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science/openbabel:

Browse Source 
- 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
This commit is contained in:
Max Brazhnikov 2012-12-11 14:19:54 +00:00
parent 4b3c9f74d5
commit 5bf9bfc399
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=308694
18 changed files with 222 additions and 305 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
MOVED
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@ -3951,3 +3951,4 @@ java/jdk16|java/openjdk6|2012-12-10|Has expired: Outdated, consider using openjd
java/linux-sun-jre15|java/linux-sun-jre16|2012-12-10|Has expired: EOLed upstream since october 2009
java/linux-sun-jdk15|java/linux-sun-jdk16|2012-12-10|Has expired: EOLed upstream since october 2009
java/jdk15-doc|java/jdk16-doc|2012-12-10|Has expired: EOLed upstream since october 2009
science/py-openbabel||2012-12-11|Merged to science/openbabel

4
biology/xdrawchem/Makefile
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@ -7,14 +7,14 @@
PORTNAME= xdrawchem
PORTVERSION= 1.9.9
PORTREVISION= 10
PORTREVISION= 11
CATEGORIES= biology
MASTER_SITES= SF
MAINTAINER= hemi@puresimplicity.net
COMMENT= Chemical drawing program
LIB_DEPENDS= openbabel.3:${PORTSDIR}/science/openbabel
LIB_DEPENDS= openbabel:${PORTSDIR}/science/openbabel
GNU_CONFIGURE= yes
USE_GMAKE= yes

11
biology/xdrawchem/files/patch-xdrawchem__application_ob.cpp Normal file
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@ -0,0 +1,11 @@
--- ./xdrawchem/application_ob.cpp.orig 2005-11-30 03:47:14.000000000 +0000
+++ ./xdrawchem/application_ob.cpp 2012-10-30 14:37:35.092762310 +0000
@@ -87,7 +87,7 @@
OBFormat *inFormat = NULL;
if (infilter.left(2) == "--") {
- inFormat = Conv.FormatFromExt(infile);
+ inFormat = Conv.FormatFromExt(infile.ascii());
if (inFormat == NULL) {
QMessageBox::warning( 0, tr("Could not determine file type"),
tr("Please select a file type from the list.") );

1
science/Makefile
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@ -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

4
science/avogadro/Makefile
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@ -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

4
science/gchemutils/Makefile
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@ -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

4
science/ghemical/Makefile
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@ -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 \

5
science/kalzium/Makefile
View File

@ -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

4
science/libghemical/Makefile
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@ -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

78
science/openbabel/Makefile
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@ -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' ${WRKSRC}/tools/Makefile.in
.if !${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.post.mk>
.include <bsd.port.mk>

4
science/openbabel/distinfo
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@ -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

23
science/openbabel/files/patch-scripts__CMakeLists.txt Normal file
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@ -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

337
science/openbabel/pkg-plist
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@ -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

30
science/py-openbabel/Makefile
View File

@ -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>

2
science/py-openbabel/distinfo
View File

@ -1,2 +0,0 @@
SHA256 (openbabel-2.2.3.tar.gz) = eabc8bdbd68431f441b6b40adde0861b2e99750efd21bbb4870ee0a233feae46
SIZE (openbabel-2.2.3.tar.gz) = 6624028

3
science/py-openbabel/pkg-descr
View File

@ -1,3 +0,0 @@
This port installs python bindings for openbabel.
WWW: http://openbabel.sourceforge.net

9
science/py-openbabel/pkg-plist
View File

@ -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%%

3
science/v_sim/Makefile
View File

@ -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