Initial import of openbabel-2.3.0 from wip/openbabel

Open Babel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing
anyone to search, convert, analyze, or store data from molecular
modeling, chemistry, solid-state materials, biochemistry, or related
areas.

7 files changed, 338 insertions, 0 deletions

diff --git a/biology/openbabel/DESCR b/biology/openbabel/DESCR
new file mode 100644
index 00000000000..c725709a987
--- /dev/null
+++ b/biology/openbabel/DESCR
@@ -0,0 +1,5 @@
+Open Babel is a chemical toolbox designed to speak the many languages
+of chemical data. It's an open, collaborative project allowing
+anyone to search, convert, analyze, or store data from molecular
+modeling, chemistry, solid-state materials, biochemistry, or related
+areas.
diff --git a/biology/openbabel/Makefile b/biology/openbabel/Makefile
new file mode 100644
index 00000000000..3a861d4829f
--- /dev/null
+++ b/biology/openbabel/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD: Makefile,v 1.1.1.1 2011/10/05 22:15:48 ryoon Exp $
+#
+
+DISTNAME=	openbabel-2.3.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=openbabel/}
+
+MAINTAINER=	oivulf@gmail.com
+HOMEPAGE=	http://openbabel.org/
+COMMENT=	Chemistry file translation program
+LICENSE=	gnu-gpl-v2
+
+PKG_DESTDIR_SUPPORT=	user-destdir
+
+USE_LANGUAGES=	c c++
+
+USE_CMAKE=	yes
+
+.include "options.mk"
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/eigen2/buildlink3.mk"
+.include "../../textproc/libxml2/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/openbabel/PLIST b/biology/openbabel/PLIST
new file mode 100644
index 00000000000..176ea911214
--- /dev/null
+++ b/biology/openbabel/PLIST
@@ -0,0 +1,257 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $
+${PLIST.wx-gui}bin/OBGUI
+bin/babel
+bin/obabel
+bin/obchiral
+bin/obconformer
+bin/obenergy
+bin/obfit
+bin/obgen
+bin/obgrep
+bin/obminimize
+bin/obprobe
+bin/obprop
+bin/obrotamer
+bin/obrotate
+bin/obspectrophore
+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/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
+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
+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/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/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/libinchi.so
+lib/libinchi.so.0
+lib/libinchi.so.0.3.1
+lib/libopenbabel.so
+lib/libopenbabel.so.4
+lib/libopenbabel.so.4.0.0
+lib/openbabel/${PKGVERSION}/APIInterface.so
+lib/openbabel/${PKGVERSION}/CSRformat.so
+lib/openbabel/${PKGVERSION}/MCDLformat.so
+lib/openbabel/${PKGVERSION}/MNAformat.so
+lib/openbabel/${PKGVERSION}/PQSformat.so
+lib/openbabel/${PKGVERSION}/acrformat.so
+lib/openbabel/${PKGVERSION}/adfformat.so
+lib/openbabel/${PKGVERSION}/alchemyformat.so
+lib/openbabel/${PKGVERSION}/amberformat.so
+lib/openbabel/${PKGVERSION}/balstformat.so
+lib/openbabel/${PKGVERSION}/bgfformat.so
+lib/openbabel/${PKGVERSION}/boxformat.so
