science/openbabel:

- Update openbabel to 2.3.2
- Switch to CMake build system
- Add PYTHON and CAIRO options
- Don't rename babel binary, mark conflict with ancient biology/babel

science/py-openbabel:
- Merge py-openbabel to openbabel

other:
- chase openbabel update

15 files changed, 209 insertions, 304 deletions

diff --git a/science/Makefile b/science/Makefile
index e2f5f032c199..f40f3206d6f4 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -166,7 +166,6 @@
     SUBDIR += py-obspy.taup
     SUBDIR += py-obspy.wav
     SUBDIR += py-obspy.xseed
-    SUBDIR += py-openbabel
     SUBDIR += py-paida
     SUBDIR += py-pydicom
     SUBDIR += py-scikit-learn
diff --git a/science/avogadro/Makefile b/science/avogadro/Makefile
index 4e138a50948a..47e78bf71778 100644
--- a/science/avogadro/Makefile
+++ b/science/avogadro/Makefile
@@ -3,7 +3,7 @@
 
 PORTNAME=	avogadro
 PORTVERSION=	1.0.3
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science
 MASTER_SITES=	SF
 
@@ -11,7 +11,7 @@ MAINTAINER=	tkjacobsen@gmail.com
 COMMENT=	Advanced molecular editor and viewer
 
 BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/eigen2.pc:${PORTSDIR}/math/eigen2
-LIB_DEPENDS=	openbabel.3:${PORTSDIR}/science/openbabel
+LIB_DEPENDS=	openbabel:${PORTSDIR}/science/openbabel
 
 USE_LDCONFIG=	yes
 USE_BZIP2=	yes
diff --git a/science/gchemutils/Makefile b/science/gchemutils/Makefile
index 387a86ee703c..d6ea8189b167 100644
--- a/science/gchemutils/Makefile
+++ b/science/gchemutils/Makefile
@@ -7,7 +7,7 @@
 
 PORTNAME=	gchemutils
 PORTVERSION=	0.12.10
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	science
 MASTER_SITES=	${MASTER_SITE_SAVANNAH}
 MASTER_SITE_SUBDIR=	${PORTNAME}/0.12
@@ -17,7 +17,7 @@ MAINTAINER=	kwm@FreeBSD.org
 COMMENT=	C++ classes and Gtk2 widgets related to chemistry
 
 LIB_DEPENDS=	gtkglext-x11-1.0.0:${PORTSDIR}/x11-toolkits/gtkglext \
-		openbabel.3:${PORTSDIR}/science/openbabel \
+		openbabel:${PORTSDIR}/science/openbabel \
 		goffice-0.8.8:${PORTSDIR}/devel/goffice
 BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/bodr.pc:${PORTSDIR}/science/bodr \
 		${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:${PORTSDIR}/science/chemical-mime-data
diff --git a/science/ghemical/Makefile b/science/ghemical/Makefile
index 2c32bdbe0176..ac6dc50bf50d 100644
--- a/science/ghemical/Makefile
+++ b/science/ghemical/Makefile
@@ -6,7 +6,7 @@
 
 PORTNAME=	ghemical
 PORTVERSION=	2.99.2
-PORTREVISION=	4
+PORTREVISION=	5
 CATEGORIES=	science
 MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20090911/ \
 		http://bioinformatics.org/ghemical/download/
@@ -15,7 +15,7 @@ MAINTAINER=	maho@FreeBSD.org
 COMMENT=	Ghemical is a computational chemistry software package
 
 BUILD_DEPENDS=	f2c:${PORTSDIR}/lang/f2c \
-		openbabel:${PORTSDIR}/science/openbabel \
+		obabel:${PORTSDIR}/science/openbabel \
 		ld:${PORTSDIR}/devel/binutils
 RUN_DEPENDS=	f2c:${PORTSDIR}/lang/f2c
 LIB_DEPENDS=	mpqc:${PORTSDIR}/science/mpqc \
diff --git a/science/kalzium/Makefile b/science/kalzium/Makefile
index 26be80628373..32bb8ed5021a 100644
--- a/science/kalzium/Makefile
+++ b/science/kalzium/Makefile
@@ -7,6 +7,7 @@
 
 PORTNAME=	kalzium
 PORTVERSION=	${KDE4_VERSION}
+PORTREVISION=	1
 CATEGORIES=	science kde
 MASTER_SITES=	${MASTER_SITE_KDE}
 MASTER_SITE_SUBDIR=	${KDE4_BRANCH}/${PORTVERSION}/src
@@ -15,8 +16,8 @@ DIST_SUBDIR=	KDE
 MAINTAINER=	kde@FreeBSD.org
 COMMENT=	Periodic table of elements for KDE 4
 
-LIB_DEPENDS=	openbabel.3:${PORTSDIR}/science/openbabel \
-		avogadro.1:${PORTSDIR}/science/avogadro
+LIB_DEPENDS=	openbabel:${PORTSDIR}/science/openbabel \
+		avogadro:${PORTSDIR}/science/avogadro
 
 BUILD_DEPENDS=	${LOCALBASE}/libdata/pkgconfig/eigen2.pc:${PORTSDIR}/math/eigen2 \
 		${LOCALBASE}/lib/ocaml/facile/facile.a:${PORTSDIR}/math/facile
diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile
index 9a1b5716490c..eab96b246daf 100644
--- a/science/libghemical/Makefile
+++ b/science/libghemical/Makefile
@@ -6,7 +6,7 @@
 
 PORTNAME=	libghemical
 PORTVERSION=	2.99.1
-PORTREVISION=	2
+PORTREVISION=	3
 CATEGORIES=	science
 MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20090911/ \
 		http://bioinformatics.org/ghemical/download/
@@ -14,7 +14,7 @@ MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/release20090911/ \
 MAINTAINER=	maho@FreeBSD.org
 COMMENT=	Support libraries of science/ghemical port
 
