diff options
Diffstat (limited to 'biology/openbabel')
| -rw-r--r-- | biology/openbabel/Makefile | 11 | ||||
| -rw-r--r-- | biology/openbabel/PLIST | 414 | ||||
| -rw-r--r-- | biology/openbabel/distinfo | 15 | ||||
| -rw-r--r-- | biology/openbabel/options.mk | 6 | ||||
| -rw-r--r-- | biology/openbabel/patches/patch-doc_CMakeLists.txt | 13 | ||||
| -rw-r--r-- | biology/openbabel/patches/patch-openbabel-3.pc.cmake | 13 | ||||
| -rw-r--r-- | biology/openbabel/patches/patch-src_conformersearch.cpp | 12 | ||||
| -rw-r--r-- | biology/openbabel/patches/patch-src_formats_confabreport.cpp | 17 | ||||
| -rw-r--r-- | biology/openbabel/patches/patch-test_addhtest.cpp | 17 |
9 files changed, 244 insertions, 274 deletions
diff --git a/biology/openbabel/Makefile b/biology/openbabel/Makefile index 898867e90aa..020206cf1c3 100644 --- a/biology/openbabel/Makefile +++ b/biology/openbabel/Makefile @@ -1,9 +1,8 @@ -# $NetBSD: Makefile,v 1.40 2020/06/02 08:22:32 adam Exp $ +# $NetBSD: Makefile,v 1.41 2020/06/29 12:10:34 ryoon Exp $ # GITHUB_PROJECT= openbabel DISTNAME= openbabel-${RELVERSION:S/-/./g} -PKGREVISION= 5 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_GITHUB:=openbabel/} GITHUB_TAG= ${PKGBASE}-${RELVERSION} @@ -13,7 +12,7 @@ HOMEPAGE= http://openbabel.org/ COMMENT= Chemistry file translation program LICENSE= gnu-gpl-v2 -RELVERSION= 3-0-0 +RELVERSION= 3-1-1 USE_LANGUAGES= c gnu++11 USE_TOOLS+= pkg-config @@ -31,8 +30,10 @@ CMAKE_ARGS+= -DLLVM_CONFIG=${LLVM_CONFIG_PATH:Q} post-extract: ${MKDIR} ${WRKDIR}/build -.include "../../graphics/cairo/buildlink3.mk" +.include "../../devel/boost-headers/buildlink3.mk" +.include "../../devel/boost-libs/buildlink3.mk" .include "../../devel/zlib/buildlink3.mk" -.include "../../math/eigen2/buildlink3.mk" +.include "../../graphics/cairo/buildlink3.mk" +.include "../../math/eigen3/buildlink3.mk" .include "../../textproc/libxml2/buildlink3.mk" .include "../../mk/bsd.pkg.mk" diff --git a/biology/openbabel/PLIST b/biology/openbabel/PLIST index 66c529188f1..389be81d73f 100644 --- a/biology/openbabel/PLIST +++ b/biology/openbabel/PLIST @@ -1,6 +1,8 @@ -@comment $NetBSD: PLIST,v 1.4 2019/11/20 17:02:12 kamil Exp $ +@comment $NetBSD: PLIST,v 1.5 2020/06/29 12:10:34 ryoon Exp $ bin/obabel bin/obconformer +bin/obdistgen +${PLIST.wx-gui}bin/obgui bin/obenergy bin/obfit bin/obfitall @@ -10,6 +12,7 @@ bin/obminimize bin/obmm bin/obprobe bin/obprop +bin/obrms bin/obrotamer bin/obrotate bin/obspectrophore @@ -17,7 +20,39 @@ bin/obsym bin/obtautomer bin/obthermo bin/roundtrip +include/coordgen/CoordgenConfig.hpp +include/coordgen/CoordgenFragmentBuilder.h +include/coordgen/CoordgenFragmenter.h +include/coordgen/CoordgenMacrocycleBuilder.h +include/coordgen/CoordgenMinimizer.h +include/coordgen/sketcherMinimizer.h +include/coordgen/sketcherMinimizerAtom.h +include/coordgen/sketcherMinimizerBendInteraction.h +include/coordgen/sketcherMinimizerBond.h +include/coordgen/sketcherMinimizerClashInteraction.h +include/coordgen/sketcherMinimizerEZConstrainInteraction.h +include/coordgen/sketcherMinimizerFragment.h +include/coordgen/sketcherMinimizerInteraction.h +include/coordgen/sketcherMinimizerMarchingSquares.h +include/coordgen/sketcherMinimizerMaths.h +include/coordgen/sketcherMinimizerMolecule.h +include/coordgen/sketcherMinimizerResidue.h +include/coordgen/sketcherMinimizerResidueInteraction.h +include/coordgen/sketcherMinimizerRing.h +include/coordgen/sketcherMinimizerStretchInteraction.h include/inchi/inchi_api.h +include/maeparser/Buffer.hpp +include/maeparser/MaeBlock.hpp +include/maeparser/MaeConstants.hpp +include/maeparser/MaeParser.hpp +include/maeparser/MaeParserConfig.hpp +include/maeparser/Reader.hpp +include/maeparser/Writer.hpp +include/openbabel3/LBFGS.h +include/openbabel3/LBFGS/LineSearchBacktracking.h +include/openbabel3/LBFGS/LineSearchBracketing.h +include/openbabel3/LBFGS/LineSearchNocedalWright.h +include/openbabel3/LBFGS/Param.h include/openbabel3/openbabel/alias.h include/openbabel3/openbabel/atom.h include/openbabel3/openbabel/babelconfig.h @@ -103,143 +138,154 @@ include/openbabel3/openbabel/text.h include/openbabel3/openbabel/tokenst.h include/openbabel3/openbabel/typer.h include/openbabel3/openbabel/xml.h +lib/cmake/coordgen-config-release.cmake +lib/cmake/coordgen-config.cmake +lib/cmake/maeparser-config-release.cmake +lib/cmake/maeparser-config.cmake lib/cmake/openbabel3/OpenBabel3Config.cmake lib/cmake/openbabel3/OpenBabel3ConfigVersion.cmake lib/cmake/openbabel3/OpenBabel3_EXPORTS-release.cmake lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake +lib/libcoordgen.so +lib/libcoordgen.so.1 +lib/libcoordgen.so.1.4.0 lib/libinchi.so lib/libinchi.so.0 lib/libinchi.so.0.4.1 +lib/libmaeparser.so +lib/libmaeparser.so.1 +lib/libmaeparser.so.1.2.3 lib/libopenbabel.so -lib/libopenbabel.so.6 -lib/libopenbabel.so.6.0.0 -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/${PKGVERSION}/abinitformat.so -lib/openbabel/${PKGVERSION}/acesformat.so -lib/openbabel/${PKGVERSION}/acrformat.so -lib/openbabel/${PKGVERSION}/adfformat.so -lib/openbabel/${PKGVERSION}/alchemyformat.so -lib/openbabel/${PKGVERSION}/amberformat.so -lib/openbabel/${PKGVERSION}/aoforceformat.so -lib/openbabel/${PKGVERSION}/asciiformat.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/${PKGVERSION}/chemdoodlejsonformat.so -lib/openbabel/${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/${PKGVERSION}/cofformat.so -lib/openbabel/${PKGVERSION}/confabreport.so -lib/openbabel/${PKGVERSION}/copyformat.so -lib/openbabel/${PKGVERSION}/crkformat.so -lib/openbabel/${PKGVERSION}/crystal09format.so -lib/openbabel/${PKGVERSION}/cssrformat.so -lib/openbabel/${PKGVERSION}/daltonformat.so -lib/openbabel/${PKGVERSION}/dlpolyformat.so -lib/openbabel/${PKGVERSION}/dmolformat.so -lib/openbabel/${PKGVERSION}/exyzformat.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}/fpsformat.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}/groformat.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}/lmpdatformat.so -lib/openbabel/${PKGVERSION}/lpmdformat.so -lib/openbabel/${PKGVERSION}/mdffformat.