+lib/openbabel/${PKGVERSION}/cacaoformat.so
+lib/openbabel/${PKGVERSION}/cacheformat.so
+lib/openbabel/${PKGVERSION}/carformat.so
+lib/openbabel/${PKGVERSION}/castepformat.so
+lib/openbabel/${PKGVERSION}/cccformat.so
+lib/openbabel/${PKGVERSION}/cdxmlformat.so
+lib/openbabel/${PKGVERSION}/chem3dformat.so
+lib/openbabel/${PKGVERSION}/chemdrawcdx.so
+lib/openbabel/${PKGVERSION}/chemdrawct.so
+lib/openbabel/${PKGVERSION}/chemkinformat.so
+lib/openbabel/${PKGVERSION}/chemtoolformat.so
+lib/openbabel/${PKGVERSION}/cifformat.so
+lib/openbabel/${PKGVERSION}/cmlformat.so
+lib/openbabel/${PKGVERSION}/cmlreactformat.so
+lib/openbabel/${PKGVERSION}/copyformat.so
+lib/openbabel/${PKGVERSION}/crkformat.so
+lib/openbabel/${PKGVERSION}/cssrformat.so
+lib/openbabel/${PKGVERSION}/dlpolyformat.so
+lib/openbabel/${PKGVERSION}/dmolformat.so
+lib/openbabel/${PKGVERSION}/fastaformat.so
+lib/openbabel/${PKGVERSION}/fastsearchformat.so
+lib/openbabel/${PKGVERSION}/fchkformat.so
+lib/openbabel/${PKGVERSION}/featformat.so
+lib/openbabel/${PKGVERSION}/fhformat.so
+lib/openbabel/${PKGVERSION}/fhiaimsformat.so
+lib/openbabel/${PKGVERSION}/fingerprintformat.so
+lib/openbabel/${PKGVERSION}/freefracformat.so
+lib/openbabel/${PKGVERSION}/gamessformat.so
+lib/openbabel/${PKGVERSION}/gamessukformat.so
+lib/openbabel/${PKGVERSION}/gausscubeformat.so
+lib/openbabel/${PKGVERSION}/gaussformat.so
+lib/openbabel/${PKGVERSION}/gausszmatformat.so
+lib/openbabel/${PKGVERSION}/ghemicalformat.so
+lib/openbabel/${PKGVERSION}/gromos96format.so
+lib/openbabel/${PKGVERSION}/gulpformat.so
+lib/openbabel/${PKGVERSION}/hinformat.so
+lib/openbabel/${PKGVERSION}/inchiformat.so
+lib/openbabel/${PKGVERSION}/jaguarformat.so
+lib/openbabel/${PKGVERSION}/mdlformat.so
+lib/openbabel/${PKGVERSION}/mmcifformat.so
+lib/openbabel/${PKGVERSION}/mmodformat.so
+lib/openbabel/${PKGVERSION}/mol2format.so
+lib/openbabel/${PKGVERSION}/moldenformat.so
+lib/openbabel/${PKGVERSION}/molproformat.so
+lib/openbabel/${PKGVERSION}/molreport.so
+lib/openbabel/${PKGVERSION}/mopacformat.so
+lib/openbabel/${PKGVERSION}/mpdformat.so
+lib/openbabel/${PKGVERSION}/mpqcformat.so
+lib/openbabel/${PKGVERSION}/msiformat.so
+lib/openbabel/${PKGVERSION}/msmsformat.so
+lib/openbabel/${PKGVERSION}/nulformat.so
+lib/openbabel/${PKGVERSION}/nwchemformat.so
+lib/openbabel/${PKGVERSION}/opendxformat.so
+lib/openbabel/${PKGVERSION}/outformat.so
+lib/openbabel/${PKGVERSION}/pcmodelformat.so
+lib/openbabel/${PKGVERSION}/pdbformat.so
+lib/openbabel/${PKGVERSION}/pdbqtformat.so
+lib/openbabel/${PKGVERSION}/plugin_charges.so
+lib/openbabel/${PKGVERSION}/plugin_descriptors.so
+lib/openbabel/${PKGVERSION}/plugin_fingerprints.so
+lib/openbabel/${PKGVERSION}/plugin_forcefields.so
+lib/openbabel/${PKGVERSION}/plugin_ops.so
+lib/openbabel/${PKGVERSION}/pngformat.so
+lib/openbabel/${PKGVERSION}/povrayformat.so
+lib/openbabel/${PKGVERSION}/pqrformat.so