-BUILD_DEPENDS=	openbabel:${PORTSDIR}/science/openbabel \
+BUILD_DEPENDS=	obabel:${PORTSDIR}/science/openbabel \
 		mopac7:${PORTSDIR}/biology/mopac \
 		intltool-update:${PORTSDIR}/textproc/intltool \
 		ld:${PORTSDIR}/devel/binutils
diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile
index 99c80626a1a3..f373a784adb3 100644
--- a/science/openbabel/Makefile
+++ b/science/openbabel/Makefile
@@ -1,45 +1,73 @@
-# ex:ts=8
-# Ports collection makefile for:	openbabel
-# Date created:			Jan 5, 2003
-# Whom:				ijliao
-#
+# Created by: ijliao
 # $FreeBSD$
-#
 
 PORTNAME=	openbabel
-PORTVERSION=	2.2.3
+PORTVERSION=	2.3.2
 CATEGORIES=	science
 MASTER_SITES=	SF
 
 MAINTAINER=	makc@FreeBSD.org
 COMMENT=	Chemistry file translation program
 
-LIB_DEPENDS=	boost_python.4:${PORTSDIR}/devel/boost-python-libs
+BUILD_DEPENDS=	${LOCALBASE}/include/eigen3/Eigen/Eigen:${PORTSDIR}/math/eigen3
 
-USE_GNOME=	gnomehack libxml2
-USE_AUTOTOOLS=	libtool
+CONFLICTS_INSTALL=	babel-*
+
+USE_GNOME=	libxml2
+USE_CMAKE=	yes
+CMAKE_ARGS=	-DBUILD_GUI=off
+CMAKE_OUTSOURCE=	yes
 USE_LDCONFIG=	yes
+MAKE_JOBS_SAFE=	yes
 
-MAN1=		obchiral.1 obconformer.1 obenergy.1 obfit.1 obgen.1 obgrep.1 \
-		obminimize.1 obprobe.1 obprop.1 obrotamer.1 obrotate.1 \
-		openbabel.1 roundtrip.1
+MAN1=		babel.1 \
+		obabel.1 \
+		obchiral.1 \
+		obconformer.1 \
+		obenergy.1 \
+		obfit.1 \
+		obgen.1 \
+		obgrep.1 \
+		obgui.1 \
+		obminimize.1 \
+		obprobe.1 \
+		obprop.1 \
+		obrotamer.1 \
+		obrotate.1 \
+		obspectrophore.1 \
+		roundtrip.1
 
 PLIST_SUB=	VERSION="${PORTVERSION}"
 
-MAKE_JOBS_SAFE=	yes
+OPTIONS_DEFINE=	CAIRO PYTHON
+OPTIONS_DEFAULT=	PYTHON
+CAIRO_DESC=	PNG support via cairo library
 
-.include <bsd.port.pre.mk>
+.include <bsd.port.options.mk>
 
-post-extract:
-	@${LN} -sf babel.1 ${WRKSRC}/doc/openbabel.1
+.if ${PORT_OPTIONS:MCAIRO}
+LIB_DEPENDS+=	cairo:${PORTSDIR}/graphics/cairo
+PLIST_SUB+=	CAIRO=""
+.else
+PLIST_SUB+=	CAIRO="@comment "
+.endif
+
+.if ${PORT_OPTIONS:MPYTHON}
+USE_PYTHON=	yes
+CMAKE_ARGS+=	-DPYTHON_BINDINGS=on
+PLIST_SUB+=	PYTHON=""
+.else
+PLIST_SUB+=	PYTHON="@comment "
+.endif
 
