Date: Wed, 17 Oct 2018 01:02:16 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r482265 - in head/science: . avogadrolibs avogadrolibs/files Message-ID: <201810170102.w9H12GG4062627@repo.freebsd.org>
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Author: yuri Date: Wed Oct 17 01:02:16 2018 New Revision: 482265 URL: https://svnweb.freebsd.org/changeset/ports/482265 Log: New port: science/avogadrolibs: Avogadro2 libraries for chemical editor and visualization applications Added: head/science/avogadrolibs/ - copied from r482264, head/science/avogadro/ head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt (contents, props changed) head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt (contents, props changed) head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp (contents, props changed) head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp (contents, props changed) head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp (contents, props changed) head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp (contents, props changed) head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt (contents, props changed) Deleted: head/science/avogadrolibs/files/patch-CMakeLists.txt head/science/avogadrolibs/files/patch-libavogadro__src__camera.cpp head/science/avogadrolibs/files/patch-libavogadro__src__glpainter_p.cpp head/science/avogadrolibs/files/patch-libavogadro__src__glwidget.cpp head/science/avogadrolibs/files/patch-libavogadro__src__tools__selectrotatetool.cpp head/science/avogadrolibs/files/patch-libavogadro_src_extensions_crystallography_crystallographyextension.cpp Modified: head/science/Makefile head/science/avogadrolibs/Makefile head/science/avogadrolibs/distinfo head/science/avogadrolibs/pkg-descr head/science/avogadrolibs/pkg-plist Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/Makefile Wed Oct 17 01:02:16 2018 (r482265) @@ -29,6 +29,7 @@ SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro + SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve SUBDIR += bft Modified: head/science/avogadrolibs/Makefile ============================================================================== --- head/science/avogadro/Makefile Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadrolibs/Makefile Wed Oct 17 01:02:16 2018 (r482265) @@ -1,66 +1,28 @@ -# Created by: Troels Kofoed Jacobsen <tkjacobsen@gmail.com> # $FreeBSD$ -PORTNAME= avogadro -PORTVERSION= 1.1.1 -PORTREVISION= 16 +PORTNAME= avogadrolibs +DISTVERSION= 1.91.0 CATEGORIES= science -MASTER_SITES= SF -MAINTAINER= kde@FreeBSD.org -COMMENT= Advanced molecular editor and viewer +MAINTAINER= yuri@FreeBSD.org +COMMENT= Avogadro2 libraries for chemical editor and visualization applications -LICENSE= GPLv2+ -LICENSE_FILE= ${WRKSRC}/COPYING +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE -BROKEN_armv6= fails to compile: eigen2/Eigen/src/Core/Assign.h: you mixed different numeric types in 'Eigen::ei_static_assert<false>' -BROKEN_armv7= fails to compile: eigen2/Eigen/src/Core/Assign.h: you mixed different numeric types in 'Eigen::ei_static_assert<false>' +LIB_DEPENDS= libjsoncpp.so:devel/jsoncpp \ + libMoleQueueClient.so:misc/molequeue \ + libmsym.so:science/libmsym \ + libsymspg.so:science/spglib -LIB_DEPENDS= libopenbabel.so:science/openbabel - -# We need to add a RUN_DEPENDS on eigen2, as the cmake file shiped with -# avogadro to use it, contains 'find_package(Eigen2 REQUIRED)'. -USES= cmake desktop-file-utils eigen:2,build,run pkgconfig qt:4 tar:bzip2 -USE_GL= glu gl -USE_QT= gui network opengl \ - linguisttools_build moc_build qmake_build rcc_build uic_build -CMAKE_ARGS= -DENABLE_GLSL=OFF \ - -DQT_MKSPECS_RELATIVE=share/qt4/mkspecs +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 -CFLAGS+= -idirafter ${LOCALBASE}/include/eigen2 \ - -idirafter ${LOCALBASE}/include \ - -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib - -OPTIONS_DEFINE= PYTHON -OPTIONS_DEFAULT=PYTHON -OPTIONS_SUB= yes - -PYTHON_USES= python:2.7 -PYTHON_BUILD_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}sip>0:devel/py-sip@${PY_FLAVOR} -PYTHON_LIB_DEPENDS= ${PY_BOOST} -PYTHON_RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}sip>0:devel/py-sip@${PY_FLAVOR} -PYTHON_CMAKE_ON= -DENABLE_PYTHON=ON \ - -DPYTHON_INCLUDE_DIR:PATH=${WRKDIR}/include/${PYTHON_VERSION} -PYTHON_CMAKE_OFF= -DENABLE_PYTHON=OFF - -post-patch: - @${REINPLACE_CMD} -e \ - '/FLAGS_RELEASE/s|^|#| ; \ - /PC_FILES/s|$${LIB_INSTALL_DIR}|libdata|' ${WRKSRC}/CMakeLists.txt - @${REINPLACE_CMD} -e \ - 's|share/man|man|' ${WRKSRC}/doc/CMakeLists.txt - -pre-configure-PYTHON-on: - @${MKDIR} ${WRKDIR}/include/${PYTHON_VERSION} - @${FIND} ${PYTHON_INCLUDEDIR} ! -name "pyport.h" -type f \ - -maxdepth 1 | ${XARGS} -J % ${LN} -sf % \ - ${WRKDIR}/include/${PYTHON_VERSION} - @${SED} -e 's|^#ifdef _PY_PORT_CTYPE_UTF8_ISSUE|#if 0|' \ - ${PYTHON_INCLUDEDIR}/pyport.h > \ - ${WRKDIR}/include/${PYTHON_VERSION}/pyport.h +post-install: + @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include <bsd.port.mk> Modified: head/science/avogadrolibs/distinfo ============================================================================== --- head/science/avogadro/distinfo Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadrolibs/distinfo Wed Oct 17 01:02:16 2018 (r482265) @@ -1,2 +1,3 @@ -SHA256 (avogadro-1.1.1.tar.bz2) = fe6f7bdea17a27a20be25b70d975145999aae9d90ef320217af2bc4d6e7a0a14 -SIZE (avogadro-1.1.1.tar.bz2) = 11118046 +TIMESTAMP = 1539728298 +SHA256 (OpenChemistry-avogadrolibs-1.91.0_GH0.tar.gz) = 752933c26b46dfbf12f7537b1f8dd9960a4fd29f0cccbed5b868b00474bb42af +SIZE (OpenChemistry-avogadrolibs-1.91.0_GH0.tar.gz) = 2706319 Added: head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_qtplugins_importpqr_CMakeLists.txt Wed Oct 17 01:02:16 2018 (r482265) @@ -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}) Added: head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_qtplugins_plugindownloader_CMakeLists.txt Wed Oct 17 01:02:16 2018 (r482265) @@ -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) Added: head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_ambientocclusionspheregeometry.cpp Wed Oct 17 01:02:16 2018 (r482265) @@ -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<GLuint>(m_numVertices), + static_cast<GLsizei>(m_numIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(NULL)); ++ (const GLvoid*)nullptr); + + m_vbo.release(); + m_ibo.release(); +@@ -1004,7 +1004,7 @@ public: + // draw + glDrawRangeElements(GL_TRIANGLES, 0, static_cast<GLuint>(m_numVertices), + static_cast<GLsizei>(m_numIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(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<GLuint>(d->numberOfVertices), + static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Added: head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_cylindergeometry.cpp Wed Oct 17 01:02:16 2018 (r482265) @@ -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<GLuint>(d->numberOfVertices), + static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Added: head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_meshgeometry.cpp Wed Oct 17 01:02:16 2018 (r482265) @@ -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<GLuint>(d->numberOfVertices - 1), + static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Added: head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-avogadro_rendering_spheregeometry.cpp Wed Oct 17 01:02:16 2018 (r482265) @@ -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<GLuint>(d->numberOfVertices), + static_cast<GLsizei>(d->numberOfIndices), GL_UNSIGNED_INT, +- reinterpret_cast<const