ports/177935: science/avogadro: Update to version 1.1.0

KATO Tsuguru tkato432 at yahoo.com
Wed Apr 17 18:10:09 UTC 2013 

>Number:         177935
>Category:       ports
>Synopsis:       science/avogadro: Update to version 1.1.0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Wed Apr 17 18:10:09 UTC 2013
>Closed-Date:
>Last-Modified:
>Originator:     KATO Tsuguru
>Release:        FreeBSD 7.4-RELEASE-p11 i386
>Organization:
>Environment:
>Description:
- Update to version 1.1.0

Remove file:
files/patch-libavogadro__CMakeLists.txt

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/science/avogadro/Makefile science/avogadro/Makefile
--- /usr/ports/science/avogadro/Makefile	2013-04-17 02:44:45.000000000 +0900
+++ science/avogadro/Makefile	2013-04-17 16:47:59.000000000 +0900
@@ -2,29 +2,34 @@
 # $FreeBSD: head/science/avogadro/Makefile 315830 2013-04-16 16:00:08Z rene $
 
 PORTNAME=	avogadro
-PORTVERSION=	1.0.3
-PORTREVISION=	2
+PORTVERSION=	1.1.0
 CATEGORIES=	science
 MASTER_SITES=	SF
 
 MAINTAINER=	ports at FreeBSD.org
 COMMENT=	Advanced molecular editor and viewer
 
+LICENSE=	GPLv2 # (or later)
+
 BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/eigen2.pc:${PORTSDIR}/math/eigen2
 LIB_DEPENDS=	openbabel:${PORTSDIR}/science/openbabel
 
-USE_LDCONFIG=	yes
+OPTIONS_DEFINE=	PYTHON
+OPTIONS_DEFAULT=PYTHON
+
 USE_BZIP2=	yes
-USE_GL=		glu
-USE_QT4=	gui opengl network linguist_build \
-		qmake_build moc_build rcc_build uic_build
 USES=		cmake
+USE_GL=		glu
+USE_QT4=	gui network opengl \
+		linguist_build moc_build qmake_build rcc_build uic_build
+USE_PKGCONFIG=	build
 CMAKE_ARGS=	-DENABLE_GLSL=OFF \
 		-DQT_MKSPECS_RELATIVE=share/qt4/mkspecs
-USE_GCC=	4.4+
+USE_LDCONFIG=	yes
 MAKE_JOBS_SAFE=	yes
 
-OPTIONS_DEFINE=	PYTHON
+CFLAGS+=	-idirafter ${LOCALBASE}/include
+LDFLAGS+=	-L${LOCALBASE}/lib
 
 MAN1=		avogadro.1 avopkg.1
 
@@ -35,9 +40,9 @@
 USE_PYTHON=	-2.7
 BUILD_DEPENDS+=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}sip>0:${PORTSDIR}/devel/py-sip
+LIB_DEPENDS+=	boost_python:${PORTSDIR}/devel/boost-python-libs
 RUN_DEPENDS+=	${PYNUMPY} \
 		${PYTHON_PKGNAMEPREFIX}sip>0:${PORTSDIR}/devel/py-sip
-LIB_DEPENDS+=	boost_python:${PORTSDIR}/devel/boost-python-libs
 PLIST_SUB+=	PYTHON=""
 .else
 CMAKE_ARGS+=	-DENABLE_PYTHON=OFF
@@ -45,6 +50,10 @@
 .endif
 
 post-patch:
-	@${REINPLACE_CMD} 's|share/man|man|' ${WRKSRC}/doc/CMakeLists.txt
+	@${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
 
 .include <bsd.port.mk>
diff -urN /usr/ports/science/avogadro/distinfo science/avogadro/distinfo
--- /usr/ports/science/avogadro/distinfo	2012-11-08 06:58:54.000000000 +0900
+++ science/avogadro/distinfo	2013-04-17 03:17:16.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (avogadro-1.0.3.tar.bz2) = efb6fda223da3c027436f0c218a47ce804f7469c58b41134230e9ebad1c98468
-SIZE (avogadro-1.0.3.tar.bz2) = 4971989
+SHA256 (avogadro-1.1.0.tar.bz2) = 6b4eaf57ae52bf43df9b103c77e6abae71e067053d5c99f82acbce9855ecceb0
+SIZE (avogadro-1.1.0.tar.bz2) = 10741835
diff -urN /usr/ports/science/avogadro/files/patch-libavogadro__CMakeLists.txt science/avogadro/files/patch-libavogadro__CMakeLists.txt
--- /usr/ports/science/avogadro/files/patch-libavogadro__CMakeLists.txt	2012-12-01 17:12:24.000000000 +0900
+++ science/avogadro/files/patch-libavogadro__CMakeLists.txt	1970-01-01 09:00:00.000000000 +0900
@@ -1,12 +0,0 @@
---- libavogadro/CMakeLists.txt.orig	2012-11-26 21:38:12.000000000 +0100
-+++ libavogadro/CMakeLists.txt	2012-11-26 21:39:47.000000000 +0100
-@@ -18,7 +18,8 @@
-   # Assume all MOC stuff is in the headers, replace .cpp and use qt4_wrap_cpp
-   # We should probably scan the header to verify the Q_OBJECT macro is used
-   string(REPLACE ".cpp" ".h" hdr_list "${src_list}")
--  qt4_wrap_cpp(moc_files ${hdr_list})
-+  qt4_wrap_cpp(moc_files ${hdr_list} OPTIONS
-+      -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED)
-   # Now sort out the ui and qrc files, process them as appropriate
-   set(ui_plugin_files)
-   set(qrc_plugin_files)
diff -urN /usr/ports/science/avogadro/pkg-plist science/avogadro/pkg-plist
--- /usr/ports/science/avogadro/pkg-plist	2012-11-08 06:58:54.000000000 +0900
+++ science/avogadro/pkg-plist	2013-04-17 16:48:45.000000000 +0900
@@ -8,6 +8,8 @@
 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
@@ -22,6 +24,7 @@
 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
@@ -38,70 +41,82 @@
 %%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_0/AvogadroBuildSettings.cmake