+lib/openbabel/${PKGVERSION}/pubchem.so
+lib/openbabel/${PKGVERSION}/pwscfformat.so
+lib/openbabel/${PKGVERSION}/qchemformat.so
+lib/openbabel/${PKGVERSION}/reportformat.so
+lib/openbabel/${PKGVERSION}/rsmiformat.so
+lib/openbabel/${PKGVERSION}/rxnformat.so
+lib/openbabel/${PKGVERSION}/shelxformat.so
+lib/openbabel/${PKGVERSION}/smilesformat.so
+lib/openbabel/${PKGVERSION}/svgformat.so
+lib/openbabel/${PKGVERSION}/textformat.so
+lib/openbabel/${PKGVERSION}/thermoformat.so
+lib/openbabel/${PKGVERSION}/tinkerformat.so
+lib/openbabel/${PKGVERSION}/titleformat.so
+lib/openbabel/${PKGVERSION}/turbomoleformat.so
+lib/openbabel/${PKGVERSION}/unichemformat.so
+lib/openbabel/${PKGVERSION}/vaspformat.so
+lib/openbabel/${PKGVERSION}/viewmolformat.so
+lib/openbabel/${PKGVERSION}/xedformat.so
+lib/openbabel/${PKGVERSION}/xmlformat.so
+lib/openbabel/${PKGVERSION}/xyzformat.so
+lib/openbabel/${PKGVERSION}/yasaraformat.so
+lib/openbabel/${PKGVERSION}/zindoformat.so
+lib/openbabel/OpenBabel2Config.cmake
+lib/openbabel/OpenBabel2ConfigVersion.cmake
+lib/openbabel/OpenBabel2_EXPORTS-relwithdebinfo.cmake
+lib/openbabel/OpenBabel2_EXPORTS.cmake
+lib/pkgconfig/openbabel-2.0.pc
+man/man1/babel.1
+man/man1/obchiral.1
+man/man1/obconformer.1
+man/man1/obenergy.1
+man/man1/obfit.1
+man/man1/obgen.1
+man/man1/obgrep.1
+man/man1/obminimize.1
+man/man1/obprobe.1
+man/man1/obprop.1
+man/man1/obrotamer.1
+man/man1/obrotate.1
+man/man1/roundtrip.1
+share/openbabel/${PKGVERSION}/MACCS.txt
+share/openbabel/${PKGVERSION}/SMARTS_InteLigand.txt
+share/openbabel/${PKGVERSION}/UFF.prm
+share/openbabel/${PKGVERSION}/aromatic.txt
+share/openbabel/${PKGVERSION}/atomtyp.txt
+share/openbabel/${PKGVERSION}/bondtyp.txt
+share/openbabel/${PKGVERSION}/element.txt
+share/openbabel/${PKGVERSION}/fragments.txt
+share/openbabel/${PKGVERSION}/gaff.dat
+share/openbabel/${PKGVERSION}/gaff.prm
+share/openbabel/${PKGVERSION}/ghemical.prm
+share/openbabel/${PKGVERSION}/isotope-small.txt
+share/openbabel/${PKGVERSION}/isotope.txt
+share/openbabel/${PKGVERSION}/logp.txt
+share/openbabel/${PKGVERSION}/mmff94.ff
+share/openbabel/${PKGVERSION}/mmff94s.ff
+share/openbabel/${PKGVERSION}/mmffang.par
+share/openbabel/${PKGVERSION}/mmffbndk.par
+share/openbabel/${PKGVERSION}/mmffbond.par
+share/openbabel/${PKGVERSION}/mmffchg.par
+share/openbabel/${PKGVERSION}/mmffdef.par
+share/openbabel/${PKGVERSION}/mmffdfsb.par
+share/openbabel/${PKGVERSION}/mmffoop.par
+share/openbabel/${PKGVERSION}/mmffpbci.par
+share/openbabel/${PKGVERSION}/mmffprop.par
+share/openbabel/${PKGVERSION}/mmffs_oop.par
+share/openbabel/${PKGVERSION}/mmffs_tor.par
+share/openbabel/${PKGVERSION}/mmffstbn.par
+share/openbabel/${PKGVERSION}/mmfftor.par
+share/openbabel/${PKGVERSION}/mmffvdw.par
+share/openbabel/${PKGVERSION}/mr.txt
+share/openbabel/${PKGVERSION}/patterns.txt
+share/openbabel/${PKGVERSION}/phmodel.txt
+share/openbabel/${PKGVERSION}/plugindefines.txt
