResEditor.pypp.hpp ├── ResEditorBase.pypp.cpp ├── ResEditorBase.pypp.hpp ├── ResFloatProperty.pypp.cpp ├── ResFloatProperty.pypp.hpp ├── ResID.pypp.cpp ├── ResID.pypp.hpp ├── ResIdx.pypp.cpp ├── ResIdx.pypp.hpp ├── ResIdxAtomCoordMatcher.pypp.cpp ├── ResIdxAtomCoordMatcher.pypp.hpp ├── ResIdxAtomMCSMatcher.pypp.cpp ├── ResIdxAtomMCSMatcher.pypp.hpp ├── ResIdxAtomNameMatcher.pypp.cpp ├── ResIdxAtomNameMatcher.pypp.hpp ├── ResIn_ChainID_.pypp.cpp ├── ResIn_ChainID_.pypp.hpp ├── ResIntProperty.pypp.cpp ├── ResIntProperty.pypp.hpp ├── ResName.pypp.cpp ├── ResName.pypp.hpp ├── ResNum.pypp.cpp ├── ResNum.pypp.hpp ├── ResNumAtomNameMatcher.pypp.cpp ├── ResNumAtomNameMatcher.pypp.hpp ├── ResProp.pypp.cpp ├── ResProp.pypp.hpp ├── ResPropertyProperty.pypp.cpp ├── ResPropertyProperty.pypp.hpp ├── ResStringProperty.pypp.cpp ├── ResStringProperty.pypp.hpp ├── ResStructureEditor.pypp.cpp ├── ResStructureEditor.pypp.hpp ├── ResVariantProperty.pypp.cpp ├── ResVariantProperty.pypp.hpp ├── ResWithAtoms.pypp.cpp ├── ResWithAtoms.pypp.hpp ├── Residue.pypp.cpp ├── Residue.pypp.hpp ├── ResidueBeading.pypp.cpp ├── ResidueBeading.pypp.hpp ├── ResidueCutting.pypp.cpp ├── ResidueCutting.pypp.hpp ├── SegAtomID.pypp.cpp ├── SegAtomID.pypp.hpp ├── SegCGID.pypp.cpp ├── SegCGID.pypp.hpp ├── SegChainID.pypp.cpp ├── SegChainID.pypp.hpp ├── SegEditor.pypp.cpp ├── SegEditor.pypp.hpp ├── SegEditorBase.pypp.cpp ├── SegEditorBase.pypp.hpp ├── SegFloatProperty.pypp.cpp ├── SegFloatProperty.pypp.hpp ├── SegID.pypp.cpp ├── SegID.pypp.hpp ├── SegIdx.pypp.cpp ├── SegIdx.pypp.hpp ├── SegIntProperty.pypp.cpp ├── SegIntProperty.pypp.hpp ├── SegName.pypp.cpp ├── SegName.pypp.hpp ├── SegProp.pypp.cpp ├── SegProp.pypp.hpp ├── SegPropertyProperty.pypp.cpp ├── SegPropertyProperty.pypp.hpp ├── SegResID.pypp.cpp ├── SegResID.pypp.hpp ├── SegStringProperty.pypp.cpp ├── SegStringProperty.pypp.hpp ├── SegStructureEditor.pypp.cpp ├── SegStructureEditor.pypp.hpp ├── SegVariantProperty.pypp.cpp ├── SegVariantProperty.pypp.hpp ├── Segment.pypp.cpp ├── Segment.pypp.hpp ├── SegsWithAtoms.pypp.cpp ├── SegsWithAtoms.pypp.hpp ├── Select.pypp.cpp ├── Select.pypp.hpp ├── SelectResult.pypp.cpp ├── SelectResult.pypp.hpp ├── SelectResultMover.pypp.cpp ├── SelectResultMover.pypp.hpp ├── SelectorM_Atom_.pypp.cpp ├── SelectorM_Atom_.pypp.hpp ├── SelectorM_Chain_.pypp.cpp ├── SelectorM_Chain_.pypp.hpp ├── SelectorM_CutGroup_.pypp.cpp ├── SelectorM_CutGroup_.pypp.hpp ├── SelectorM_Residue_.pypp.cpp ├── SelectorM_Residue_.pypp.hpp ├── SelectorM_Segment_.pypp.cpp ├── SelectorM_Segment_.pypp.hpp ├── SelectorMol.pypp.cpp ├── SelectorMol.pypp.hpp ├── Selector_Atom_.pypp.cpp ├── Selector_Atom_.pypp.hpp ├── Selector_Chain_.pypp.cpp ├── Selector_Chain_.pypp.hpp ├── Selector_CutGroup_.pypp.cpp ├── Selector_CutGroup_.pypp.hpp ├── Selector_Residue_.pypp.cpp ├── Selector_Residue_.pypp.hpp ├── Selector_Segment_.pypp.cpp ├── Selector_Segment_.pypp.hpp ├── SireMol_containers.cpp ├── SireMol_containers.h ├── SireMol_properties.cpp ├── SireMol_properties.h ├── SireMol_registrars.cpp ├── SireMol_registrars.h ├── SpecifyMol.pypp.cpp ├── SpecifyMol.pypp.hpp ├── Specify_AtomID_.pypp.cpp ├── Specify_AtomID_.pypp.hpp ├── Specify_CGID_.pypp.cpp ├── Specify_CGID_.pypp.hpp ├── Specify_ChainID_.pypp.cpp ├── Specify_ChainID_.pypp.hpp ├── Specify_MGID_.pypp.cpp ├── Specify_MGID_.pypp.hpp ├── Specify_ResID_.pypp.cpp ├── Specify_ResID_.pypp.hpp ├── Specify_SegID_.pypp.cpp ├── Specify_SegID_.pypp.hpp ├── Stereochemistry.pypp.cpp ├── Stereochemistry.pypp.hpp ├── Trajectory.pypp.cpp ├── Trajectory.pypp.hpp ├── TrajectoryAligner.pypp.cpp ├── TrajectoryAligner.pypp.hpp ├── UserBeading.pypp.cpp ├── UserBeading.pypp.hpp ├── Velocity3D.pypp.cpp ├── Velocity3D.pypp.hpp ├── VolumeMap.pypp.cpp ├── VolumeMap.pypp.hpp ├── WeightFunction.pypp.cpp ├── WeightFunction.pypp.hpp ├── Within.pypp.cpp ├── Within.pypp.hpp ├── _Mol.main.cpp ├── _Mol_free_functions.pypp.cpp ├── _Mol_free_functions.pypp.hpp ├── __init__.py ├── active_headers.h ├── convertviewsofmol.hpp └── special_code.py ├── Move ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── CMakeNoOpenMM.txt ├── CMakeNoOpenMMFile.txt ├── CMakeOpenMM.txt ├── CMakeOpenMMFile.txt ├── DLMRigidBody.pypp.cpp ├── DLMRigidBody.pypp.hpp ├── DofID.pypp.cpp ├── DofID.pypp.hpp ├── Dynamics.pypp.cpp ├── Dynamics.pypp.hpp ├── Ensemble.pypp.cpp ├── Ensemble.pypp.hpp ├── Flexibility.pypp.cpp ├── Flexibility.pypp.hpp ├── GetCOGPoint.pypp.cpp ├── GetCOGPoint.pypp.hpp ├── GetCOMPoint.pypp.cpp ├── GetCOMPoint.pypp.hpp ├── GetCentroidPoint.pypp.cpp ├── GetCentroidPoint.pypp.hpp ├── GetPoint.pypp.cpp ├── GetPoint.pypp.hpp ├── HMCGenerator.pypp.cpp ├── HMCGenerator.pypp.hpp ├── HMCVelGen.pypp.cpp ├── HMCVelGen.pypp.hpp ├── HybridMC.pypp.cpp ├── HybridMC.pypp.hpp ├── Integrator.pypp.cpp ├── Integrator.pypp.hpp ├── InternalMove.pypp.cpp ├── InternalMove.pypp.hpp ├── InternalMoveSingle.pypp.cpp ├── InternalMoveSingle.pypp.hpp ├── MTSMC.pypp.cpp ├── MTSMC.pypp.hpp ├── MaxwellBoltzmann.pypp.cpp ├── MaxwellBoltzmann.pypp.hpp ├── MolDeleter.pypp.cpp ├── MolDeleter.pypp.hpp ├── MolInserter.pypp.cpp ├── MolInserter.pypp.hpp ├── MolecularDynamics.pypp.cpp ├── MolecularDynamics.pypp.hpp ├── MonteCarlo.pypp.cpp ├── MonteCarlo.pypp.hpp ├── Move.pypp.cpp ├── Move.pypp.hpp ├── Moves.pypp.cpp ├── Moves.pypp.hpp ├── NoOpenMM │ ├── OpenMMFrEnergyDT.pypp.cpp │ ├── OpenMMFrEnergyDT.pypp.hpp │ ├── OpenMMFrEnergyST.pypp.cpp │ ├── OpenMMFrEnergyST.pypp.hpp │ ├── OpenMMMDIntegrator.pypp.cpp │ ├── OpenMMMDIntegrator.pypp.hpp │ ├── OpenMMPMEFEP.pypp.cpp │ └── OpenMMPMEFEP.pypp.hpp ├── NullDeleter.pypp.cpp ├── NullDeleter.pypp.hpp ├── NullGetPoint.pypp.cpp ├── NullGetPoint.pypp.hpp ├── NullInserter.pypp.cpp ├── NullInserter.pypp.hpp ├── NullIntegrator.pypp.cpp ├── NullIntegrator.pypp.hpp ├── NullMove.pypp.cpp ├── NullMove.pypp.hpp ├── NullSupraMove.pypp.cpp ├── NullSupraMove.pypp.hpp ├── NullSupraSubMove.pypp.cpp ├── NullSupraSubMove.pypp.hpp ├── NullVelocityGenerator.pypp.cpp ├── NullVelocityGenerator.pypp.hpp ├── NullVolumeChanger.pypp.cpp ├── NullVolumeChanger.pypp.hpp ├── OpenMMFrEnergyDT.pypp.cpp ├── OpenMMFrEnergyDT.pypp.hpp ├── OpenMMFrEnergyST.pypp.cpp ├── OpenMMFrEnergyST.pypp.hpp ├── OpenMMMDIntegrator.pypp.cpp ├── OpenMMMDIntegrator.pypp.hpp ├── OpenMMPMEFEP.pypp.cpp ├── OpenMMPMEFEP.pypp.hpp ├── PrefSampler.pypp.cpp ├── PrefSampler.pypp.hpp ├── RBWorkspaceJM.pypp.cpp ├── RBWorkspaceJM.pypp.hpp ├── RepExMove.pypp.cpp ├── RepExMove.pypp.hpp ├── RepExMove2.pypp.cpp ├── RepExMove2.pypp.hpp ├── RepExSubMove.pypp.cpp ├── RepExSubMove.pypp.hpp ├── Replica.pypp.cpp ├── Replica.pypp.hpp ├── Replicas.pypp.cpp ├── Replicas.pypp.hpp ├── RigidBodyMC.pypp.cpp ├── RigidBodyMC.pypp.hpp ├── SameMoves.pypp.cpp ├── SameMoves.pypp.hpp ├── SameSupraMoves.pypp.cpp ├── SameSupraMoves.pypp.hpp ├── SameSupraSubMoves.pypp.cpp ├── SameSupraSubMoves.pypp.hpp ├── Sampler.pypp.cpp ├── Sampler.pypp.hpp ├── ScaleVolumeFromCenter.pypp.cpp ├── ScaleVolumeFromCenter.pypp.hpp ├── SimPacket.pypp.cpp ├── SimPacket.pypp.hpp ├── SimStore.pypp.cpp ├── SimStore.pypp.hpp ├── Simulation.pypp.cpp ├── Simulation.pypp.hpp ├── SireMove_containers.cpp ├── SireMove_containers.h ├── SireMove_properties.cpp ├── SireMove_properties.h ├── SireMove_registrars.cpp ├── SireMove_registrars.h ├── SpecifiedGroupsDeleter.pypp.cpp ├── SpecifiedGroupsDeleter.pypp.hpp ├── SupraMove.pypp.cpp ├── SupraMove.pypp.hpp ├── SupraMoves.pypp.cpp ├── SupraMoves.pypp.hpp ├── SupraSim.pypp.cpp ├── SupraSim.pypp.hpp ├── SupraSimPacket.pypp.cpp ├── SupraSimPacket.pypp.hpp ├── SupraSubMove.pypp.cpp ├── SupraSubMove.pypp.hpp ├── SupraSubMoves.pypp.cpp ├── SupraSubMoves.pypp.hpp ├── SupraSubSim.pypp.cpp ├── SupraSubSim.pypp.hpp ├── SupraSubSimPacket.pypp.cpp ├── SupraSubSimPacket.pypp.hpp ├── SupraSubSystem.pypp.cpp ├── SupraSubSystem.pypp.hpp ├── SupraSystem.pypp.cpp ├── SupraSystem.pypp.hpp ├── SystemWideDeleter.pypp.cpp ├── SystemWideDeleter.pypp.hpp ├── TitrationMove.pypp.cpp ├── TitrationMove.pypp.hpp ├── Titrator.pypp.cpp ├── Titrator.pypp.hpp ├── UniformInserter.pypp.cpp ├── UniformInserter.pypp.hpp ├── UniformSampler.pypp.cpp ├── UniformSampler.pypp.hpp ├── VelocitiesFromProperty.pypp.cpp ├── VelocitiesFromProperty.pypp.hpp ├── VelocityGenerator.pypp.cpp ├── VelocityGenerator.pypp.hpp ├── VelocityVerlet.pypp.cpp ├── VelocityVerlet.pypp.hpp ├── VolumeChanger.pypp.cpp ├── VolumeChanger.pypp.hpp ├── VolumeMove.pypp.cpp ├── VolumeMove.pypp.hpp ├── WeightedMoves.pypp.cpp ├── WeightedMoves.pypp.hpp ├── ZMatMove.pypp.cpp ├── ZMatMove.pypp.hpp ├── ZMatrix.pypp.cpp ├── ZMatrix.pypp.hpp ├── ZMatrixCoords.pypp.cpp ├── ZMatrixCoords.pypp.hpp ├── ZMatrixCoordsLine.pypp.cpp ├── ZMatrixCoordsLine.pypp.hpp ├── ZMatrixLine.pypp.cpp ├── ZMatrixLine.pypp.hpp ├── _Move.main.cpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Py++ └── pyplusplus-r1247.tgz ├── Qt ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── QByteArray.pypp.cpp ├── QByteArray.pypp.hpp ├── QDate.pypp.cpp ├── QDate.pypp.hpp ├── QDateTime.pypp.cpp ├── QDateTime.pypp.hpp ├── QDir.pypp.cpp ├── QDir.pypp.hpp ├── QElapsedTimer.pypp.cpp ├── QElapsedTimer.pypp.hpp ├── QFileInfo.pypp.cpp ├── QFileInfo.pypp.hpp ├── QTime.pypp.cpp ├── QTime.pypp.hpp ├── QUuid.pypp.cpp ├── QUuid.pypp.hpp ├── _Qt.main.cpp ├── __array_1.pypp.hpp ├── __init__.py ├── autoconvert_QChar.cpp ├── autoconvert_QString.cpp ├── create_qt_wrappers.py ├── named_tuple.py ├── qdatastream.hpp ├── qtheaders │ ├── README │ ├── qbytearray.h │ ├── qdatetime.h │ └── quuid.h ├── sireqt_containers.cpp ├── sireqt_containers.h └── sireqt_headers.h ├── README.md ├── Search ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── _Search.main.cpp ├── _Search_free_functions.pypp.cpp ├── _Search_free_functions.pypp.hpp ├── __init__.py └── active_headers.h ├── Squire ├── AM1BCC.pypp.cpp ├── AM1BCC.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ChargeElementParameterNames3D.pypp.cpp ├── ChargeElementParameterNames3D.pypp.hpp ├── ElementParameterName.pypp.cpp ├── ElementParameterName.pypp.hpp ├── ElementParameterName3D.pypp.cpp ├── ElementParameterName3D.pypp.hpp ├── GTO.pypp.cpp ├── GTO.pypp.hpp ├── GTOPair.pypp.cpp ├── GTOPair.pypp.hpp ├── HF.pypp.cpp ├── HF.pypp.hpp ├── Molpro.pypp.cpp ├── Molpro.pypp.hpp ├── Mopac.pypp.cpp ├── Mopac.pypp.hpp ├── NullQM.pypp.cpp ├── NullQM.pypp.hpp ├── NullQMChargeCalculator.pypp.cpp ├── NullQMChargeCalculator.pypp.hpp ├── Orbital.pypp.cpp ├── Orbital.pypp.hpp ├── OrbitalShell.pypp.cpp ├── OrbitalShell.pypp.hpp ├── PP_GTO.pypp.cpp ├── PP_GTO.pypp.hpp ├── PP_GTOs.pypp.cpp ├── PP_GTOs.pypp.hpp ├── PS_GTO.pypp.cpp ├── PS_GTO.pypp.hpp ├── PS_GTOs.pypp.cpp ├── PS_GTOs.pypp.hpp ├── P_GTO.pypp.cpp ├── P_GTO.pypp.hpp ├── PointCharge.pypp.cpp ├── PointCharge.pypp.hpp ├── PointDipole.pypp.cpp ├── PointDipole.pypp.hpp ├── QMChargeCalculator.pypp.cpp ├── QMChargeCalculator.pypp.hpp ├── QMChargeConstraint.pypp.cpp ├── QMChargeConstraint.pypp.hpp ├── QMComponent.pypp.cpp ├── QMComponent.pypp.hpp ├── QMFF.pypp.cpp ├── QMFF.pypp.hpp ├── QMMMFF.pypp.cpp ├── QMMMFF.pypp.hpp ├── QMProgram.pypp.cpp ├── QMProgram.pypp.hpp ├── SQM.pypp.cpp ├── SQM.pypp.hpp ├── SS_GTO.pypp.cpp ├── SS_GTO.pypp.hpp ├── SS_GTOs.pypp.cpp ├── SS_GTOs.pypp.hpp ├── S_GTO.pypp.cpp ├── S_GTO.pypp.hpp ├── ShellPair.pypp.cpp ├── ShellPair.pypp.hpp ├── Squire_containers.cpp ├── Squire_containers.h ├── Squire_properties.cpp ├── Squire_properties.h ├── Squire_registrars.cpp ├── Squire_registrars.h ├── _Squire.main.cpp ├── _Squire_free_functions.pypp.cpp ├── _Squire_free_functions.pypp.hpp ├── __init__.py └── active_headers.h ├── Stream ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── FileHeader.pypp.cpp ├── FileHeader.pypp.hpp ├── MD5Sum.pypp.cpp ├── MD5Sum.pypp.hpp ├── SireStream_functions.cpp ├── SireStream_registrars.cpp ├── SireStream_registrars.h ├── _Stream.main.cpp ├── _Stream_free_functions.pypp.cpp ├── _Stream_free_functions.pypp.hpp ├── __init__.py ├── active_headers.h └── special_code.py ├── System ├── AngleComponent.pypp.cpp ├── AngleComponent.pypp.hpp ├── AssignerGroup.pypp.cpp ├── AssignerGroup.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── ChargeConstraint.pypp.cpp ├── ChargeConstraint.pypp.hpp ├── CheckPoint.pypp.cpp ├── CheckPoint.pypp.hpp ├── CloseMols.pypp.cpp ├── CloseMols.pypp.hpp ├── ComponentConstraint.pypp.cpp ├── ComponentConstraint.pypp.hpp ├── Constraint.pypp.cpp ├── Constraint.pypp.hpp ├── Constraints.pypp.cpp ├── Constraints.pypp.hpp ├── DihedralComponent.pypp.cpp ├── DihedralComponent.pypp.hpp ├── DistanceComponent.pypp.cpp ├── DistanceComponent.pypp.hpp ├── DoubleDistanceComponent.pypp.cpp ├── DoubleDistanceComponent.pypp.hpp ├── EnergyMonitor.pypp.cpp ├── EnergyMonitor.pypp.hpp ├── ForceFieldInfo.pypp.cpp ├── ForceFieldInfo.pypp.hpp ├── FreeEnergyMonitor.pypp.cpp ├── FreeEnergyMonitor.pypp.hpp ├── GeometryComponent.pypp.cpp ├── GeometryComponent.pypp.hpp ├── IDAndSet_MonitorID_.pypp.cpp ├── IDAndSet_MonitorID_.pypp.hpp ├── IDAndSet_SysID_.pypp.cpp ├── IDAndSet_SysID_.pypp.hpp ├── IDAssigner.pypp.cpp ├── IDAssigner.pypp.hpp ├── IDOrSet_MonitorID_.pypp.cpp ├── IDOrSet_MonitorID_.pypp.hpp ├── IDOrSet_SysID_.pypp.cpp ├── IDOrSet_SysID_.pypp.hpp ├── IdentityConstraint.pypp.cpp ├── IdentityConstraint.pypp.hpp ├── MoleculeConstraint.pypp.cpp ├── MoleculeConstraint.pypp.hpp ├── MonitorComponent.pypp.cpp ├── MonitorComponent.pypp.hpp ├── MonitorComponents.pypp.cpp ├── MonitorComponents.pypp.hpp ├── MonitorID.pypp.cpp ├── MonitorID.pypp.hpp ├── MonitorIdx.pypp.cpp ├── MonitorIdx.pypp.hpp ├── MonitorMonitor.pypp.cpp ├── MonitorMonitor.pypp.hpp ├── MonitorName.pypp.cpp ├── MonitorName.pypp.hpp ├── MonitorProperty.pypp.cpp ├── MonitorProperty.pypp.hpp ├── NullConstraint.pypp.cpp ├── NullConstraint.pypp.hpp ├── NullMonitor.pypp.cpp ├── NullMonitor.pypp.hpp ├── PerturbationConstraint.pypp.cpp ├── PerturbationConstraint.pypp.hpp ├── PolariseCharges.pypp.cpp ├── PolariseCharges.pypp.hpp ├── PolariseChargesFF.pypp.cpp ├── PolariseChargesFF.pypp.hpp ├── PropertyConstraint.pypp.cpp ├── PropertyConstraint.pypp.hpp ├── SireSystem_containers.cpp ├── SireSystem_containers.h ├── SireSystem_properties.cpp ├── SireSystem_properties.h ├── SireSystem_registrars.cpp ├── SireSystem_registrars.h ├── SpaceWrapper.pypp.cpp ├── SpaceWrapper.pypp.hpp ├── Specify_MonitorID_.pypp.cpp ├── Specify_MonitorID_.pypp.hpp ├── Specify_SysID_.pypp.cpp ├── Specify_SysID_.pypp.hpp ├── SysID.pypp.cpp ├── SysID.pypp.hpp ├── SysIdx.pypp.cpp ├── SysIdx.pypp.hpp ├── SysName.pypp.cpp ├── SysName.pypp.hpp ├── System.pypp.cpp ├── System.pypp.hpp ├── SystemMonitor.pypp.cpp ├── SystemMonitor.pypp.hpp ├── SystemMonitors.pypp.cpp ├── SystemMonitors.pypp.hpp ├── TripleDistanceComponent.pypp.cpp ├── TripleDistanceComponent.pypp.hpp ├── VolMapMonitor.pypp.cpp ├── VolMapMonitor.pypp.hpp ├── WindowedComponent.pypp.cpp ├── WindowedComponent.pypp.hpp ├── _System.main.cpp ├── _System_free_functions.pypp.cpp ├── _System_free_functions.pypp.hpp ├── __init__.py ├── active_headers.h └── special_code.py ├── Tools ├── AmberLoader.py ├── BoreschAnalyticalCorrection.py ├── BoreschNumericalCorrection.py ├── CMakeLists.txt ├── DCDFile.py ├── FreeEnergyAnalysis.py ├── LJcutoff.py ├── LSRC.py ├── Nautilus.py ├── OpenMMMD.py ├── PSRC.py ├── Plot.py ├── QuantumToMM.py ├── StandardState.py ├── WSRC.py ├── WaterChanger.py ├── WaterView.py ├── __init__.py ├── ap.py └── deprecated │ ├── FDTISingleBound.py │ └── FDTISingleFree.py ├── Units ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Celsius.pypp.cpp ├── Celsius.pypp.hpp ├── Fahrenheit.pypp.cpp ├── Fahrenheit.pypp.hpp ├── GeneralUnit.pypp.cpp ├── GeneralUnit.pypp.hpp ├── SireUnits_containers.cpp ├── SireUnits_containers.h ├── SireUnits_registrars.cpp ├── SireUnits_registrars.h ├── TempBase.pypp.cpp ├── TempBase.pypp.hpp ├── Unit.pypp.cpp ├── Unit.pypp.hpp ├── _Units.main.cpp ├── _Units_free_functions.pypp.cpp ├── _Units_free_functions.pypp.hpp ├── _Units_global_variables.pyman.cpp ├── _Units_global_variables.pyman.hpp ├── __init__.py ├── active_headers.h ├── sireunits_dimensions.cpp ├── sireunits_dimensions.h └── special_code.py ├── Vol ├── AABox.pypp.cpp ├── AABox.pypp.hpp ├── BoxPatching.pypp.cpp ├── BoxPatching.pypp.hpp ├── CMakeAutogenFile.txt ├── CMakeLists.txt ├── Cartesian.pypp.cpp ├── Cartesian.pypp.hpp ├── CombineSpaces.pypp.cpp ├── CombineSpaces.pypp.hpp ├── CombinedSpace.pypp.cpp ├── CombinedSpace.pypp.hpp ├── CoordGroup.pypp.cpp ├── CoordGroup.pypp.hpp ├── CoordGroupArray.pypp.cpp ├── CoordGroupArray.pypp.hpp ├── CoordGroupArrayArray.pypp.cpp ├── CoordGroupArrayArray.pypp.hpp ├── CoordGroupBase.pypp.cpp ├── CoordGroupBase.pypp.hpp ├── CoordGroupEditor.pypp.cpp ├── CoordGroupEditor.pypp.hpp ├── Grid.pypp.cpp ├── Grid.pypp.hpp ├── GridIndex.pypp.cpp ├── GridIndex.pypp.hpp ├── GridInfo.pypp.cpp ├── GridInfo.pypp.hpp ├── NullGrid.pypp.cpp ├── NullGrid.pypp.hpp ├── NullPatching.pypp.cpp ├── NullPatching.pypp.hpp ├── Patching.pypp.cpp ├── Patching.pypp.hpp ├── PeriodicBox.pypp.cpp ├── PeriodicBox.pypp.hpp ├── RegularGrid.pypp.cpp ├── RegularGrid.pypp.hpp ├── SireVol_containers.cpp ├── SireVol_containers.h ├── SireVol_properties.cpp ├── SireVol_properties.h ├── SireVol_registrars.cpp ├── SireVol_registrars.h ├── Space.pypp.cpp ├── Space.pypp.hpp ├── TransformedSpace.pypp.cpp ├── TransformedSpace.pypp.hpp ├── TriclinicBox.pypp.cpp ├── TriclinicBox.pypp.hpp ├── _Vol.main.cpp ├── __init__.py ├── active_headers.h └── special_code.py ├── __init__.py ├── build ├── clang_boost_macos_crash │ ├── README.md │ ├── clean.sh │ ├── compile.sh │ ├── test.py │ └── test_bp.cpp ├── cmake │ ├── Config__init__.py.in │ ├── FindOpenMM.cmake │ ├── FindRDKit.cmake │ ├── FindSire.cmake │ ├── GetGitVersion.cmake │ ├── GetSvnVersion.cmake │ ├── LimitSirePythonExportSymbols.cmake │ ├── LogVariables.cmake │ ├── cmake_strip.in │ ├── 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