-lib/avogadro/1_0/AvogadroLibraryDeps.cmake
-lib/avogadro/1_0/AvogadroUse.cmake
-lib/avogadro/1_0/cmake/FindEigen2.cmake
-lib/avogadro/1_0/cmake/FindGLEW.cmake
-lib/avogadro/1_0/colors/atomindexcolor.so
-lib/avogadro/1_0/colors/chargecolor.so
-lib/avogadro/1_0/colors/customcolor.so
-lib/avogadro/1_0/colors/distancecolor.so
-lib/avogadro/1_0/colors/residuecolor.so
-lib/avogadro/1_0/engines/axesengine.so
-lib/avogadro/1_0/engines/cartoonengine.so
-lib/avogadro/1_0/engines/dipoleengine.so
-lib/avogadro/1_0/engines/forceengine.so
-lib/avogadro/1_0/engines/hbondengine.so
-lib/avogadro/1_0/engines/labelengine.so
-lib/avogadro/1_0/engines/overlayengine.so
-lib/avogadro/1_0/engines/polygonengine.so
-lib/avogadro/1_0/engines/ribbonengine.so
-lib/avogadro/1_0/engines/ringengine.so
-lib/avogadro/1_0/engines/simplewireengine.so
-lib/avogadro/1_0/engines/sphereengine.so
-lib/avogadro/1_0/engines/stickengine.so
-lib/avogadro/1_0/engines/surfaceengine.so
-lib/avogadro/1_0/engines/wireengine.so
-lib/avogadro/1_0/extensions/animationextension.so
-lib/avogadro/1_0/extensions/fileimportextension.so
-lib/avogadro/1_0/extensions/forcefieldextension.so
-lib/avogadro/1_0/extensions/gamessextension.so
-lib/avogadro/1_0/extensions/h2methylextension.so
-lib/avogadro/1_0/extensions/hydrogenextension.so
-lib/avogadro/1_0/extensions/inputfileextension.so
-lib/avogadro/1_0/extensions/insertfragmentextension.so
-lib/avogadro/1_0/extensions/insertpeptideextension.so
-lib/avogadro/1_0/extensions/molecularpropextension.so
-lib/avogadro/1_0/extensions/networkfetchextension.so
-lib/avogadro/1_0/extensions/povrayextension.so
-lib/avogadro/1_0/extensions/propextension.so
-%%PYTHON%%lib/avogadro/1_0/extensions/pythonterminal.so
-lib/avogadro/1_0/extensions/selectextension.so
-lib/avogadro/1_0/extensions/spectraextension.so
-lib/avogadro/1_0/extensions/supercellextension.so
-lib/avogadro/1_0/extensions/surfaceextension.so
-lib/avogadro/1_0/extensions/unitcellextension.so
-lib/avogadro/1_0/extensions/vibrationextension.so
-lib/avogadro/1_0/tools/aligntool.so
-lib/avogadro/1_0/tools/autoopttool.so
-lib/avogadro/1_0/tools/autorotatetool.so
-lib/avogadro/1_0/tools/bondcentrictool.so
-lib/avogadro/1_0/tools/clickmeasuretool.so
-lib/avogadro/1_0/tools/drawtool.so
-lib/avogadro/1_0/tools/manipulatetool.so
-lib/avogadro/1_0/tools/navigatetool.so
-lib/avogadro/1_0/tools/selectrotatetool.so
+lib/avogadro/1_1/AvogadroUse.cmake
+lib/avogadro/1_1/cmake/FindEigen2.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/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-release.cmake
+lib/avogadro/AvogadroTargets.cmake
 lib/libavogadro.so
 lib/libavogadro.so.1
-lib/libavogadro.so.1.0.3
+lib/libavogadro.so.1.1.0
+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
+share/applications/avogadro.desktop
 %%DATADIR%%/builder/amino/d-ala.zmat
 %%DATADIR%%/builder/amino/d-arg.zmat
 %%DATADIR%%/builder/amino/d-asn.zmat
@@ -143,18 +158,574 @@
 %%DATADIR%%/builder/amino/l-trp.zmat
 %%DATADIR%%/builder/amino/l-tyr.zmat
 %%DATADIR%%/builder/amino/l-val.zmat
+%%DATADIR%%/crystals/antimonides/AlSb.cif
+%%DATADIR%%/crystals/antimonides/GaSb.cif
+%%DATADIR%%/crystals/antimonides/InSb.cif
+%%DATADIR%%/crystals/arsenides/AlAs.cif
+%%DATADIR%%/crystals/arsenides/BAs.cif
+%%DATADIR%%/crystals/arsenides/Co.87Fe.11Ni.13As3-Skutterudite.cif
+%%DATADIR%%/crystals/arsenides/CoAs3-Skutterudite.cif
+%%DATADIR%%/crystals/arsenides/GaAs.cif
+%%DATADIR%%/crystals/arsenides/InAs.cif
+%%DATADIR%%/crystals/arsenides/NiAs-Nickeline.cif
+%%DATADIR%%/crystals/carbides/SiC-2H-Moissanite.cif
+%%DATADIR%%/crystals/carbides/SiC-3C-beta.cif
+%%DATADIR%%/crystals/carbides/SiC-6H-alpha.cif
+%%DATADIR%%/crystals/carbides/SiC-Moissanite.cif
+%%DATADIR%%/crystals/carbides/SiC.cif
+%%DATADIR%%/crystals/carbides/W2C.cif
+%%DATADIR%%/crystals/carbides/WC.cif
+%%DATADIR%%/crystals/carbonates/CaCO3-Calcite.cif
+%%DATADIR%%/crystals/carbonates/CaMgC2O6-Dolomite.cif
+%%DATADIR%%/crystals/carbonates/Li2CO3-Zabuyelite.cif
+%%DATADIR%%/crystals/carbonates/MgCO3-Magnesite.cif
+%%DATADIR%%/crystals/carbonates/Na2CO3-Natrite.cif
+%%DATADIR%%/crystals/clays/Al2Si2O9H4-Dickite.cif
+%%DATADIR%%/crystals/clays/Al2Si2O9H4-Kaolinite.cif
+%%DATADIR%%/crystals/clays/Al2Si2O9H4-Nacrite.cif
+%%DATADIR%%/crystals/clays/Al2Si4O12Ca0.5-Montmorillonite.cif
+%%DATADIR%%/crystals/clays/Al4KSi2O12-Illite.cif
+%%DATADIR%%/crystals/clays/AlSi2O6H-Pyrophyllite.cif
+%%DATADIR%%/crystals/clays/Fe2.25Cl0.5H2.75-Fougerite.cif
