[Midnightbsd-cvs] mports: science/openbabel: add openbabel

ctriv at midnightbsd.org ctriv at midnightbsd.org
Fri Dec 19 03:45:22 EST 2008 

Log Message:
-----------
add openbabel

Added Files:
-----------
    mports/science/openbabel:
        Makefile (r1.1)
        distinfo (r1.1)
        pkg-descr (r1.1)
        pkg-plist (r1.1)

-------------- next part --------------
--- /dev/null
+++ science/openbabel/pkg-descr
@@ -0,0 +1,19 @@
+Open Babel is a project designed to pick up where Babel left off, as a
+cross-platform program and library designed to interconvert between many
+file formats used in molecular modeling and computational chemistry.
+
+Features currently include:
+   * A huge variety of common chemical file formats
+   * Recognition of file type based on filename extension
+   * SMARTS matcher
+   * Flexible atom typer
+   * Gasteiger partial charge calculation
+   * Hydrogen addition and deletion
+   * Automatic feature perception (rings, hybridization, aromaticity)
+   * Multiple conformer storage within molecules
+   * Command line interface development class
+   * Bitvector class
+   * Open-source/Free Software under the GNU General Public License
+   * Cross platform (Windows, Linux, Mac OS X, SGI, Solaris, Dreamcast...)
+
+WWW: http://openbabel.sourceforge.net/
--- /dev/null
+++ science/openbabel/pkg-plist
@@ -0,0 +1,365 @@
+bin/obchiral
+bin/obconformer
+bin/obenergy
+bin/obfit
+bin/obgen
+bin/obgrep
+bin/obminimize
+bin/obprobe
+bin/obprop
+bin/obrotamer
+bin/obrotate
+bin/openbabel
+bin/roundtrip
+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
+include/openbabel-2.0/openbabel/babelconfig.h
+include/openbabel-2.0/openbabel/base.h
+include/openbabel-2.0/openbabel/bitvec.h
+include/openbabel-2.0/openbabel/bond.h
+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/chemdrawcdx.h
+include/openbabel-2.0/openbabel/chiral.h
+include/openbabel-2.0/openbabel/data.h
+include/openbabel-2.0/openbabel/descriptor.h
+include/openbabel-2.0/openbabel/dlhandler.h
+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/grid.h
+include/openbabel-2.0/openbabel/griddata.h
+include/openbabel-2.0/openbabel/groupcontrib.h
+include/openbabel-2.0/openbabel/internalcoord.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/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/mol.h
+include/openbabel-2.0/openbabel/molchrg.h
+include/openbabel-2.0/openbabel/obconversion.h
+include/openbabel-2.0/openbabel/oberror.h
+include/openbabel-2.0/openbabel/obiter.h
+include/openbabel-2.0/openbabel/obmolecformat.h
+include/openbabel-2.0/openbabel/obutil.h
+include/openbabel-2.0/openbabel/op.h
+include/openbabel-2.0/openbabel/optransform.h
+include/openbabel-2.0/openbabel/parsmart.h
+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/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/tokenst.h
+include/openbabel-2.0/openbabel/typer.h
+include/openbabel-2.0/openbabel/xml.h
+lib/libopenbabel.a
+lib/libopenbabel.la
+lib/libopenbabel.so
+lib/libopenbabel.so.3
+lib/openbabel/%%VERSION%%/APIInterface.a
+lib/openbabel/%%VERSION%%/APIInterface.la
+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%%/PQSformat.so
+lib/openbabel/%%VERSION%%/acrformat.a
+lib/openbabel/%%VERSION%%/acrformat.la
+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%%/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%%/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%%/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%%/cssrformat.so
+lib/openbabel/%%VERSION%%/dmolformat.a
+lib/openbabel/%%VERSION%%/dmolformat.la
+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%%/fingerprintformat.so
+lib/openbabel/%%VERSION%%/freefracformat.a
+lib/openbabel/%%VERSION%%/freefracformat.la