 post-patch:
-	@${REINPLACE_CMD} -e \
-		's|/usr/local/|${LOCALBASE}|g' ${WRKSRC}/configure
-	@${REINPLACE_CMD} -e \
-		's|= babel|= openbabel|g' ${WRKSRC}/doc/Makefile.in
-	@${REINPLACE_CMD} -e 's| babel| openbabel|g ; \
-		 s|"babel|"openbabel|g' ${WRKSRC}/doc/o*.1
-	@${REINPLACE_CMD} -e 's|babel$$(EXEEXT)|openbabel$$(EXEEXT)|g' ${WRKSRC}/tools/Makefile.in
-
-.include <bsd.port.post.mk>
+.if !${PORT_OPTIONS:MCAIRO}
+	${REINPLACE_CMD} -e '/find_package(Cairo)/d' \
+		${WRKSRC}/CMakeLists.txt
+.endif
+	${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \
+		${WRKSRC}/CMakeLists.txt
+	${REINPLACE_CMD} -e 's,share/man,man,' \
+		${WRKSRC}/doc/CMakeLists.txt
+
+.include <bsd.port.mk>
diff --git a/science/openbabel/distinfo b/science/openbabel/distinfo
index a506de08caea..084378dc32a9 100644
--- a/science/openbabel/distinfo
+++ b/science/openbabel/distinfo
@@ -1,2 +1,2 @@
-SHA256 (openbabel-2.2.3.tar.gz) = eabc8bdbd68431f441b6b40adde0861b2e99750efd21bbb4870ee0a233feae46
-SIZE (openbabel-2.2.3.tar.gz) = 6624028
+SHA256 (openbabel-2.3.2.tar.gz) = 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188
+SIZE (openbabel-2.3.2.tar.gz) = 20509105
diff --git a/science/openbabel/files/patch-scripts__CMakeLists.txt b/science/openbabel/files/patch-scripts__CMakeLists.txt
new file mode 100644
index 000000000000..eaf5df494a63
--- /dev/null
+++ b/science/openbabel/files/patch-scripts__CMakeLists.txt
@@ -0,0 +1,23 @@
+--- ./scripts/CMakeLists.txt.orig	2012-10-03 19:08:52.000000000 +0000
++++ ./scripts/CMakeLists.txt	2012-10-29 23:15:24.219796263 +0000
+@@ -50,6 +50,7 @@
+ 
+     if(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+       set(DO_PYTHON_BINDINGS ON BOOL)
++      set(PYTHON_SITE_PACKAGES_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages CACHE PATH "The directory where python modules will be installed to.")
+       message(STATUS "Python bindings will be compiled")
+     endif(PYTHONLIBS_FOUND AND PYTHONINTERP_FOUND)
+ 
+@@ -91,9 +92,9 @@
+             PREFIX ""
+             SUFFIX .so )
+         add_dependencies(bindings_python openbabel)
+-        install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR})
+-        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR})
+-        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR})
++        install(TARGETS bindings_python LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
++        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
++        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${PYTHON_SITE_PACKAGES_INSTALL_DIR})
+     else(NOT WIN32)
+         set_target_properties(bindings_python PROPERTIES
+             OUTPUT_NAME _openbabel
diff --git a/science/openbabel/pkg-plist b/science/openbabel/pkg-plist
index 2866be216886..2269910c3c90 100644
--- a/science/openbabel/pkg-plist
+++ b/science/openbabel/pkg-plist
@@ -1,3 +1,5 @@
+bin/babel
+bin/obabel
 bin/obchiral
 bin/obconformer
 bin/obenergy
@@ -7,11 +9,12 @@ bin/obgrep
 bin/obminimize
 bin/obprobe
 bin/obprop
+bin/obrms
 bin/obrotamer
 bin/obrotate
-bin/openbabel
+bin/obspectrophore
 bin/roundtrip
-include/inchi102/inchi_api.h
+include/inchi/inchi_api.h
 include/openbabel-2.0/openbabel/alias.h
 include/openbabel-2.0/openbabel/atom.h
 include/openbabel-2.0/openbabel/atomclass.h
@@ -23,8 +26,10 @@ include/openbabel-2.0/openbabel/bondtyper.h
 include/openbabel-2.0/openbabel/builder.h
 include/openbabel-2.0/openbabel/canon.h
 include/openbabel-2.0/openbabel/chains.h
+include/openbabel-2.0/openbabel/chargemodel.h
 include/openbabel-2.0/openbabel/chemdrawcdx.h
 include/openbabel-2.0/openbabel/chiral.h
+include/openbabel-2.0/openbabel/conformersearch.h
 include/openbabel-2.0/openbabel/data.h
 include/openbabel-2.0/openbabel/descriptor.h
 include/openbabel-2.0/openbabel/dlhandler.h
@@ -32,18 +37,24 @@ include/openbabel-2.0/openbabel/fingerprint.h
 include/openbabel-2.0/openbabel/forcefield.h
 include/openbabel-2.0/openbabel/format.h
 include/openbabel-2.0/openbabel/generic.h
+include/openbabel-2.0/openbabel/graphsym.h
 include/openbabel-2.0/openbabel/grid.h
 include/openbabel-2.0/openbabel/griddata.h
 include/openbabel-2.0/openbabel/groupcontrib.h