+%%DATADIR%%/crystals/clays/FeSi2O6H-Nontronite.cif
+%%DATADIR%%/crystals/clays/Lepidolite.cif
+%%DATADIR%%/crystals/clays/Mg2Al2SiO9H4-Amesite.cif
+%%DATADIR%%/crystals/clays/Mg3(O12Si4)H2-Vermiculite.cif
+%%DATADIR%%/crystals/clays/Mg4Si6O22.82H13.64-Sepiolite.cif
+%%DATADIR%%/crystals/clays/Mn1.854Fe1.656Mg0.537Si0.953O9H4-Guidottiite.cif
+%%DATADIR%%/crystals/clays/Zn2SiO5H2-Hemimorphite.cif
+%%DATADIR%%/crystals/elements/Ac-Actinium.cif
+%%DATADIR%%/crystals/elements/Ag-Silver.cif
+%%DATADIR%%/crystals/elements/Al-Aluminum.cif
+%%DATADIR%%/crystals/elements/Am-Americium.cif
+%%DATADIR%%/crystals/elements/Ar-Argon.cif
+%%DATADIR%%/crystals/elements/As-Arsenic.cif
+%%DATADIR%%/crystals/elements/As-Arsenolamprite.cif
+%%DATADIR%%/crystals/elements/Au-Gold.cif
+%%DATADIR%%/crystals/elements/B-Boron.cif
+%%DATADIR%%/crystals/elements/Ba-Barium.cif
+%%DATADIR%%/crystals/elements/Be-Beryllium.cif
+%%DATADIR%%/crystals/elements/Bi-Bismuth.cif
+%%DATADIR%%/crystals/elements/Br-Bromine.cif
+%%DATADIR%%/crystals/elements/C-Diamond.cif
+%%DATADIR%%/crystals/elements/C-Graphite.cif
+%%DATADIR%%/crystals/elements/C-Lonsdaleite.cif
+%%DATADIR%%/crystals/elements/Ca-Calcium-alpha.cif
+%%DATADIR%%/crystals/elements/Ca-Calcium-beta.cif
+%%DATADIR%%/crystals/elements/Ca-Calcium-gamma.cif
+%%DATADIR%%/crystals/elements/Cd-Cadmium.cif
+%%DATADIR%%/crystals/elements/Ce-Cerium.cif
+%%DATADIR%%/crystals/elements/Cl-Chlorine.cif
+%%DATADIR%%/crystals/elements/Co-Cobalt.cif
+%%DATADIR%%/crystals/elements/Cr-Chromium.cif
+%%DATADIR%%/crystals/elements/Cs-Cesium.cif
+%%DATADIR%%/crystals/elements/Cu-Copper.cif
+%%DATADIR%%/crystals/elements/Dy-Dysprosium.cif
+%%DATADIR%%/crystals/elements/Er-Erbium.cif
+%%DATADIR%%/crystals/elements/Eu-Europium.cif
+%%DATADIR%%/crystals/elements/Fe-Iron-alpha.cif
+%%DATADIR%%/crystals/elements/Fe-Iron-beta.cif
+%%DATADIR%%/crystals/elements/Fe-Iron-delta.cif
+%%DATADIR%%/crystals/elements/Fe-Iron-gamma.cif
+%%DATADIR%%/crystals/elements/Ga-Gallium.cif
+%%DATADIR%%/crystals/elements/Gd-Gadolinium.cif
+%%DATADIR%%/crystals/elements/Ge-Germanium.cif
+%%DATADIR%%/crystals/elements/He-Helium.cif
+%%DATADIR%%/crystals/elements/Hf-Hafnium.cif
+%%DATADIR%%/crystals/elements/Ho-Holmium.cif
+%%DATADIR%%/crystals/elements/I-Iodine.cif
+%%DATADIR%%/crystals/elements/In-Indium.cif
+%%DATADIR%%/crystals/elements/Ir-Iridium.cif
+%%DATADIR%%/crystals/elements/K-Potassium.cif
+%%DATADIR%%/crystals/elements/Kr-Krypton.cif
+%%DATADIR%%/crystals/elements/La-Lanthanum.cif
+%%DATADIR%%/crystals/elements/Li-Lithium.cif
+%%DATADIR%%/crystals/elements/Lu-Lutetium.cif
+%%DATADIR%%/crystals/elements/Mg-Magnesium.cif
+%%DATADIR%%/crystals/elements/Mn-Manganese-alpha.cif
+%%DATADIR%%/crystals/elements/Mn-Manganese-delta.cif
+%%DATADIR%%/crystals/elements/Mn-Manganese-gamma.cif
+%%DATADIR%%/crystals/elements/Mo-Molybdenum.cif
+%%DATADIR%%/crystals/elements/N-Nitrogen.cif
+%%DATADIR%%/crystals/elements/Na-Sodium.cif
+%%DATADIR%%/crystals/elements/Nb-Niobium.cif
+%%DATADIR%%/crystals/elements/Nd-Neodymium.cif
+%%DATADIR%%/crystals/elements/Ne-Neon.cif
+%%DATADIR%%/crystals/elements/Ni-Nickel.cif
+%%DATADIR%%/crystals/elements/Np-Neptunium-alpha.cif
+%%DATADIR%%/crystals/elements/Np-Neptunium-beta.cif
+%%DATADIR%%/crystals/elements/Np-Neptunium-gamma.cif
+%%DATADIR%%/crystals/elements/Os-Osmium.cif
+%%DATADIR%%/crystals/elements/P-Phosphorus-black.cif
+%%DATADIR%%/crystals/elements/P-Phosphorus.cif
+%%DATADIR%%/crystals/elements/Pb-Lead.cif
+%%DATADIR%%/crystals/elements/Pd-Palladium.cif
+%%DATADIR%%/crystals/elements/Pr-Praseodymium.cif
+%%DATADIR%%/crystals/elements/Pt-Platinum.cif
+%%DATADIR%%/crystals/elements/Pu-Plutonium-alpha.cif
+%%DATADIR%%/crystals/elements/Pu-Plutonium-epsilon.cif
+%%DATADIR%%/crystals/elements/Pu-Plutonium-gamma.cif
+%%DATADIR%%/crystals/elements/Rb-Rubidium.cif
+%%DATADIR%%/crystals/elements/Re-Rhenium.cif
+%%DATADIR%%/crystals/elements/Rh-Rhodium.cif
+%%DATADIR%%/crystals/elements/Ru-Ruthenium.cif
+%%DATADIR%%/crystals/elements/S6-Sulfur.cif
+%%DATADIR%%/crystals/elements/S8-Sulfur-alpha.cif
+%%DATADIR%%/crystals/elements/S8-Sulfur-beta.cif
+%%DATADIR%%/crystals/elements/S8-Sulfur-gamma.cif
+%%DATADIR%%/crystals/elements/Sb-Antimony.cif
+%%DATADIR%%/crystals/elements/Sc-Scandium.cif
+%%DATADIR%%/crystals/elements/Se-Selenium.cif
+%%DATADIR%%/crystals/elements/Si-Silicon.cif
+%%DATADIR%%/crystals/elements/Sm-Samarium.cif
+%%DATADIR%%/crystals/elements/Sn-Tin-alpha.cif