+share/openbabel/${PKGVERSION}/psa.txt
+share/openbabel/${PKGVERSION}/qeq.txt
+share/openbabel/${PKGVERSION}/resdata.txt
+share/openbabel/${PKGVERSION}/ringtyp.txt
+share/openbabel/${PKGVERSION}/space-groups.txt
+share/openbabel/${PKGVERSION}/superatom.txt
+share/openbabel/${PKGVERSION}/svgformat.script
+share/openbabel/${PKGVERSION}/torlib.txt
+share/openbabel/${PKGVERSION}/types.txt
diff --git a/biology/openbabel/buildlink3.mk b/biology/openbabel/buildlink3.mk
new file mode 100644
index 00000000000..35ae4aed82f
--- /dev/null
+++ b/biology/openbabel/buildlink3.mk
@@ -0,0 +1,16 @@
+# $NetBSD: buildlink3.mk,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $
+
+BUILDLINK_TREE+=	openbabel
+
+.if !defined(OPENBABEL_BUILDLINK3_MK)
+OPENBABEL_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.openbabel+=	openbabel>=2.3.0
+BUILDLINK_PKGSRCDIR.openbabel?=	../../biology/openbabel
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../math/eigen2/buildlink3.mk"
+.include "../../textproc/libxml2/buildlink3.mk"
+.endif	# OPENBABEL_BUILDLINK3_MK
+
+BUILDLINK_TREE+=	-openbabel
diff --git a/biology/openbabel/distinfo b/biology/openbabel/distinfo
new file mode 100644
index 00000000000..cb553f308ec
--- /dev/null
+++ b/biology/openbabel/distinfo
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1.1.1 2011/10/05 22:15:48 ryoon Exp $
+
+SHA1 (openbabel-2.3.0.tar.gz) = 408a4bddb7f052fd89c57ea51b4204b721856b16
+RMD160 (openbabel-2.3.0.tar.gz) = 96dafa3c2aca544f79e08b5617ab0da845c28a16
+Size (openbabel-2.3.0.tar.gz) = 14321281 bytes
+SHA1 (patch-doc_CMakeLists.txt) = aad6a7c17783949667d43cf41bfdf268166f1208
diff --git a/biology/openbabel/options.mk b/biology/openbabel/options.mk
new file mode 100644
index 00000000000..21c82567c5e
--- /dev/null
+++ b/biology/openbabel/options.mk
@@ -0,0 +1,17 @@
+# $NetBSD: options.mk,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $
+
+PKG_OPTIONS_VAR=	PKG_OPTIONS.openbabel
+PKG_SUPPORTED_OPTIONS=	wx-gui
+PKG_SUGGESTED_OPTIONS=
+
+PLIST_VARS+=		wx-gui
+
+.include "../../mk/bsd.options.mk"
+
+.if !empty(PKG_OPTIONS:Mwx-gui)
+.  include "../../x11/wxGTK28/buildlink3.mk"
+CMAKE_ARGS+=	-DBUILD_GUI=ON
+PLIST.wx-gui=	yes
+.else
+CMAKE_ARGS+=	-DBUILD_GUI=OFF
+.endif
diff --git a/biology/openbabel/patches/patch-doc_CMakeLists.txt b/biology/openbabel/patches/patch-doc_CMakeLists.txt
new file mode 100644
index 00000000000..e86c81f655e
--- /dev/null
+++ b/biology/openbabel/patches/patch-doc_CMakeLists.txt
@@ -0,0 +1,13 @@
+$NetBSD: patch-doc_CMakeLists.txt,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $
+
+Fix man path.
+
+--- doc/CMakeLists.txt.orig	2010-07-12 13:05:06.000000000 +0000
++++ doc/CMakeLists.txt
+@@ -1,5 +1,5 @@
+ file(GLOB man_1 *.1)
+-install(FILES ${man_1} DESTINATION share/man/man1)
++install(FILES ${man_1} DESTINATION man/man1)
+ 
+ OPTION(BUILD_DOCS "Build Open Babel documentation" OFF)
+ IF(BUILD_DOCS)