+include/openbabel-2.0/openbabel/inchiformat.h
 include/openbabel-2.0/openbabel/internalcoord.h
+include/openbabel-2.0/openbabel/isomorphism.h
 include/openbabel-2.0/openbabel/kinetics.h
 include/openbabel-2.0/openbabel/lineend.h
 include/openbabel-2.0/openbabel/locale.h
+include/openbabel-2.0/openbabel/math/align.h
+include/openbabel-2.0/openbabel/math/erf.h
 include/openbabel-2.0/openbabel/math/matrix3x3.h
 include/openbabel-2.0/openbabel/math/spacegroup.h
 include/openbabel-2.0/openbabel/math/transform3d.h
 include/openbabel-2.0/openbabel/math/vector3.h
 include/openbabel-2.0/openbabel/matrix.h
+include/openbabel-2.0/openbabel/mcdlutil.h
 include/openbabel-2.0/openbabel/mol.h
 include/openbabel-2.0/openbabel/molchrg.h
 include/openbabel-2.0/openbabel/obconversion.h
@@ -58,318 +69,204 @@ include/openbabel-2.0/openbabel/patty.h
 include/openbabel-2.0/openbabel/phmodel.h
 include/openbabel-2.0/openbabel/plugin.h
 include/openbabel-2.0/openbabel/pointgroup.h
+include/openbabel-2.0/openbabel/query.h
 include/openbabel-2.0/openbabel/rand.h
 include/openbabel-2.0/openbabel/reaction.h
 include/openbabel-2.0/openbabel/residue.h
 include/openbabel-2.0/openbabel/ring.h
 include/openbabel-2.0/openbabel/rotamer.h
 include/openbabel-2.0/openbabel/rotor.h
+include/openbabel-2.0/openbabel/shared_ptr.h
+include/openbabel-2.0/openbabel/spectrophore.h
+include/openbabel-2.0/openbabel/stereo/bindings.h
+include/openbabel-2.0/openbabel/stereo/cistrans.h
+include/openbabel-2.0/openbabel/stereo/squareplanar.h
+include/openbabel-2.0/openbabel/stereo/stereo.h
+include/openbabel-2.0/openbabel/stereo/tetrahedral.h
+include/openbabel-2.0/openbabel/stereo/tetranonplanar.h
+include/openbabel-2.0/openbabel/stereo/tetraplanar.h
+include/openbabel-2.0/openbabel/text.h
 include/openbabel-2.0/openbabel/tokenst.h
 include/openbabel-2.0/openbabel/typer.h
 include/openbabel-2.0/openbabel/xml.h
-lib/libopenbabel.a
-lib/libopenbabel.la
+lib/cmake/openbabel2/OpenBabel2Config.cmake
+lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake
+lib/cmake/openbabel2/OpenBabel2_EXPORTS-%%CMAKE_BUILD_TYPE%%.cmake
+lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake
+lib/libinchi.so
+lib/libinchi.so.0
+lib/libinchi.so.0.4.1
 lib/libopenbabel.so
-lib/libopenbabel.so.3
-lib/openbabel/%%VERSION%%/APIInterface.a
-lib/openbabel/%%VERSION%%/APIInterface.la
+lib/libopenbabel.so.4
+lib/libopenbabel.so.4.0.2
 lib/openbabel/%%VERSION%%/APIInterface.so
-lib/openbabel/%%VERSION%%/CSRformat.a
-lib/openbabel/%%VERSION%%/CSRformat.la
 lib/openbabel/%%VERSION%%/CSRformat.so
-lib/openbabel/%%VERSION%%/MCDLformat.a
-lib/openbabel/%%VERSION%%/MCDLformat.la
 lib/openbabel/%%VERSION%%/MCDLformat.so
-lib/openbabel/%%VERSION%%/PQSformat.a
-lib/openbabel/%%VERSION%%/PQSformat.la
+lib/openbabel/%%VERSION%%/MNAformat.so
 lib/openbabel/%%VERSION%%/PQSformat.so
-lib/openbabel/%%VERSION%%/acrformat.a
-lib/openbabel/%%VERSION%%/acrformat.la
+lib/openbabel/%%VERSION%%/abinitformat.so
+lib/openbabel/%%VERSION%%/acesformat.so
 lib/openbabel/%%VERSION%%/acrformat.so
-lib/openbabel/%%VERSION%%/adfformat.a
-lib/openbabel/%%VERSION%%/adfformat.la
 lib/openbabel/%%VERSION%%/adfformat.so
-lib/openbabel/%%VERSION%%/alchemyformat.a
-lib/openbabel/%%VERSION%%/alchemyformat.la
 lib/openbabel/%%VERSION%%/alchemyformat.so
-lib/openbabel/%%VERSION%%/amberformat.a
-lib/openbabel/%%VERSION%%/amberformat.la
 lib/openbabel/%%VERSION%%/amberformat.so
-lib/openbabel/%%VERSION%%/balstformat.a
-lib/openbabel/%%VERSION%%/balstformat.la
+lib/openbabel/%%VERSION%%/asciiformat.so
 lib/openbabel/%%VERSION%%/balstformat.so
-lib/openbabel/%%VERSION%%/bgfformat.a
-lib/openbabel/%%VERSION%%/bgfformat.la
 lib/openbabel/%%VERSION%%/bgfformat.so
-lib/openbabel/%%VERSION%%/boxformat.a
-lib/openbabel/%%VERSION%%/boxformat.la
 lib/openbabel/%%VERSION%%/boxformat.so
-lib/openbabel/%%VERSION%%/cacaoformat.a
-lib/openbabel/%%VERSION%%/cacaoformat.la
 lib/openbabel/%%VERSION%%/cacaoformat.so
-lib/openbabel/%%VERSION%%/cacheformat.a
-lib/openbabel/%%VERSION%%/cacheformat.la
 lib/openbabel/%%VERSION%%/cacheformat.so
-lib/openbabel/%%VERSION%%/carformat.a
-lib/openbabel/%%VERSION%%/carformat.la