+%%DATADIR%%/crystals/elements/Sn-Tin-beta.cif
+%%DATADIR%%/crystals/elements/Sr-Strontium.cif
+%%DATADIR%%/crystals/elements/Ta-Tantalum.cif
+%%DATADIR%%/crystals/elements/Tb-Terbium.cif
+%%DATADIR%%/crystals/elements/Te-Tellurium.cif
+%%DATADIR%%/crystals/elements/Th-Thorium.cif
+%%DATADIR%%/crystals/elements/Ti-Titanium-alpha.cif
+%%DATADIR%%/crystals/elements/Ti-Titanium-beta.cif
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+%%DATADIR%%/crystals/zeolites/ZON.cif
+%%DATADIR%%/crystals/zeolites/ZSM-5.cif
+%%DATADIR%%/fragments/alcohols/2-aminoethanol.cml
+%%DATADIR%%/fragments/alcohols/but-2-yne-1_4-diol.cml
+%%DATADIR%%/fragments/alcohols/cyclohexanol.cml
+%%DATADIR%%/fragments/alcohols/cyclopentanol.cml
+%%DATADIR%%/fragments/alcohols/ethane-1_2-diol.cml
 %%DATADIR%%/fragments/alcohols/ethanol.cml
 %%DATADIR%%/fragments/alcohols/methanol.cml
 %%DATADIR%%/fragments/alcohols/propan-1-ol.cml
 %%DATADIR%%/fragments/alcohols/propan-2-ol.cml
+%%DATADIR%%/fragments/alcohols/propane-1_2_3-triol.cml
 %%DATADIR%%/fragments/aldehydes/acetaldehyde.cml
 %%DATADIR%%/fragments/aldehydes/formaldehyde.cml
 %%DATADIR%%/fragments/alkanes/2-methylpropane.cml
+%%DATADIR%%/fragments/alkanes/butane.cml
+%%DATADIR%%/fragments/alkanes/decane.cml
+%%DATADIR%%/fragments/alkanes/dodecane.cml
+%%DATADIR%%/fragments/alkanes/eicosane.cml
 %%DATADIR%%/fragments/alkanes/ethane.cml
+%%DATADIR%%/fragments/alkanes/heptane.cml
+%%DATADIR%%/fragments/alkanes/hexadecane.cml
+%%DATADIR%%/fragments/alkanes/hexane.cml
 %%DATADIR%%/fragments/alkanes/methane.cml
+%%DATADIR%%/fragments/alkanes/nonane.cml
+%%DATADIR%%/fragments/alkanes/octane.cml
+%%DATADIR%%/fragments/alkanes/pentadecane.cml
+%%DATADIR%%/fragments/alkanes/pentane.cml
 %%DATADIR%%/fragments/alkanes/propane.cml
+%%DATADIR%%/fragments/alkanes/tetracosane.cml
+%%DATADIR%%/fragments/alkanes/tetradecane.cml
+%%DATADIR%%/fragments/alkanes/tridecane.cml
+%%DATADIR%%/fragments/alkanes/undecane.cml
+%%DATADIR%%/fragments/alkenes/2-methylbut-2-ene.cml
+%%DATADIR%%/fragments/alkenes/2-methylbuta-1_3-diene.cml
+%%DATADIR%%/fragments/alkenes/3E-penta-1_3-diene.cml
+%%DATADIR%%/fragments/alkenes/3Z-penta-1_3-diene.cml
+%%DATADIR%%/fragments/alkenes/3Z_3-ethylhepta-1_3-diene.cml
+%%DATADIR%%/fragments/alkenes/E-but-2-ene.cml
+%%DATADIR%%/fragments/alkenes/E-hept-2-ene.cml
+%%DATADIR%%/fragments/alkenes/E-hept-3-ene.cml
+%%DATADIR%%/fragments/alkenes/E-hex-2-ene.cml
+%%DATADIR%%/fragments/alkenes/E-hex-3-ene.cml
+%%DATADIR%%/fragments/alkenes/E-oct-2-ene.cml
+%%DATADIR%%/fragments/alkenes/E-oct-3-ene.cml
+%%DATADIR%%/fragments/alkenes/E-oct-4-ene.cml
+%%DATADIR%%/fragments/alkenes/E-pent-2-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-but-2-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-hept-2-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-hept-3-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-hex-2-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-hex-3-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-oct-2-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-oct-3-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-oct-4-ene.cml
+%%DATADIR%%/fragments/alkenes/Z-pent-2-ene.cml
 %%DATADIR%%/fragments/alkenes/but-1-ene.cml
 %%DATADIR%%/fragments/alkenes/ethene.cml
+%%DATADIR%%/fragments/alkenes/hept-1-ene.cml
+%%DATADIR%%/fragments/alkenes/hex-1-ene.cml
+%%DATADIR%%/fragments/alkenes/oct-1-ene.cml
+%%DATADIR%%/fragments/alkenes/pent-1-ene.cml
+%%DATADIR%%/fragments/alkenes/propene.cml
 %%DATADIR%%/fragments/alkynes/acetylene.cml
 %%DATADIR%%/fragments/alkynes/propyne.cml
 %%DATADIR%%/fragments/amides/N_N-dimethylacetamide.cml
@@ -162,10 +733,22 @@
 %%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
 %%DATADIR%%/fragments/amino_acids/D-alanine.cml
 %%DATADIR%%/fragments/amino_acids/D-allo-threonine.cml
 %%DATADIR%%/fragments/amino_acids/D-arginine.cml
@@ -209,19 +792,43 @@
 %%DATADIR%%/fragments/amino_acids/L-valine.cml
 %%DATADIR%%/fragments/amino_acids/glycine.cml
 %%DATADIR%%/fragments/aromatics/1H-indene.cml
+%%DATADIR%%/fragments/aromatics/1H-indole.cml
+%%DATADIR%%/fragments/aromatics/1_10-phenanthroline.cml
+%%DATADIR%%/fragments/aromatics/1_8-naphthyridine.cml
+%%DATADIR%%/fragments/aromatics/2H-chromene.cml
+%%DATADIR%%/fragments/aromatics/4H-chromene.cml
+%%DATADIR%%/fragments/aromatics/7H-purine.cml
+%%DATADIR%%/fragments/aromatics/9H-carbazole.cml
+%%DATADIR%%/fragments/aromatics/9H-fluorene.cml
+%%DATADIR%%/fragments/aromatics/9H-xanthene.cml