+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%%/gromos96format.so
+lib/openbabel/%%VERSION%%/hinformat.a
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+lib/openbabel/%%VERSION%%/hinformat.so
+lib/openbabel/%%VERSION%%/inchiformat.a
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+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%%/mdlformat.so
+lib/openbabel/%%VERSION%%/mmcifformat.a
+lib/openbabel/%%VERSION%%/mmcifformat.la
+lib/openbabel/%%VERSION%%/mmcifformat.so
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+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%%/molreportformat.a
+lib/openbabel/%%VERSION%%/molreportformat.la
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+lib/openbabel/%%VERSION%%/mopacformat.a
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+lib/openbabel/%%VERSION%%/msmsformat.la
+lib/openbabel/%%VERSION%%/msmsformat.so
+lib/openbabel/%%VERSION%%/nwchemformat.a
+lib/openbabel/%%VERSION%%/nwchemformat.la
+lib/openbabel/%%VERSION%%/nwchemformat.so
+lib/openbabel/%%VERSION%%/opendxformat.a
+lib/openbabel/%%VERSION%%/opendxformat.la
+lib/openbabel/%%VERSION%%/opendxformat.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%%/pngformat.so
+lib/openbabel/%%VERSION%%/povrayformat.a
+lib/openbabel/%%VERSION%%/povrayformat.la
+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
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+lib/openbabel/%%VERSION%%/qchemformat.a
+lib/openbabel/%%VERSION%%/qchemformat.la
+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
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+lib/openbabel/%%VERSION%%/rxnformat.a
+lib/openbabel/%%VERSION%%/rxnformat.la
+lib/openbabel/%%VERSION%%/rxnformat.so
+lib/openbabel/%%VERSION%%/shelxformat.a
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+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%%/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
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+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%%/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
+libdata/pkgconfig/openbabel-2.0.pc
+%%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
+ at dirrm %%DATADIR%%/%%VERSION%%
+ at dirrm %%DATADIR%%
+ at dirrm lib/openbabel/%%VERSION%%
+ at dirrm lib/openbabel
+ at dirrm include/openbabel-2.0/openbabel/math
+ at dirrm include/openbabel-2.0/openbabel
+ at dirrm include/openbabel-2.0
+ at dirrm include/inchi
--- /dev/null
+++ science/openbabel/Makefile
@@ -0,0 +1,47 @@
+# ex:ts=8
+#
+# $MidnightBSD: mports/science/openbabel/Makefile,v 1.1 2008/12/19 08:45:22 ctriv Exp $
+#
+
+PORTNAME=	openbabel
+PORTVERSION=	2.2.0
+PORTREVISION=	1
+CATEGORIES=	science
+MASTER_SITES=	SF
+
+MAINTAINER=	ports at MidnightBSD.org
+COMMENT=	Chemistry file translation program
+LICENSE=	gpl2
+
+USE_GNOME=	gnomehack gnometarget libxml2
+USE_AUTOTOOLS=	libtool:15
+USE_LDCONFIG=	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
+
+LIB_DEPENDS=	boost_thread.4:${PORTSDIR}/devel/boost-python
+
+PLIST_SUB=	VERSION="${PORTVERSION}"
+
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} == "ia64"
+BROKEN=		does not compile on ia64 (gcc internal error)
+.endif
+
+
+post-extract:
+	@${LN} -sf babel.1 ${WRKSRC}/doc/openbabel.1
+
+post-patch:
+	@${REINPLACE_CMD} -e \
+		'/test/s| == | = |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>
--- /dev/null
+++ science/openbabel/distinfo
@@ -0,0 +1,3 @@
+MD5 (openbabel-2.2.0.tar.gz) = 643a18c7ba09254d36e93afd6277346f
+SHA256 (openbabel-2.2.0.tar.gz) = a898b79336c7372c901bcc7e5f83db7b8e79f8e864be6a262f515b3e088bc607
+SIZE (openbabel-2.2.0.tar.gz) = 6127264

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