 lib/openbabel/%%VERSION%%/carformat.so
-lib/openbabel/%%VERSION%%/cccformat.a
-lib/openbabel/%%VERSION%%/cccformat.la
+lib/openbabel/%%VERSION%%/castepformat.so
 lib/openbabel/%%VERSION%%/cccformat.so
-lib/openbabel/%%VERSION%%/cdxmlformat.a
-lib/openbabel/%%VERSION%%/cdxmlformat.la
 lib/openbabel/%%VERSION%%/cdxmlformat.so
-lib/openbabel/%%VERSION%%/chem3dformat.a
-lib/openbabel/%%VERSION%%/chem3dformat.la
 lib/openbabel/%%VERSION%%/chem3dformat.so
-lib/openbabel/%%VERSION%%/chemdrawcdxformat.a
-lib/openbabel/%%VERSION%%/chemdrawcdxformat.la
-lib/openbabel/%%VERSION%%/chemdrawcdxformat.so
-lib/openbabel/%%VERSION%%/chemdrawctformat.a
-lib/openbabel/%%VERSION%%/chemdrawctformat.la
-lib/openbabel/%%VERSION%%/chemdrawctformat.so
-lib/openbabel/%%VERSION%%/chemkinformat.a
-lib/openbabel/%%VERSION%%/chemkinformat.la
+lib/openbabel/%%VERSION%%/chemdrawcdx.so
+lib/openbabel/%%VERSION%%/chemdrawct.so
 lib/openbabel/%%VERSION%%/chemkinformat.so
-lib/openbabel/%%VERSION%%/chemtoolformat.a
-lib/openbabel/%%VERSION%%/chemtoolformat.la
 lib/openbabel/%%VERSION%%/chemtoolformat.so
-lib/openbabel/%%VERSION%%/cifformat.a
-lib/openbabel/%%VERSION%%/cifformat.la
 lib/openbabel/%%VERSION%%/cifformat.so
-lib/openbabel/%%VERSION%%/cmlformat.a
-lib/openbabel/%%VERSION%%/cmlformat.la
 lib/openbabel/%%VERSION%%/cmlformat.so
-lib/openbabel/%%VERSION%%/cmlreactformat.a
-lib/openbabel/%%VERSION%%/cmlreactformat.la
 lib/openbabel/%%VERSION%%/cmlreactformat.so
-lib/openbabel/%%VERSION%%/copyformat.a
-lib/openbabel/%%VERSION%%/copyformat.la
 lib/openbabel/%%VERSION%%/copyformat.so
-lib/openbabel/%%VERSION%%/crkformat.a
-lib/openbabel/%%VERSION%%/crkformat.la
 lib/openbabel/%%VERSION%%/crkformat.so
-lib/openbabel/%%VERSION%%/cssrformat.a
-lib/openbabel/%%VERSION%%/cssrformat.la
+lib/openbabel/%%VERSION%%/crystal09format.so
 lib/openbabel/%%VERSION%%/cssrformat.so
-lib/openbabel/%%VERSION%%/dmolformat.a
-lib/openbabel/%%VERSION%%/dmolformat.la
+lib/openbabel/%%VERSION%%/dlpolyformat.so
 lib/openbabel/%%VERSION%%/dmolformat.so
-lib/openbabel/%%VERSION%%/fastaformat.a
-lib/openbabel/%%VERSION%%/fastaformat.la
 lib/openbabel/%%VERSION%%/fastaformat.so
-lib/openbabel/%%VERSION%%/fastsearchformat.a
-lib/openbabel/%%VERSION%%/fastsearchformat.la
 lib/openbabel/%%VERSION%%/fastsearchformat.so
-lib/openbabel/%%VERSION%%/fchkformat.a
-lib/openbabel/%%VERSION%%/fchkformat.la
 lib/openbabel/%%VERSION%%/fchkformat.so
-lib/openbabel/%%VERSION%%/featformat.a
-lib/openbabel/%%VERSION%%/featformat.la
 lib/openbabel/%%VERSION%%/featformat.so
-lib/openbabel/%%VERSION%%/fhformat.a
-lib/openbabel/%%VERSION%%/fhformat.la
 lib/openbabel/%%VERSION%%/fhformat.so
-lib/openbabel/%%VERSION%%/fingerprintformat.a
-lib/openbabel/%%VERSION%%/fingerprintformat.la
+lib/openbabel/%%VERSION%%/fhiaimsformat.so
 lib/openbabel/%%VERSION%%/fingerprintformat.so
-lib/openbabel/%%VERSION%%/freefracformat.a
-lib/openbabel/%%VERSION%%/freefracformat.la
+lib/openbabel/%%VERSION%%/fpsformat.so
 lib/openbabel/%%VERSION%%/freefracformat.so
-lib/openbabel/%%VERSION%%/gamessformat.a
-lib/openbabel/%%VERSION%%/gamessformat.la
 lib/openbabel/%%VERSION%%/gamessformat.so
-lib/openbabel/%%VERSION%%/gamessukformat.a
-lib/openbabel/%%VERSION%%/gamessukformat.la
 lib/openbabel/%%VERSION%%/gamessukformat.so
-lib/openbabel/%%VERSION%%/gausscubeformat.a
-lib/openbabel/%%VERSION%%/gausscubeformat.la
 lib/openbabel/%%VERSION%%/gausscubeformat.so
-lib/openbabel/%%VERSION%%/gaussformat.a
-lib/openbabel/%%VERSION%%/gaussformat.la
 lib/openbabel/%%VERSION%%/gaussformat.so
-lib/openbabel/%%VERSION%%/gausszmatformat.a
-lib/openbabel/%%VERSION%%/gausszmatformat.la
 lib/openbabel/%%VERSION%%/gausszmatformat.so
-lib/openbabel/%%VERSION%%/ghemicalformat.a
-lib/openbabel/%%VERSION%%/ghemicalformat.la
 lib/openbabel/%%VERSION%%/ghemicalformat.so
-lib/openbabel/%%VERSION%%/gromos96format.a
-lib/openbabel/%%VERSION%%/gromos96format.la
+lib/openbabel/%%VERSION%%/groformat.so
 lib/openbabel/%%VERSION%%/gromos96format.so
-lib/openbabel/%%VERSION%%/hinformat.a
-lib/openbabel/%%VERSION%%/hinformat.la
+lib/openbabel/%%VERSION%%/gulpformat.so
 lib/openbabel/%%VERSION%%/hinformat.so
-lib/openbabel/%%VERSION%%/inchiformat.a