+%%DATADIR%%/fragments/aromatics/acenaphthene.cml
+%%DATADIR%%/fragments/aromatics/acenaphthenequinone.cml
+%%DATADIR%%/fragments/aromatics/acenaphthylene.cml
+%%DATADIR%%/fragments/aromatics/acridine.cml
 %%DATADIR%%/fragments/aromatics/aniline.cml
 %%DATADIR%%/fragments/aromatics/anisole.cml
 %%DATADIR%%/fragments/aromatics/anthracene.cml
 %%DATADIR%%/fragments/aromatics/benzaldehyde.cml
 %%DATADIR%%/fragments/aromatics/benzene.cml
+%%DATADIR%%/fragments/aromatics/benzofuran.cml
 %%DATADIR%%/fragments/aromatics/benzoic_acid.cml
+%%DATADIR%%/fragments/aromatics/benzothiophene.cml
 %%DATADIR%%/fragments/aromatics/benzoyl_chloride.cml
 %%DATADIR%%/fragments/aromatics/caffeine.cml
+%%DATADIR%%/fragments/aromatics/chromone.cml
+%%DATADIR%%/fragments/aromatics/cinnoline.cml
+%%DATADIR%%/fragments/aromatics/coumarin.cml
+%%DATADIR%%/fragments/aromatics/isoquinoline.cml
 %%DATADIR%%/fragments/aromatics/naphthalene.cml
 %%DATADIR%%/fragments/aromatics/nitrobenzene.cml
+%%DATADIR%%/fragments/aromatics/phenanthrene.cml
 %%DATADIR%%/fragments/aromatics/phenol.cml
+%%DATADIR%%/fragments/aromatics/phthalimide.cml
+%%DATADIR%%/fragments/aromatics/quinazoline.cml
+%%DATADIR%%/fragments/aromatics/quinoline.cml
+%%DATADIR%%/fragments/aromatics/tetralin.cml
 %%DATADIR%%/fragments/aromatics/toluene.cml
-%%DATADIR%%/fragments/buckminsterfullerene.cml
+%%DATADIR%%/fragments/aromatics/uric_acid.cml
 %%DATADIR%%/fragments/carbamides/urea.cml
 %%DATADIR%%/fragments/carbohydrates/d-allose.cml
 %%DATADIR%%/fragments/carbohydrates/d-altrose.cml
@@ -252,6 +859,8 @@
 %%DATADIR%%/fragments/carboxylic_acids/D-lactic_acid.cml
 %%DATADIR%%/fragments/carboxylic_acids/D-malic_acid.cml
 %%DATADIR%%/fragments/carboxylic_acids/D-tartaric_acid.cml
+%%DATADIR%%/fragments/carboxylic_acids/E-butanoic_acid.cml
+%%DATADIR%%/fragments/carboxylic_acids/E-butenedioic_acid.cml
 %%DATADIR%%/fragments/carboxylic_acids/L-ascorbic_acid.cml
 %%DATADIR%%/fragments/carboxylic_acids/L-lactic_acid.cml
 %%DATADIR%%/fragments/carboxylic_acids/L-malic_acid.cml
@@ -270,58 +879,82 @@
 %%DATADIR%%/fragments/coordination/5-square-pyramidal.cml
 %%DATADIR%%/fragments/coordination/5-trigonal-bipyramidal.cml
 %%DATADIR%%/fragments/coordination/6-octahedral.cml
-%%DATADIR%%/fragments/cyclic alkanes/adamantane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cubane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cyclobutane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cycloheptane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cyclohexane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cyclopentane.cml
-%%DATADIR%%/fragments/cyclic alkanes/cyclopropane.cml
-%%DATADIR%%/fragments/cyclic alkanes/norbornane.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-allopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-arabinopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-fucopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-galactopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-galacturonopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-glucopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-glucuronopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-gulopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-idopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-lyxopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-mannopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-psicopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-rhamnopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-ribopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-tagatopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-talopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-D-xylopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-arabinopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-fucopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-galactopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-lyxopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-rhamnopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-ribopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-sorbopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/alpha-L-xylopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-allopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-arabinopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-fructopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-fucopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-galactopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-glucopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-gulopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-idopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-lyxopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-mannopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-rhamnopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-ribopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-tagatopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-talopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-D-xylopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-L-arabinopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-L-lyxopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-L-ribopyranose.cml
-%%DATADIR%%/fragments/cyclic sugars/beta-L-xylopyranose.cml
+%%DATADIR%%/fragments/cyclic_alkanes/1R-camphene.cml
+%%DATADIR%%/fragments/cyclic_alkanes/1R-camphor.cml
+%%DATADIR%%/fragments/cyclic_alkanes/abietic_acid.cml
+%%DATADIR%%/fragments/cyclic_alkanes/adamantane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cis-decahydronaphthalene.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cubane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclobutane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclodecane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cycloheptane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclohexane-chair.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclohexane-twist-boat.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclohexane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclononane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclooctane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclopentane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/cyclopropane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/norbornane.cml
+%%DATADIR%%/fragments/cyclic_alkanes/trans-decahydronaphthalene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/Z-cycloheptene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/Z-cyclooctene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohepta-1_3-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohepta-1_3_5-triene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohepta-1_4-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohexa-1_3-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohexa-1_4-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclohexene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cycloocta-1_3-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cycloocta-1_3_5-triene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cycloocta-1_3_5_7-tetraene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclopenta-1_3-diene.cml
+%%DATADIR%%/fragments/cyclic_alkenes/cyclopentene.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-allopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-arabinopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-fucopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-galactopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-galacturonopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-glucopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-glucuronopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-gulopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-idopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-lyxopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-mannopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-psicopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-rhamnopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-ribopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-tagatopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-talopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-D-xylopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-arabinopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-fucopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-galactopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-lyxopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-rhamnopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-ribopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-sorbopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/alpha-L-xylopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-allopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-arabinopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-fructopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-fucopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-galactopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-glucopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-gulopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-idopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-lyxopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-mannopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-rhamnopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-ribopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-tagatopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-talopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-D-xylopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-L-arabinopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-L-lyxopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-L-ribopyranose.cml
+%%DATADIR%%/fragments/cyclic_sugars/beta-L-xylopyranose.cml
+%%DATADIR%%/fragments/ethers/1_4-dioxane.cml
 %%DATADIR%%/fragments/ethers/di-tert-butylether.cml
 %%DATADIR%%/fragments/ethers/dibutylether.cml
 %%DATADIR%%/fragments/ethers/diethylether.cml
@@ -330,14 +963,37 @@
 %%DATADIR%%/fragments/ethers/dipropylether.cml
 %%DATADIR%%/fragments/ethers/ethylmethylether.cml
 %%DATADIR%%/fragments/ethers/tetrahydrofuran.cml
-%%DATADIR%%/fragments/fatty acids/decanoic_acid.cml
-%%DATADIR%%/fragments/fatty acids/hexanoic_acid.cml
-%%DATADIR%%/fragments/fatty acids/lauric_acid.cml
-%%DATADIR%%/fragments/fatty acids/linoleic_acid.cml
-%%DATADIR%%/fragments/fatty acids/octanoic_acid.cml
-%%DATADIR%%/fragments/fatty acids/oleic_acid.cml
-%%DATADIR%%/fragments/fatty acids/palmitic_acid.cml
-%%DATADIR%%/fragments/fatty acids/stearic_acid.cml
+%%DATADIR%%/fragments/ethers/tetrahydropyran.cml
+%%DATADIR%%/fragments/fatty_acids/arachidonic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/cervonic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/decanoic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/hexanoic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/lauric_acid.cml
+%%DATADIR%%/fragments/fatty_acids/linoleic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/linolenic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/myristic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/octanoic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/oleic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/palmitic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/pentanoic_acid.cml
+%%DATADIR%%/fragments/fatty_acids/stearic_acid.cml
+%%DATADIR%%/fragments/fullerenes/C180.cml
+%%DATADIR%%/fragments/fullerenes/C20.cml
+%%DATADIR%%/fragments/fullerenes/C24.cml
+%%DATADIR%%/fragments/fullerenes/C240.cml
+%%DATADIR%%/fragments/fullerenes/C26.cml
+%%DATADIR%%/fragments/fullerenes/C28.cml
+%%DATADIR%%/fragments/fullerenes/C30.cml
+%%DATADIR%%/fragments/fullerenes/C32.cml
+%%DATADIR%%/fragments/fullerenes/C36.cml
+%%DATADIR%%/fragments/fullerenes/C50.cml
+%%DATADIR%%/fragments/fullerenes/C60-buckminsterfullerene.cml
+%%DATADIR%%/fragments/fullerenes/C70.cml
+%%DATADIR%%/fragments/fullerenes/C76.cml
+%%DATADIR%%/fragments/fullerenes/C78.cml
+%%DATADIR%%/fragments/fullerenes/C80.cml
+%%DATADIR%%/fragments/fullerenes/PC70BM.cml
+%%DATADIR%%/fragments/fullerenes/PCBM.cml
 %%DATADIR%%/fragments/heteroaromatics/1H-indole.cml
 %%DATADIR%%/fragments/heteroaromatics/1H-pyrazole.cml
 %%DATADIR%%/fragments/heteroaromatics/1H-pyrrole.cml
@@ -348,11 +1004,27 @@
 %%DATADIR%%/fragments/heteroaromatics/benzofuran.cml
 %%DATADIR%%/fragments/heteroaromatics/benzothiophene.cml
 %%DATADIR%%/fragments/heteroaromatics/furan.cml
+%%DATADIR%%/fragments/heteroaromatics/isonicotinamide.cml
+%%DATADIR%%/fragments/heteroaromatics/isonicotinic_acid.cml
+%%DATADIR%%/fragments/heteroaromatics/nicotinamide.cml
+%%DATADIR%%/fragments/heteroaromatics/nicotinic_acid.cml
+%%DATADIR%%/fragments/heteroaromatics/picolinamide.cml
+%%DATADIR%%/fragments/heteroaromatics/picolinic_acid.cml
 %%DATADIR%%/fragments/heteroaromatics/pyridine.cml
 %%DATADIR%%/fragments/heteroaromatics/thiophene.cml
 %%DATADIR%%/fragments/ketones/acetone.cml
 %%DATADIR%%/fragments/ketones/butanone.cml
+%%DATADIR%%/fragments/ketones/cyclohexanone.cml
+%%DATADIR%%/fragments/ketones/methyl_vinyl_ketone.cml