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}/orcaformat.so -lib/openbabel/${PKGVERSION}/outformat.so -lib/openbabel/${PKGVERSION}/painterformat.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/${PKGVERSION}/png2format.so -lib/openbabel/${PKGVERSION}/pngformat.so -lib/openbabel/${PKGVERSION}/pointcloudformat.so -lib/openbabel/${PKGVERSION}/posformat.so -lib/openbabel/${PKGVERSION}/povrayformat.so -lib/openbabel/${PKGVERSION}/pqrformat.so -lib/openbabel/${PKGVERSION}/pubchem.so -lib/openbabel/${PKGVERSION}/pubchemjsonformat.so -lib/openbabel/${PKGVERSION}/pwscfformat.so -lib/openbabel/${PKGVERSION}/qchemformat.so -lib/openbabel/${PKGVERSION}/reportformat.so -lib/openbabel/${PKGVERSION}/rinchiformat.so -lib/openbabel/${PKGVERSION}/rsmiformat.so -lib/openbabel/${PKGVERSION}/rxnformat.so -lib/openbabel/${PKGVERSION}/shelxformat.so -lib/openbabel/${PKGVERSION}/siestaformat.so -lib/openbabel/${PKGVERSION}/smilesformat.so -lib/openbabel/${PKGVERSION}/smileyformat.so -lib/openbabel/${PKGVERSION}/stlformat.so -lib/openbabel/${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/${PKGVERSION}/xsfformat.so -lib/openbabel/${PKGVERSION}/xyzformat.so -lib/openbabel/${PKGVERSION}/yasaraformat.so -lib/openbabel/${PKGVERSION}/zindoformat.so +lib/libopenbabel.so.7 +lib/libopenbabel.so.7.0.0 +lib/openbabel/3.1.0/APIInterface.so +lib/openbabel/3.1.0/CSRformat.so +lib/openbabel/3.1.0/MCDLformat.so +lib/openbabel/3.1.0/MNAformat.so +lib/openbabel/3.1.0/PQSformat.so +lib/openbabel/3.1.0/abinitformat.so +lib/openbabel/3.1.0/acesformat.so +lib/openbabel/3.1.0/acrformat.so +lib/openbabel/3.1.0/adfformat.so +lib/openbabel/3.1.0/alchemyformat.so +lib/openbabel/3.1.0/amberformat.so +lib/openbabel/3.1.0/aoforceformat.so +lib/openbabel/3.1.0/asciiformat.so +lib/openbabel/3.1.0/balstformat.so +lib/openbabel/3.1.0/bgfformat.so +lib/openbabel/3.1.0/boxformat.so +lib/openbabel/3.1.0/cacaoformat.so +lib/openbabel/3.1.0/cacheformat.so +lib/openbabel/3.1.0/carformat.so +lib/openbabel/3.1.0/castepformat.so +lib/openbabel/3.1.0/cccformat.so +lib/openbabel/3.1.0/cdxmlformat.so +lib/openbabel/3.1.0/chem3dformat.so +lib/openbabel/3.1.0/chemdoodlejsonformat.so +lib/openbabel/3.1.0/chemdrawcdx.so +lib/openbabel/3.1.0/chemdrawct.so +lib/openbabel/3.1.0/chemkinformat.so +lib/openbabel/3.1.0/chemtoolformat.so +lib/openbabel/3.1.0/cifformat.so +lib/openbabel/3.1.0/cmlformat.so +lib/openbabel/3.1.0/cmlreactformat.so +lib/openbabel/3.1.0/cofformat.so +lib/openbabel/3.1.0/confabreport.so +lib/openbabel/3.1.0/copyformat.so +lib/openbabel/3.1.0/crkformat.so +lib/openbabel/3.1.0/crystal09format.so +lib/openbabel/3.1.0/cssrformat.so +lib/openbabel/3.1.0/daltonformat.so +lib/openbabel/3.1.0/dlpolyformat.so +lib/openbabel/3.1.0/dmolformat.so +lib/openbabel/3.1.0/exyzformat.so +lib/openbabel/3.1.0/fastaformat.so +lib/openbabel/3.1.0/fastsearchformat.so +lib/openbabel/3.1.0/fchkformat.so +lib/openbabel/3.1.0/featformat.so +lib/openbabel/3.1.0/fhformat.so +lib/openbabel/3.1.0/fhiaimsformat.so +lib/openbabel/3.1.0/fingerprintformat.so +lib/openbabel/3.1.0/fpsformat.so +lib/openbabel/3.1.0/freefracformat.so +lib/openbabel/3.1.0/gamessformat.so +lib/openbabel/3.1.0/gamessukformat.so +lib/openbabel/3.1.0/gausscubeformat.so +lib/openbabel/3.1.0/gaussformat.so +lib/openbabel/3.1.0/gausszmatformat.so +lib/openbabel/3.1.0/ghemicalformat.so +lib/openbabel/3.1.0/groformat.so +lib/openbabel/3.1.0/gromos96format.so +lib/openbabel/3.1.0/gulpformat.so +lib/openbabel/3.1.0/hinformat.so +lib/openbabel/3.1.0/inchiformat.so +lib/openbabel/3.1.0/jaguarformat.so +lib/openbabel/3.1.0/lmpdatformat.so +lib/openbabel/3.1.0/lpmdformat.so +lib/openbabel/3.1.0/maeformat.so +lib/openbabel/3.1.0/mdffformat.so +lib/openbabel/3.1.0/mdlformat.so +lib/openbabel/3.1.0/mmcifformat.so +lib/openbabel/3.1.0/mmodformat.so +lib/openbabel/3.1.0/mol2format.so +lib/openbabel/3.1.0/moldenformat.so +lib/openbabel/3.1.0/molproformat.so +lib/openbabel/3.1.0/molreport.so +lib/openbabel/3.1.0/mopacformat.so +lib/openbabel/3.1.0/mpdformat.so +lib/openbabel/3.1.0/mpqcformat.so +lib/openbabel/3.1.0/msiformat.so +lib/openbabel/3.1.0/msmsformat.so +lib/openbabel/3.1.0/nulformat.so +lib/openbabel/3.1.0/nwchemformat.so +lib/openbabel/3.1.0/opendxformat.so +lib/openbabel/3.1.0/orcaformat.so +lib/openbabel/3.1.0/outformat.so +lib/openbabel/3.1.0/painterformat.so +lib/openbabel/3.1.0/pcmodelformat.so +lib/openbabel/3.1.0/pdbformat.so +lib/openbabel/3.1.0/pdbqtformat.so +lib/openbabel/3.1.0/plugin_charges.so +lib/openbabel/3.1.0/plugin_descriptors.so +lib/openbabel/3.1.0/plugin_fingerprints.so +lib/openbabel/3.1.0/plugin_forcefields.so +lib/openbabel/3.1.0/plugin_ops.so +lib/openbabel/3.1.0/png2format.so +lib/openbabel/3.1.0/pngformat.so +lib/openbabel/3.1.0/pointcloudformat.so +lib/openbabel/3.1.0/posformat.so +lib/openbabel/3.1.0/povrayformat.so +lib/openbabel/3.1.0/pqrformat.so +lib/openbabel/3.1.0/pubchem.so +lib/openbabel/3.1.0/pubchemjsonformat.so +lib/openbabel/3.1.0/pwscfformat.so +lib/openbabel/3.1.0/qchemformat.so +lib/openbabel/3.1.0/reportformat.so +lib/openbabel/3.1.0/rinchiformat.so +lib/openbabel/3.1.0/rsmiformat.so +lib/openbabel/3.1.0/rxnformat.so +lib/openbabel/3.1.0/shelxformat.so +lib/openbabel/3.1.0/siestaformat.so +lib/openbabel/3.1.0/smilesformat.so +lib/openbabel/3.1.0/smileyformat.so +lib/openbabel/3.1.0/stlformat.so +lib/openbabel/3.1.0/svgformat.so +lib/openbabel/3.1.0/textformat.so +lib/openbabel/3.1.0/thermoformat.so +lib/openbabel/3.1.0/tinkerformat.so +lib/openbabel/3.1.0/titleformat.so +lib/openbabel/3.1.0/turbomoleformat.so +lib/openbabel/3.1.0/unichemformat.so +lib/openbabel/3.1.0/vaspformat.so +lib/openbabel/3.1.0/viewmolformat.so +lib/openbabel/3.1.0/wlnformat.so +lib/openbabel/3.1.0/xedformat.so +lib/openbabel/3.1.0/xmlformat.so +lib/openbabel/3.1.0/xsfformat.so +lib/openbabel/3.1.0/xyzformat.so +lib/openbabel/3.1.0/yasaraformat.so +lib/openbabel/3.1.0/zindoformat.so lib/pkgconfig/openbabel-3.pc -man/man1/babel.1 man/man1/obabel.1 man/man1/obchiral.1 man/man1/obconformer.1 @@ -260,58 +306,58 @@ man/man1/obsym.1 