-lib/openbabel/%%VERSION%%/inchiformat.la
 lib/openbabel/%%VERSION%%/inchiformat.so
-lib/openbabel/%%VERSION%%/jaguarformat.a
-lib/openbabel/%%VERSION%%/jaguarformat.la
 lib/openbabel/%%VERSION%%/jaguarformat.so
-lib/openbabel/%%VERSION%%/mdlformat.a
-lib/openbabel/%%VERSION%%/mdlformat.la
+lib/openbabel/%%VERSION%%/lmpdatformat.so
 lib/openbabel/%%VERSION%%/mdlformat.so
-lib/openbabel/%%VERSION%%/mmcifformat.a
-lib/openbabel/%%VERSION%%/mmcifformat.la
 lib/openbabel/%%VERSION%%/mmcifformat.so
-lib/openbabel/%%VERSION%%/mmodformat.a
-lib/openbabel/%%VERSION%%/mmodformat.la
 lib/openbabel/%%VERSION%%/mmodformat.so
-lib/openbabel/%%VERSION%%/mol2format.a
-lib/openbabel/%%VERSION%%/mol2format.la
 lib/openbabel/%%VERSION%%/mol2format.so
-lib/openbabel/%%VERSION%%/moldenformat.a
-lib/openbabel/%%VERSION%%/moldenformat.la
 lib/openbabel/%%VERSION%%/moldenformat.so
-lib/openbabel/%%VERSION%%/molproformat.a
-lib/openbabel/%%VERSION%%/molproformat.la
 lib/openbabel/%%VERSION%%/molproformat.so
-lib/openbabel/%%VERSION%%/molreportformat.a
-lib/openbabel/%%VERSION%%/molreportformat.la
-lib/openbabel/%%VERSION%%/molreportformat.so
-lib/openbabel/%%VERSION%%/mopacformat.a
-lib/openbabel/%%VERSION%%/mopacformat.la
+lib/openbabel/%%VERSION%%/molreport.so
 lib/openbabel/%%VERSION%%/mopacformat.so
-lib/openbabel/%%VERSION%%/mpdformat.a
-lib/openbabel/%%VERSION%%/mpdformat.la
 lib/openbabel/%%VERSION%%/mpdformat.so
-lib/openbabel/%%VERSION%%/mpqcformat.a
-lib/openbabel/%%VERSION%%/mpqcformat.la
 lib/openbabel/%%VERSION%%/mpqcformat.so
-lib/openbabel/%%VERSION%%/msiformat.a
-lib/openbabel/%%VERSION%%/msiformat.la
 lib/openbabel/%%VERSION%%/msiformat.so
-lib/openbabel/%%VERSION%%/msmsformat.a
-lib/openbabel/%%VERSION%%/msmsformat.la
 lib/openbabel/%%VERSION%%/msmsformat.so
-lib/openbabel/%%VERSION%%/nwchemformat.a
-lib/openbabel/%%VERSION%%/nwchemformat.la
+lib/openbabel/%%VERSION%%/nulformat.so
 lib/openbabel/%%VERSION%%/nwchemformat.so
-lib/openbabel/%%VERSION%%/opendxformat.a
-lib/openbabel/%%VERSION%%/opendxformat.la
 lib/openbabel/%%VERSION%%/opendxformat.so
-lib/openbabel/%%VERSION%%/outformat.a
-lib/openbabel/%%VERSION%%/outformat.la
 lib/openbabel/%%VERSION%%/outformat.so
-lib/openbabel/%%VERSION%%/pcmodelformat.a
-lib/openbabel/%%VERSION%%/pcmodelformat.la
 lib/openbabel/%%VERSION%%/pcmodelformat.so
-lib/openbabel/%%VERSION%%/pdbformat.a
-lib/openbabel/%%VERSION%%/pdbformat.la
 lib/openbabel/%%VERSION%%/pdbformat.so
-lib/openbabel/%%VERSION%%/pngformat.a
-lib/openbabel/%%VERSION%%/pngformat.la
+lib/openbabel/%%VERSION%%/pdbqtformat.so
+lib/openbabel/%%VERSION%%/plugin_charges.so
+lib/openbabel/%%VERSION%%/plugin_descriptors.so
+lib/openbabel/%%VERSION%%/plugin_fingerprints.so
+lib/openbabel/%%VERSION%%/plugin_forcefields.so
+lib/openbabel/%%VERSION%%/plugin_ops.so
+%%CAIRO%%lib/openbabel/%%VERSION%%/png2format.so
 lib/openbabel/%%VERSION%%/pngformat.so
-lib/openbabel/%%VERSION%%/povrayformat.a
-lib/openbabel/%%VERSION%%/povrayformat.la
+lib/openbabel/%%VERSION%%/posformat.so
 lib/openbabel/%%VERSION%%/povrayformat.so
-lib/openbabel/%%VERSION%%/pqrformat.a
-lib/openbabel/%%VERSION%%/pqrformat.la
 lib/openbabel/%%VERSION%%/pqrformat.so
-lib/openbabel/%%VERSION%%/pubchem.a
-lib/openbabel/%%VERSION%%/pubchem.la
 lib/openbabel/%%VERSION%%/pubchem.so
-lib/openbabel/%%VERSION%%/qchemformat.a
-lib/openbabel/%%VERSION%%/qchemformat.la
+lib/openbabel/%%VERSION%%/pwscfformat.so
 lib/openbabel/%%VERSION%%/qchemformat.so
-lib/openbabel/%%VERSION%%/reportformat.a
-lib/openbabel/%%VERSION%%/reportformat.la
 lib/openbabel/%%VERSION%%/reportformat.so
-lib/openbabel/%%VERSION%%/rsmiformat.a
-lib/openbabel/%%VERSION%%/rsmiformat.la
 lib/openbabel/%%VERSION%%/rsmiformat.so
-lib/openbabel/%%VERSION%%/rxnformat.a
-lib/openbabel/%%VERSION%%/rxnformat.la
 lib/openbabel/%%VERSION%%/rxnformat.so
-lib/openbabel/%%VERSION%%/shelxformat.a
-lib/openbabel/%%VERSION%%/shelxformat.la
 lib/openbabel/%%VERSION%%/shelxformat.so
-lib/openbabel/%%VERSION%%/smilesformat.a
-lib/openbabel/%%VERSION%%/smilesformat.la
 lib/openbabel/%%VERSION%%/smilesformat.so
-lib/openbabel/%%VERSION%%/thermoformat.a
-lib/openbabel/%%VERSION%%/thermoformat.la