+%%DATADIR%%/fragments/ketones/p-benzoquinone.cml
+%%DATADIR%%/fragments/ligands/Cp-cyclopentadienyl.cml
+%%DATADIR%%/fragments/macrocycles/phthalocyanine.cml
 %%DATADIR%%/fragments/macrocycles/porphin.cml
+%%DATADIR%%/fragments/nitriles/1_1_1-trichloroacetonitrile.cml
+%%DATADIR%%/fragments/nitriles/acetonitrile.cml
+%%DATADIR%%/fragments/nitriles/butyronitrile.cml
+%%DATADIR%%/fragments/nitriles/isobutyronitrile.cml
+%%DATADIR%%/fragments/nitriles/propionitrile.cml
 %%DATADIR%%/fragments/nucleobases/adenine.cml
 %%DATADIR%%/fragments/nucleobases/cytosine.cml
 %%DATADIR%%/fragments/nucleobases/guanine.cml
@@ -362,9 +1034,18 @@
 %%DATADIR%%/fragments/steroids/estradiol.cml
 %%DATADIR%%/fragments/steroids/testosterone.cml
 %%DATADIR%%/fragments/sulfoxides/dimethyl_sulfoxide.cml
+%%DATADIR%%/fragments/thiols/2-methylproprane-2-thiol.cml
+%%DATADIR%%/fragments/thiols/R_butane-2-thiol.cml
+%%DATADIR%%/fragments/thiols/butane-1-thiol.cml
+%%DATADIR%%/fragments/thiols/ethane-1_2-dithiol.cml
 %%DATADIR%%/fragments/thiols/ethanethiol.cml
+%%DATADIR%%/fragments/thiols/heptane-1-thiol.cml
+%%DATADIR%%/fragments/thiols/hexane-1-thiol.cml
 %%DATADIR%%/fragments/thiols/methanethiol.cml
+%%DATADIR%%/fragments/thiols/octane-1-thiol.cml
 %%DATADIR%%/fragments/thiols/pentane-1-thiol.cml
+%%DATADIR%%/fragments/thiols/proprane-1-thiol.cml
+%%DATADIR%%/fragments/thiols/proprane-2-thiol.cml
 %%DATADIR%%/fragments/water.cml
 %%DATADIR%%/i18n/avogadro_af.qm
 %%DATADIR%%/i18n/avogadro_ar.qm
@@ -451,6 +1132,7 @@
 %%DATADIR%%/i18n/libavogadro_zh_TW.qm
 %%PYTHON%%share/libavogadro/engineScripts/wireframe.py
 %%PYTHON%%share/libavogadro/extensionScripts/example.py
+share/pixmaps/avogadro-icon.png
 share/qt4/mkspecs/features/avogadro.prf
 %%PYTHON%%@dirrm share/libavogadro/extensionScripts
 %%PYTHON%%@dirrm share/libavogadro/engineScripts
@@ -460,13 +1142,17 @@
 @dirrm %%DATADIR%%/fragments/sulfoxides
 @dirrm %%DATADIR%%/fragments/steroids
 @dirrm %%DATADIR%%/fragments/nucleobases
+ at dirrm %%DATADIR%%/fragments/nitriles
 @dirrm %%DATADIR%%/fragments/macrocycles
+ at dirrm %%DATADIR%%/fragments/ligands
 @dirrm %%DATADIR%%/fragments/ketones
 @dirrm %%DATADIR%%/fragments/heteroaromatics
- at dirrm %%DATADIR%%/fragments/fatty acids
+ at dirrm %%DATADIR%%/fragments/fullerenes
+ at dirrm %%DATADIR%%/fragments/fatty_acids
 @dirrm %%DATADIR%%/fragments/ethers
- at dirrm %%DATADIR%%/fragments/cyclic sugars
- at dirrm %%DATADIR%%/fragments/cyclic alkanes
+ at dirrm %%DATADIR%%/fragments/cyclic_sugars
+ at dirrm %%DATADIR%%/fragments/cyclic_alkenes
+ at dirrm %%DATADIR%%/fragments/cyclic_alkanes
 @dirrm %%DATADIR%%/fragments/coordination
 @dirrm %%DATADIR%%/fragments/carboxylic_acids
 @dirrm %%DATADIR%%/fragments/carbohydrates
@@ -481,14 +1167,38 @@
 @dirrm %%DATADIR%%/fragments/aldehydes
 @dirrm %%DATADIR%%/fragments/alcohols
 @dirrm %%DATADIR%%/fragments
+ at dirrm %%DATADIR%%/crystals/zeolites
+ at dirrm %%DATADIR%%/crystals/titanates
+ at dirrm %%DATADIR%%/crystals/telurides
+ at dirrm %%DATADIR%%/crystals/sulfides
+ at dirrm %%DATADIR%%/crystals/sulfates
+ at dirrm %%DATADIR%%/crystals/silicates
+ at dirrm %%DATADIR%%/crystals/selenides
+ at dirrm %%DATADIR%%/crystals/phosphides
+ at dirrm %%DATADIR%%/crystals/oxides
+ at dirrm %%DATADIR%%/crystals/other
+ at dirrm %%DATADIR%%/crystals/nitrides
+ at dirrm %%DATADIR%%/crystals/intermetallics
+ at dirrm %%DATADIR%%/crystals/ice
+ at dirrm %%DATADIR%%/crystals/hydroxides
+ at dirrm %%DATADIR%%/crystals/hydrides
+ at dirrm %%DATADIR%%/crystals/halides
+ at dirrm %%DATADIR%%/crystals/elements
+ at dirrm %%DATADIR%%/crystals/clays
+ at dirrm %%DATADIR%%/crystals/carbonates
+ at dirrm %%DATADIR%%/crystals/carbides
+ at dirrm %%DATADIR%%/crystals/arsenides
+ at dirrm %%DATADIR%%/crystals/antimonides
+ at dirrm %%DATADIR%%/crystals
 @dirrm %%DATADIR%%/builder/amino
 @dirrm %%DATADIR%%/builder
 @dirrm %%DATADIR%%
- at dirrm lib/avogadro/1_0/tools
- at dirrm lib/avogadro/1_0/extensions
- at dirrm lib/avogadro/1_0/engines
- at dirrm lib/avogadro/1_0/colors
- at dirrm lib/avogadro/1_0/cmake
- at dirrm lib/avogadro/1_0
+ at dirrmtry share/applications
+ at dirrm lib/avogadro/1_1/tools
+ at dirrm lib/avogadro/1_1/extensions
+ at dirrm lib/avogadro/1_1/engines
+ at dirrm lib/avogadro/1_1/colors
+ at dirrm lib/avogadro/1_1/cmake
+ at dirrm lib/avogadro/1_1
 @dirrm lib/avogadro
 @dirrm include/avogadro
>Release-Note:
>Audit-Trail:
>Unformatted:

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