GLvoid*>(NULL)); ++ (const GLvoid*)nullptr); + + d->vbo.release(); + d->ibo.release(); Added: head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/avogadrolibs/files/patch-thirdparty_CMakeLists.txt Wed Oct 17 01:02:16 2018 (r482265) @@ -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) Modified: head/science/avogadrolibs/pkg-descr ============================================================================== --- head/science/avogadro/pkg-descr Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadrolibs/pkg-descr Wed Oct 17 01:02:16 2018 (r482265) @@ -1,6 +1,24 @@ -Avogadro is an advanced molecular editor designed for cross-platform use in -computational chemistry, molecular modeling, bioinformatics, materials science, -and related areas. It offers flexible rendering and a powerful plugin -architecture. +Libraries that are a foundation of the Avogadro 2 project. -WWW: http://avogadro.cc/ +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/ Modified: head/science/avogadrolibs/pkg-plist ============================================================================== --- head/science/avogadro/pkg-plist Tue Oct 16 22:58:17 2018 (r482264) +++ head/science/avogadrolibs/pkg-plist Wed Oct 17 01:02:16 2018 (r482265) @@ -1,1150 +1,210 @@ -bin/avogadro -bin/avopkg -include/avogadro/animation.h -include/avogadro/atom.h -include/avogadro/bond.h -include/avogadro/camera.h -include/avogadro/color.h -include/avogadro/color3f.h -include/avogadro/colorbutton.h -include/avogadro/cube.h -include/avogadro/dockextension.h -include/avogadro/dockwidget.h -include/avogadro/elementtranslator.h -include/avogadro/engine.h -include/avogadro/extension.h -include/avogadro/fragment.h -include/avogadro/glhit.h -include/avogadro/global.h -include/avogadro/glwidget.h -include/avogadro/idlist.h -include/avogadro/mesh.h -include/avogadro/meshgenerator.h -include/avogadro/molecule.h -include/avogadro/moleculefile.h -include/avogadro/navigate.h -include/avogadro/neighborlist.h -include/avogadro/obeigenconv.h -include/avogadro/painter.h -include/avogadro/painterdevice.h -include/avogadro/periodictableview.h -include/avogadro/plotaxis.h -include/avogadro/plotobject.h -include/avogadro/plotpoint.h -include/avogadro/plotwidget.h -include/avogadro/plugin.h -include/avogadro/pluginmanager.h -include/avogadro/primitive.h -include/avogadro/primitivelist.h -include/avogadro/protein.h -%%PYTHON%%include/avogadro/pythonerror.h -%%PYTHON%%include/avogadro/pythoninterpreter.h -%%PYTHON%%include/avogadro/pythonscript.h -include/avogadro/residue.h -include/avogadro/textmatrixeditor.h -include/avogadro/tool.h -include/avogadro/toolgroup.h -include/avogadro/undosequence.h -include/avogadro/zmatrix.h -lib/avogadro/1_1/AvogadroUse.cmake -lib/avogadro/1_1/cmake/FindEigen2.cmake -lib/avogadro/1_1/cmake/FindEigen3.cmake -lib/avogadro/1_1/cmake/FindGLEW.cmake -lib/avogadro/1_1/colors/atomindexcolor.so -lib/avogadro/1_1/colors/chargecolor.so -lib/avogadro/1_1/colors/customcolor.so -lib/avogadro/1_1/colors/distancecolor.so -lib/avogadro/1_1/colors/residuecolor.so -lib/avogadro/1_1/colors/smartscolor.so -lib/avogadro/1_1/engines/axesengine.so -lib/avogadro/1_1/engines/cartoonengine.so -lib/avogadro/1_1/engines/dipoleengine.so -lib/avogadro/1_1/engines/forceengine.so -lib/avogadro/1_1/engines/hbondengine.so -lib/avogadro/1_1/engines/labelengine.so -lib/avogadro/1_1/engines/polygonengine.so -lib/avogadro/1_1/engines/qtaimengine.so -lib/avogadro/1_1/engines/ribbonengine.so -lib/avogadro/1_1/engines/ringengine.so -lib/avogadro/1_1/engines/simplewireengine.so -lib/avogadro/1_1/engines/sphereengine.so -lib/avogadro/1_1/engines/stickengine.so -lib/avogadro/1_1/engines/surfaceengine.so -lib/avogadro/1_1/engines/wireengine.so -lib/avogadro/1_1/extensions/animationextension.so -lib/avogadro/1_1/extensions/cartesianextension.so -lib/avogadro/1_1/extensions/crystallographyextension.so -lib/avogadro/1_1/extensions/fileimportextension.so -lib/avogadro/1_1/extensions/forcefieldextension.so -lib/avogadro/1_1/extensions/gamessextension.so -lib/avogadro/1_1/extensions/gl2psextension.so -lib/avogadro/1_1/extensions/h2methylextension.so -lib/avogadro/1_1/extensions/hydrogensextension.so -lib/avogadro/1_1/extensions/inputfileextension.so -lib/avogadro/1_1/extensions/insertdnaextension.so -lib/avogadro/1_1/extensions/insertfragmentextension.so -lib/avogadro/1_1/extensions/insertpeptideextension.so -lib/avogadro/1_1/extensions/invertchiralextension.so -lib/avogadro/1_1/extensions/molecularpropextension.so -lib/avogadro/1_1/extensions/networkfetchextension.so -lib/avogadro/1_1/extensions/orbitalextension.so -lib/avogadro/1_1/extensions/povrayextension.so -lib/avogadro/1_1/extensions/propextension.so -%%PYTHON%%lib/avogadro/1_1/extensions/pythonterminal.so -lib/avogadro/1_1/extensions/qtaimextension.so -lib/avogadro/1_1/extensions/selectextension.so -lib/avogadro/1_1/extensions/spectraextension.so -lib/avogadro/1_1/extensions/supercellextension.so -lib/avogadro/1_1/extensions/surfaceextension.so -lib/avogadro/1_1/extensions/swcntbuilderextension.so -lib/avogadro/1_1/extensions/vibrationextension.so -lib/avogadro/1_1/tools/aligntool.so -lib/avogadro/1_1/tools/autoopttool.so -lib/avogadro/1_1/tools/autorotatetool.so -lib/avogadro/1_1/tools/bondcentrictool.so -lib/avogadro/1_1/tools/clickmeasuretool.so -lib/avogadro/1_1/tools/drawtool.so -lib/avogadro/1_1/tools/manipulatetool.so -lib/avogadro/1_1/tools/selectrotatetool.so -lib/avogadro/AvogadroConfig.cmake -lib/avogadro/AvogadroConfigVersion.cmake -lib/avogadro/AvogadroTargets-%%CMAKE_BUILD_TYPE%%.cmake -lib/avogadro/AvogadroTargets.cmake -lib/libavogadro.so -lib/libavogadro.so.1 -lib/libavogadro.so.1.1.1 -lib/libavogadro_OpenQube.so -lib/libavogadro_OpenQube.so.0 -lib/libavogadro_OpenQube.so.0.1.0 -%%PYTHON%%%%PYTHON_SITELIBDIR%%/Avogadro.so -libdata/pkgconfig/avogadro.pc -man/man1/avogadro.1.gz -man/man1/avopkg.1.gz -share/applications/avogadro.desktop -%%DATADIR%%/builder/amino/d-ala.zmat -%%DATADIR%%/builder/amino/d-arg.zmat -%%DATADIR%%/builder/amino/d-asn.zmat -%%DATADIR%%/builder/amino/d-asp.zmat -%%DATADIR%%/builder/amino/d-cys.zmat -%%DATADIR%%/builder/amino/d-gln.zmat -%%DATADIR%%/builder/amino/d-glu.zmat -%%DATADIR%%/builder/amino/d-his.zmat -%%DATADIR%%/builder/amino/d-ile.zmat -%%DATADIR%%/builder/amino/d-leu.zmat -%%DATADIR%%/builder/amino/d-lys.zmat -%%DATADIR%%/builder/amino/d-met.zmat -%%DATADIR%%/builder/amino/d-phe.zmat -%%DATADIR%%/builder/amino/d-pro.zmat -%%DATADIR%%/builder/amino/d-ser.zmat 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-%%DATADIR%%/fragments/amides/N_N-dimethylformamide.cml -%%DATADIR%%/fragments/amides/acetamide.cml -%%DATADIR%%/fragments/amides/ethyl_carbamate.cml -%%DATADIR%%/fragments/amides/oxamide.cml -%%DATADIR%%/fragments/amines/1H-azepine.cml -%%DATADIR%%/fragments/amines/2-aminopropane.cml -%%DATADIR%%/fragments/amines/S-sec-butylamine.cml -%%DATADIR%%/fragments/amines/ammonia.cml -%%DATADIR%%/fragments/amines/azepane.cml -%%DATADIR%%/fragments/amines/diethylamine.cml -%%DATADIR%%/fragments/amines/dimethylamine.cml -%%DATADIR%%/fragments/amines/ethylamine.cml -%%DATADIR%%/fragments/amines/methylamine.cml -%%DATADIR%%/fragments/amines/piperazine.cml -%%DATADIR%%/fragments/amines/piperidine.cml -%%DATADIR%%/fragments/amines/pyrrolidine.cml -%%DATADIR%%/fragments/amines/tert-butylamine.cml -%%DATADIR%%/fragments/amines/triethylamine.cml -%%DATADIR%%/fragments/amines/triethylenediamine.cml -%%DATADIR%%/fragments/amines/trimethylamine.cml *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***
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