+lib/openbabel/%%VERSION%%/svgformat.so
+lib/openbabel/%%VERSION%%/textformat.so
 lib/openbabel/%%VERSION%%/thermoformat.so
-lib/openbabel/%%VERSION%%/tinkerformat.a
-lib/openbabel/%%VERSION%%/tinkerformat.la
 lib/openbabel/%%VERSION%%/tinkerformat.so
-lib/openbabel/%%VERSION%%/titleformat.a
-lib/openbabel/%%VERSION%%/titleformat.la
 lib/openbabel/%%VERSION%%/titleformat.so
-lib/openbabel/%%VERSION%%/turbomoleformat.a
-lib/openbabel/%%VERSION%%/turbomoleformat.la
 lib/openbabel/%%VERSION%%/turbomoleformat.so
-lib/openbabel/%%VERSION%%/unichemformat.a
-lib/openbabel/%%VERSION%%/unichemformat.la
 lib/openbabel/%%VERSION%%/unichemformat.so
-lib/openbabel/%%VERSION%%/vaspformat.a
-lib/openbabel/%%VERSION%%/vaspformat.la
 lib/openbabel/%%VERSION%%/vaspformat.so
-lib/openbabel/%%VERSION%%/viewmolformat.a
-lib/openbabel/%%VERSION%%/viewmolformat.la
 lib/openbabel/%%VERSION%%/viewmolformat.so
-lib/openbabel/%%VERSION%%/xedformat.a
-lib/openbabel/%%VERSION%%/xedformat.la
 lib/openbabel/%%VERSION%%/xedformat.so
-lib/openbabel/%%VERSION%%/xmlformat.a
-lib/openbabel/%%VERSION%%/xmlformat.la
 lib/openbabel/%%VERSION%%/xmlformat.so
-lib/openbabel/%%VERSION%%/xtcformat.a
-lib/openbabel/%%VERSION%%/xtcformat.la
-lib/openbabel/%%VERSION%%/xtcformat.so
-lib/openbabel/%%VERSION%%/xyzformat.a
-lib/openbabel/%%VERSION%%/xyzformat.la
+lib/openbabel/%%VERSION%%/xsfformat.so
 lib/openbabel/%%VERSION%%/xyzformat.so
-lib/openbabel/%%VERSION%%/yasaraformat.a
-lib/openbabel/%%VERSION%%/yasaraformat.la
 lib/openbabel/%%VERSION%%/yasaraformat.so
-lib/openbabel/%%VERSION%%/zindoformat.a
-lib/openbabel/%%VERSION%%/zindoformat.la
 lib/openbabel/%%VERSION%%/zindoformat.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/_openbabel.so
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/openbabel.py
+%%PYTHON%%%%PYTHON_SITELIBDIR%%/pybel.py
 libdata/pkgconfig/openbabel-2.0.pc
-%%DATADIR%%/%%VERSION%%/MACCS.txt
-%%DATADIR%%/%%VERSION%%/SMARTS_InteLigand.txt
-%%DATADIR%%/%%VERSION%%/UFF.prm
-%%DATADIR%%/%%VERSION%%/aromatic.txt
-%%DATADIR%%/%%VERSION%%/atomtyp.txt
-%%DATADIR%%/%%VERSION%%/bondtyp.txt
-%%DATADIR%%/%%VERSION%%/element.txt
-%%DATADIR%%/%%VERSION%%/fragments.txt
-%%DATADIR%%/%%VERSION%%/ghemical.prm
-%%DATADIR%%/%%VERSION%%/isotope-small.txt
-%%DATADIR%%/%%VERSION%%/isotope.txt
-%%DATADIR%%/%%VERSION%%/logp.txt
-%%DATADIR%%/%%VERSION%%/mmff94.ff
-%%DATADIR%%/%%VERSION%%/mmff94s.ff
-%%DATADIR%%/%%VERSION%%/mmffang.par
-%%DATADIR%%/%%VERSION%%/mmffbndk.par
-%%DATADIR%%/%%VERSION%%/mmffbond.par
-%%DATADIR%%/%%VERSION%%/mmffchg.par
-%%DATADIR%%/%%VERSION%%/mmffdef.par
-%%DATADIR%%/%%VERSION%%/mmffdfsb.par
-%%DATADIR%%/%%VERSION%%/mmffoop.par
-%%DATADIR%%/%%VERSION%%/mmffpbci.par
-%%DATADIR%%/%%VERSION%%/mmffprop.par
-%%DATADIR%%/%%VERSION%%/mmffs_oop.par
-%%DATADIR%%/%%VERSION%%/mmffs_tor.par
-%%DATADIR%%/%%VERSION%%/mmffstbn.par
-%%DATADIR%%/%%VERSION%%/mmfftor.par
-%%DATADIR%%/%%VERSION%%/mmffvdw.par
-%%DATADIR%%/%%VERSION%%/mr.txt
-%%DATADIR%%/%%VERSION%%/patterns.txt
-%%DATADIR%%/%%VERSION%%/phmodel.txt
-%%DATADIR%%/%%VERSION%%/plugindefines.txt
-%%DATADIR%%/%%VERSION%%/psa.txt
-%%DATADIR%%/%%VERSION%%/resdata.txt
-%%DATADIR%%/%%VERSION%%/ringtyp.txt
-%%DATADIR%%/%%VERSION%%/space-groups.txt
-%%DATADIR%%/%%VERSION%%/torlib.txt
-%%DATADIR%%/%%VERSION%%/types.txt
-@dirrm %%DATADIR%%/%%VERSION%%
-@dirrm %%DATADIR%%
+share/openbabel/%%VERSION%%/MACCS.txt
+share/openbabel/%%VERSION%%/SMARTS_InteLigand.txt
+share/openbabel/%%VERSION%%/UFF.prm
+share/openbabel/%%VERSION%%/aromatic.txt
+share/openbabel/%%VERSION%%/atomtyp.txt
+share/openbabel/%%VERSION%%/babel_povray3.inc
+share/openbabel/%%VERSION%%/bondtyp.txt
+share/openbabel/%%VERSION%%/element.txt
+share/openbabel/%%VERSION%%/fragments.txt
+share/openbabel/%%VERSION%%/gaff.dat
+share/openbabel/%%VERSION%%/gaff.prm
+share/openbabel/%%VERSION%%/ghemical.prm
+share/openbabel/%%VERSION%%/isotope-small.txt
+share/openbabel/%%VERSION%%/isotope.txt
+share/openbabel/%%VERSION%%/logp.txt
+share/openbabel/%%VERSION%%/mmff94.ff
+share/openbabel/%%VERSION%%/mmff94s.ff
+share/openbabel/%%VERSION%%/mmffang.par
+share/openbabel/%%VERSION%%/mmffbndk.par
+share/openbabel/%%VERSION%%/mmffbond.par
