Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 482264) +++ head/science/Makefile (revision 482265) @@ -1,296 +1,297 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro + SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += colt SUBDIR += coot SUBDIR += cp2k SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += elk SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += lm SUBDIR += luscus SUBDIR += madness SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += molgif SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openmx SUBDIR += openstructure SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-PyFR SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-ase SUBDIR += py-cdo SUBDIR += py-chempy SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qmcpack SUBDIR += qtresistors SUBDIR += quantum-espresso SUBDIR += qwalk SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tinker SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += wxmacmolplt SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/avogadrolibs/Makefile =================================================================== --- head/science/avogadrolibs/Makefile (nonexistent) +++ head/science/avogadrolibs/Makefile (revision 482265) @@ -0,0 +1,28 @@ +# $FreeBSD$ + +PORTNAME= avogadrolibs +DISTVERSION= 1.91.0 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Avogadro2 libraries for chemical editor and visualization applications + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +LIB_DEPENDS= libjsoncpp.so:devel/jsoncpp \ + libMoleQueueClient.so:misc/molequeue \ + libmsym.so:science/libmsym \ + libsymspg.so:science/spglib + +USES= cmake:outsource compiler:c++11-lang eigen:3,build,run gl libarchive qt:5 # eigen needs to be 'run' because it is written into cmake files +USE_GITHUB= yes +GH_ACCOUNT= OpenChemistry +USE_QT= core concurrent gui network widgets buildtools_build qmake_build +USE_GL= gl glew glu +USE_LDCONFIG= yes + +post-install: + @${RM} -r ${STAGEDIR}${PREFIX}/share/doc + +.include Property changes on: head/science/avogadrolibs/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/distinfo =================================================================== --- head/science/avogadrolibs/distinfo (nonexistent) +++ head/science/avogadrolibs/distinfo (revision 482265) @@ -0,0 +1,3 @@ +TIMESTAMP = 1539728298 +SHA256 (OpenChemistry-avogadrolibs-1.91.0_GH0.tar.gz) = 752933c26b46dfbf12f7537b1f8dd9960a4fd29f0cccbed5b868b00474bb42af +SIZE (OpenChemistry-avogadrolibs-1.91.0_GH0.tar.gz) = 2706319 Property changes on: head/science/avogadrolibs/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt (revision 482265) @@ -0,0 +1,8 @@ +--- avogadro/qtplugins/importpqr/CMakeLists.txt.orig 2018-10-17 00:20:17 UTC ++++ avogadro/qtplugins/importpqr/CMakeLists.txt +@@ -17,4 +17,4 @@ avogadro_plugin(ImportPQR + "" + ) + +-target_link_libraries(ImportPQR LINK_PRIVATE ${Qt5Network_LIBRARIES} jsoncpp) ++target_link_libraries(ImportPQR LINK_PUBLIC ${CMAKE_INSTALL_PREFIX}/lib/libjsoncpp.so LINK_PRIVATE ${Qt5Network_LIBRARIES}) Property changes on: head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt (revision 482265) @@ -0,0 +1,8 @@ +--- avogadro/qtplugins/plugindownloader/CMakeLists.txt.orig 2018-10-16 23:37:42 UTC ++++ avogadro/qtplugins/plugindownloader/CMakeLists.txt +@@ -20,4 +20,4 @@ avogadro_plugin(PluginDownloader + ) + + target_link_libraries(PluginDownloader LINK_PRIVATE ${Qt5Network_LIBRARIES} +- ${LIBARCHIVE_LIBRARIES} jsoncpp) ++ ${LIBARCHIVE_LIBRARIES} ${CMAKE_INSTALL_PREFIX}/lib/libjsoncpp.so) Property changes on: head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp (revision 482265) @@ -0,0 +1,29 @@ +--- avogadro/rendering/ambientocclusionspheregeometry.cpp.orig 2018-10-16 22:25:02 UTC ++++ avogadro/rendering/ambientocclusionspheregeometry.cpp +@@ -930,7 +930,7 @@ public: + // draw + glDrawRangeElements(GL_TRIANGLES, 0, static_cast(m_numVertices), + static_cast(m_numIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + m_vbo.release(); + m_ibo.release(); +@@ -1004,7 +1004,7 @@ public: + // draw + glDrawRangeElements(GL_TRIANGLES, 0, static_cast(m_numVertices), + static_cast(m_numIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + m_vbo.release(); + m_ibo.release(); +@@ -1326,7 +1326,7 @@ void AmbientOcclusionSphereGeometry::ren + // Render the loaded spheres using the shader and bound VBO. + glDrawRangeElements(GL_TRIANGLES, 0, static_cast(d->numberOfVertices), + static_cast(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Property changes on: head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp (revision 482265) @@ -0,0 +1,11 @@ +--- avogadro/rendering/cylindergeometry.cpp.orig 2018-10-16 22:23:29 UTC ++++ avogadro/rendering/cylindergeometry.cpp +@@ -223,7 +223,7 @@ void CylinderGeometry::render(const Came + // Render the loaded spheres using the shader and bound VBO. + glDrawRangeElements(GL_TRIANGLES, 0, static_cast(d->numberOfVertices), + static_cast(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Property changes on: head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp (revision 482265) @@ -0,0 +1,11 @@ +--- avogadro/rendering/meshgeometry.cpp.orig 2018-10-16 22:24:31 UTC ++++ avogadro/rendering/meshgeometry.cpp +@@ -171,7 +171,7 @@ void MeshGeometry::render(const Camera& + glDrawRangeElements(GL_TRIANGLES, 0, + static_cast(d->numberOfVertices - 1), + static_cast(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Property changes on: head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp =================================================================== --- head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp (nonexistent) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp (revision 482265) @@ -0,0 +1,11 @@ +--- avogadro/rendering/spheregeometry.cpp.orig 2018-10-16 22:26:03 UTC ++++ avogadro/rendering/spheregeometry.cpp +@@ -196,7 +196,7 @@ void SphereGeometry::render(const Camera + // Render the loaded spheres using the shader and bound VBO. + glDrawRangeElements(GL_TRIANGLES, 0, static_cast(d->numberOfVertices), + static_cast(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Property changes on: head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt =================================================================== --- head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt (nonexistent) +++ head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt (revision 482265) @@ -0,0 +1,7 @@ +--- thirdparty/CMakeLists.txt.orig 2018-10-16 23:17:59 UTC ++++ thirdparty/CMakeLists.txt +@@ -1,3 +1,3 @@ +-add_subdirectory(jsoncpp) ++#add_subdirectory(jsoncpp) + add_subdirectory(struct) + add_subdirectory(libgwavi) Property changes on: head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/pkg-descr =================================================================== --- head/science/avogadrolibs/pkg-descr (nonexistent) +++ head/science/avogadrolibs/pkg-descr (revision 482265) @@ -0,0 +1,24 @@ +Libraries that are a foundation of the Avogadro 2 project. + +Avogadro 2 is a chemical editor and visualization application, it is also a set +of reusable software libraries written in C++ using principles of modularity for +maximum reuse. The development of the first generation Avogadro application and +library is documented in our paper, and this remains the preferred method of +citation at present. The motivation for rewriting Avogadro, along with +improvements and changes made in Avogadro 2 are summarized in our Source +article. We provide a set of permissively licensed, open source, cross platform +software components in the Avogadro 2 libraries, along with an end-user +application with full source code, and binaries. + +The library features updated and improved rendering, where we built upon the +abstraction provided by previous API, but implemented a simple scene graph. This +makes use of features such as impostor sphere rendering, resulting in +significant rendering speed improvements while improving the quality of the +visualization. The core is built for scalability, looking to enable the analysis +of larger chemical structures and simulations being produced by computational +chemistry codes today. Emphasis has also been placed on making it even easier to +extend, using simple Python scripts to add simulation input capabilities, and +data input/output along with access to full-blown C++ plugin APIs where more +control is required. + +WWW: https://www.openchemistry.org/projects/avogadro2/ Property changes on: head/science/avogadrolibs/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/avogadrolibs/pkg-plist =================================================================== --- head/science/avogadrolibs/pkg-plist (nonexistent) +++ head/science/avogadrolibs/pkg-plist (revision 482265) @@ -0,0 +1,210 @@ +include/avogadro/core/array.h +include/avogadro/core/atom.h +include/avogadro/core/atomtyper-inline.h +include/avogadro/core/atomtyper.h +include/avogadro/core/avogadrocore.h +include/avogadro/core/avogadrocoreexport.h +include/avogadro/core/avospglib.h +include/avogadro/core/basisset.h +include/avogadro/core/bond.h +include/avogadro/core/color3f.h +include/avogadro/core/coordinateblockgenerator.h +include/avogadro/core/coordinateset.h +include/avogadro/core/crystaltools.h +include/avogadro/core/cube.h +include/avogadro/core/elements.h +include/avogadro/core/gaussianset.h +include/avogadro/core/gaussiansettools.h +include/avogadro/core/graph.h +include/avogadro/core/matrix.h +include/avogadro/core/mesh.h +include/avogadro/core/molecule.h +include/avogadro/core/mutex.h +include/avogadro/core/nameatomtyper.h +include/avogadro/core/residue.h +include/avogadro/core/ringperceiver.h +include/avogadro/core/slaterset.h +include/avogadro/core/slatersettools.h +include/avogadro/core/spacegroups.h +include/avogadro/core/symbolatomtyper.h +include/avogadro/core/types.h +include/avogadro/core/unitcell.h +include/avogadro/core/utilities.h +include/avogadro/core/variant-inline.h +include/avogadro/core/variant.h +include/avogadro/core/variantmap.h +include/avogadro/core/vector.h +include/avogadro/core/version.h +include/avogadro/io/avogadroioexport.h +include/avogadro/io/cjsonformat.h +include/avogadro/io/cmlformat.h +include/avogadro/io/dcdformat.h +include/avogadro/io/fileformat.h +include/avogadro/io/fileformatmanager.h +include/avogadro/io/gromacsformat.h +include/avogadro/io/lammpsformat.h +include/avogadro/io/mdlformat.h +include/avogadro/io/pdbformat.h +include/avogadro/io/trrformat.h +include/avogadro/io/vaspformat.h +include/avogadro/io/xyzformat.h +include/avogadro/molequeue/avogadromolequeueexport.h +include/avogadro/molequeue/batchjob.h +include/avogadro/molequeue/inputgenerator.h +include/avogadro/molequeue/inputgeneratordialog.h +include/avogadro/molequeue/inputgeneratorwidget.h +include/avogadro/molequeue/molequeuedialog.h +include/avogadro/molequeue/molequeuemanager.h +include/avogadro/molequeue/molequeuequeuelistmodel.h +include/avogadro/molequeue/molequeuewidget.h +include/avogadro/qtgui/avogadroqtguiexport.h +include/avogadro/qtgui/containerwidget.h +include/avogadro/qtgui/customelementdialog.h +include/avogadro/qtgui/elementtranslator.h +include/avogadro/qtgui/extensionplugin.h +include/avogadro/qtgui/filebrowsewidget.h +include/avogadro/qtgui/fileformatdialog.h +include/avogadro/qtgui/generichighlighter.h +include/avogadro/qtgui/hydrogentools.h +include/avogadro/qtgui/interfacescript.h +include/avogadro/qtgui/interfacewidget.h +include/avogadro/qtgui/meshgenerator.h +include/avogadro/qtgui/molecule.h +include/avogadro/qtgui/moleculemodel.h +include/avogadro/qtgui/multiviewwidget.h +include/avogadro/qtgui/periodictableview.h +include/avogadro/qtgui/persistentatom.h +include/avogadro/qtgui/persistentbond.h +include/avogadro/qtgui/pythonscript.h +include/avogadro/qtgui/rwmolecule.h 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