+share/openbabel/%%VERSION%%/mmffchg.par
+share/openbabel/%%VERSION%%/mmffdef.par
+share/openbabel/%%VERSION%%/mmffdfsb.par
+share/openbabel/%%VERSION%%/mmffoop.par
+share/openbabel/%%VERSION%%/mmffpbci.par
+share/openbabel/%%VERSION%%/mmffprop.par
+share/openbabel/%%VERSION%%/mmffs_oop.par
+share/openbabel/%%VERSION%%/mmffs_tor.par
+share/openbabel/%%VERSION%%/mmffstbn.par
+share/openbabel/%%VERSION%%/mmfftor.par
+share/openbabel/%%VERSION%%/mmffvdw.par
+share/openbabel/%%VERSION%%/mr.txt
+share/openbabel/%%VERSION%%/patterns.txt
+share/openbabel/%%VERSION%%/phmodel.txt
+share/openbabel/%%VERSION%%/plugindefines.txt
+share/openbabel/%%VERSION%%/psa.txt
+share/openbabel/%%VERSION%%/qeq.txt
+share/openbabel/%%VERSION%%/resdata.txt
+share/openbabel/%%VERSION%%/ringtyp.txt
+share/openbabel/%%VERSION%%/space-groups.txt
+share/openbabel/%%VERSION%%/splash.png
+share/openbabel/%%VERSION%%/superatom.txt
+share/openbabel/%%VERSION%%/svgformat.script
+share/openbabel/%%VERSION%%/torlib.txt
+share/openbabel/%%VERSION%%/types.txt
+@dirrm share/openbabel/%%VERSION%%
+@dirrm share/openbabel
+%%PYTHON%%@dirrmtry %%PYTHON_SITELIBDIR%%
+%%PYTHON%%@dirrmtry %%PYTHON_LIBDIR%%
 @dirrm lib/openbabel/%%VERSION%%
 @dirrm lib/openbabel
+@dirrm lib/cmake/openbabel2
+@dirrmtry lib/cmake
+@dirrm include/openbabel-2.0/openbabel/stereo
 @dirrm include/openbabel-2.0/openbabel/math
 @dirrm include/openbabel-2.0/openbabel
 @dirrm include/openbabel-2.0
-@dirrm include/inchi102
+@dirrm include/inchi
diff --git a/science/py-openbabel/Makefile b/science/py-openbabel/Makefile
deleted file mode 100644
index c4243a87f5f4..000000000000
--- a/science/py-openbabel/Makefile
+++ /dev/null
@@ -1,30 +0,0 @@
-# New ports collection makefile for:	py-openbabel
-# Date created:		2008-07-18
-# Whom:			Max Brazhnikov <makc@issp.ac.ru>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	openbabel
-PORTVERSION=	2.2.3
-CATEGORIES=	science python
-MASTER_SITES=	SF
-PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-
-MAINTAINER=	makc@FreeBSD.org
-COMMENT=	Python bindings for openbabel
-
-LIB_DEPENDS=	openbabel.3:${PORTSDIR}/science/openbabel
-
-USE_PYTHON=	yes
-USE_PYDISTUTILS=	yes
-BUILD_WRKSRC=	${WRKSRC}/scripts/python
-INSTALL_WRKSRC=	${BUILD_WRKSRC}
-
-PYDISTUTILS_PKGVERSION=	1.5
-
-#Fix build with non-default LOCALBASE
-CONFIGURE_ENV+=	OPENBABEL_INSTALL=${LOCALBASE}
-MAKE_ENV+=	OPENBABEL_INSTALL=${LOCALBASE}
-
-.include <bsd.port.mk>
diff --git a/science/py-openbabel/distinfo b/science/py-openbabel/distinfo
deleted file mode 100644
index a506de08caea..000000000000
--- a/science/py-openbabel/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (openbabel-2.2.3.tar.gz) = eabc8bdbd68431f441b6b40adde0861b2e99750efd21bbb4870ee0a233feae46
-SIZE (openbabel-2.2.3.tar.gz) = 6624028
diff --git a/science/py-openbabel/pkg-descr b/science/py-openbabel/pkg-descr
deleted file mode 100644
index 62d28d8e61af..000000000000
--- a/science/py-openbabel/pkg-descr
+++ /dev/null
@@ -1,3 +0,0 @@
-This port installs python bindings for openbabel.
-
-WWW:	http://openbabel.sourceforge.net
diff --git a/science/py-openbabel/pkg-plist b/science/py-openbabel/pkg-plist
deleted file mode 100644
index 8ae081ce5f37..000000000000
--- a/science/py-openbabel/pkg-plist
+++ /dev/null
@@ -1,9 +0,0 @@
-%%PYTHON_SITELIBDIR%%/_openbabel.so
-%%PYTHON_SITELIBDIR%%/openbabel.py
-%%PYTHON_SITELIBDIR%%/openbabel.pyc
-%%PYTHON_SITELIBDIR%%/openbabel.pyo
-%%PYTHON_SITELIBDIR%%/pybel.py
-%%PYTHON_SITELIBDIR%%/pybel.pyc
-%%PYTHON_SITELIBDIR%%/pybel.pyo
-@dirrmtry %%PYTHON_SITELIBDIR%%
-@dirrmtry %%PYTHON_LIBDIR%%
diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile
index 48b5a020d4bb..d62dbc4253f6 100644
--- a/science/v_sim/Makefile
+++ b/science/v_sim/Makefile
@@ -3,6 +3,7 @@
 
 PORTNAME=	v_sim
 PORTVERSION=	3.6.1.1
+PORTREVISION=	1
 CATEGORIES=	science
 MASTER_SITES=	http://www-drfmc.cea.fr/sp2m/L_Sim/V_Sim/download/
 
@@ -49,7 +50,7 @@ PLIST_SUB+=	CDF="@comment "
 .endif
 
 .if !defined(WITHOUT_BABEL)
-LIB_DEPENDS+=	openbabel.3:${PORTSDIR}/science/openbabel
+LIB_DEPENDS+=	openbabel:${PORTSDIR}/science/openbabel
 CONFIGURE_ARGS+=--with-openbabel
 PLIST_SUB+=	BABEL=""
 .else