man/man1/obtautomer.1 man/man1/obthermo.1 man/man1/roundtrip.1 -share/openbabel/${PKGVERSION}/MACCS.txt -share/openbabel/${PKGVERSION}/SMARTS_InteLigand.txt -share/openbabel/${PKGVERSION}/UFF.prm -share/openbabel/${PKGVERSION}/atomization-energies.txt -share/openbabel/${PKGVERSION}/atomtyp.txt -share/openbabel/${PKGVERSION}/babel_povray3.inc -share/openbabel/${PKGVERSION}/bondtyp.txt -share/openbabel/${PKGVERSION}/eem.txt -share/openbabel/${PKGVERSION}/eem2015ba.txt -share/openbabel/${PKGVERSION}/eem2015bm.txt -share/openbabel/${PKGVERSION}/eem2015bn.txt -share/openbabel/${PKGVERSION}/eem2015ha.txt -share/openbabel/${PKGVERSION}/eem2015hm.txt -share/openbabel/${PKGVERSION}/eem2015hn.txt -share/openbabel/${PKGVERSION}/eqeqIonizations.txt -share/openbabel/${PKGVERSION}/gaff.dat -share/openbabel/${PKGVERSION}/gaff.prm -share/openbabel/${PKGVERSION}/ghemical.prm -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}/mpC.txt -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}/rigid-fragments-index.txt -share/openbabel/${PKGVERSION}/rigid-fragments.txt -share/openbabel/${PKGVERSION}/ring-fragments.txt -share/openbabel/${PKGVERSION}/ringtyp.txt -share/openbabel/${PKGVERSION}/space-groups.txt -share/openbabel/${PKGVERSION}/splash.png -share/openbabel/${PKGVERSION}/superatom.txt -share/openbabel/${PKGVERSION}/svgformat.script -share/openbabel/${PKGVERSION}/templates.sdf -share/openbabel/${PKGVERSION}/torlib.txt -share/openbabel/${PKGVERSION}/torsion.txt -share/openbabel/${PKGVERSION}/types.txt +share/openbabel/3.1.0/MACCS.txt +share/openbabel/3.1.0/SMARTS_InteLigand.txt +share/openbabel/3.1.0/UFF.prm +share/openbabel/3.1.0/atomization-energies.txt +share/openbabel/3.1.0/atomtyp.txt +share/openbabel/3.1.0/babel_povray3.inc +share/openbabel/3.1.0/bondtyp.txt +share/openbabel/3.1.0/eem.txt +share/openbabel/3.1.0/eem2015ba.txt +share/openbabel/3.1.0/eem2015bm.txt +share/openbabel/3.1.0/eem2015bn.txt +share/openbabel/3.1.0/eem2015ha.txt +share/openbabel/3.1.0/eem2015hm.txt +share/openbabel/3.1.0/eem2015hn.txt +share/openbabel/3.1.0/eqeqIonizations.txt +share/openbabel/3.1.0/gaff.dat +share/openbabel/3.1.0/gaff.prm +share/openbabel/3.1.0/ghemical.prm +share/openbabel/3.1.0/logp.txt +share/openbabel/3.1.0/mmff94.ff +share/openbabel/3.1.0/mmff94s.ff +share/openbabel/3.1.0/mmffang.par +share/openbabel/3.1.0/mmffbndk.par +share/openbabel/3.1.0/mmffbond.par +share/openbabel/3.1.0/mmffchg.par +share/openbabel/3.1.0/mmffdef.par +share/openbabel/3.1.0/mmffdfsb.par +share/openbabel/3.1.0/mmffoop.par +share/openbabel/3.1.0/mmffpbci.par +share/openbabel/3.1.0/mmffprop.par +share/openbabel/3.1.0/mmffs_oop.par +share/openbabel/3.1.0/mmffs_tor.par +share/openbabel/3.1.0/mmffstbn.par +share/openbabel/3.1.0/mmfftor.par +share/openbabel/3.1.0/mmffvdw.par +share/openbabel/3.1.0/mpC.txt +share/openbabel/3.1.0/mr.txt +share/openbabel/3.1.0/patterns.txt +share/openbabel/3.1.0/phmodel.txt +share/openbabel/3.1.0/plugindefines.txt +share/openbabel/3.1.0/psa.txt +share/openbabel/3.1.0/qeq.txt +share/openbabel/3.1.0/resdata.txt +share/openbabel/3.1.0/rigid-fragments-index.txt +share/openbabel/3.1.0/rigid-fragments.txt +share/openbabel/3.1.0/ring-fragments.txt +share/openbabel/3.1.0/ringtyp.txt +share/openbabel/3.1.0/space-groups.txt +share/openbabel/3.1.0/splash.png +share/openbabel/3.1.0/superatom.txt +share/openbabel/3.1.0/svgformat.script +share/openbabel/3.1.0/templates.sdf +share/openbabel/3.1.0/torlib.txt +share/openbabel/3.1.0/torsion.txt +share/openbabel/3.1.0/types.txt diff --git a/biology/openbabel/distinfo b/biology/openbabel/distinfo index e38809dcdfa..c5ba9cd5dff 100644 --- a/biology/openbabel/distinfo +++ b/biology/openbabel/distinfo @@ -1,11 +1,6 @@ -$NetBSD: distinfo,v 1.10 2020/05/02 15:05:30 wiedi Exp $ +$NetBSD: distinfo,v 1.11 2020/06/29 12:10:34 ryoon Exp $ -SHA1 (openbabel-3.0.0.tar.gz) = 8e1428127f00e39f5f05f58b9b186cd8e50f2486 -RMD160 (openbabel-3.0.0.tar.gz) = 333fd2af6dd6e59ca88258c2f228932a728321c6 -SHA512 (openbabel-3.0.0.tar.gz) = 94af7cffec7de3a7c9d18ea0e1f7b95b0fc64ec563ddb9d420bfb8e9dfa6ac2365338e55e0444e1f5aa2a9f35f5f53961212193c0fdb9d4fd348bd8f61a1684e -Size (openbabel-3.0.0.tar.gz) = 36571060 bytes -SHA1 (patch-doc_CMakeLists.txt) = c4a46fd0ddd253fb755680d7eb91799c74a6489d -SHA1 (patch-openbabel-3.pc.cmake) = abae8cf74db7d45d340f17e5ef9749b6bafa5a70 -SHA1 (patch-src_conformersearch.cpp) = 0f16cc0d0a45e30c6bf00af3b67fac435013a337 -SHA1 (patch-src_formats_confabreport.cpp) = d9f81b6dfeff8ce7e94be5fdb375972ca8d422f2 -SHA1 (patch-test_addhtest.cpp) = 995f7b532517ef9cee8ee924181c3103aa6f3b6c +SHA1 (openbabel-3.1.1.tar.gz) = 22d5eea2492d4ea55fd29f9dcea34fd972af2a27 +RMD160 (openbabel-3.1.1.tar.gz) = 74c74c3129d47ecf70f37d17c1caa42693f6be28 +SHA512 (openbabel-3.1.1.tar.gz) = d46807e8f4e2f0f691e69943e5c5eda9c271271cfca6f66b6df136bbf384502fd3b65a4adf134a4e9e1f2452e1316c9515aa92292b73205b9eb4d7e4d7a85f18 +Size (openbabel-3.1.1.tar.gz) = 36688499 bytes diff --git a/biology/openbabel/options.mk b/biology/openbabel/options.mk index 21c82567c5e..0f247d1336f 100644 --- a/biology/openbabel/options.mk +++ b/biology/openbabel/options.mk @@ -1,14 +1,14 @@ -# $NetBSD: options.mk,v 1.1.1.1 2011/10/05 22:15:49 ryoon Exp $ +# $NetBSD: options.mk,v 1.2 2020/06/29 12:10:34 ryoon Exp $ PKG_OPTIONS_VAR= PKG_OPTIONS.openbabel -PKG_SUPPORTED_OPTIONS= wx-gui +PKG_SUPPORTED_OPTIONS= wxwidgets PKG_SUGGESTED_OPTIONS= PLIST_VARS+= wx-gui .include "../../mk/bsd.options.mk" -.if !empty(PKG_OPTIONS:Mwx-gui) +.if !empty(PKG_OPTIONS:Mwxwidgets) . include "../../x11/wxGTK28/buildlink3.mk" CMAKE_ARGS+= -DBUILD_GUI=ON PLIST.wx-gui= yes diff --git a/biology/openbabel/patches/patch-doc_CMakeLists.txt b/biology/openbabel/patches/patch-doc_CMakeLists.txt deleted file mode 100644 index 9bf7c6f9396..00000000000 --- a/biology/openbabel/patches/patch-doc_CMakeLists.txt +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-doc_CMakeLists.txt,v 1.5 2019/11/20 17:02:12 kamil Exp $ - ---- doc/CMakeLists.txt.orig 2019-10-07 16:39:17.000000000 +0000 -+++ doc/CMakeLists.txt -@@ -1,5 +1,7 @@ -+include(GNUInstallDirs) -+ - file(GLOB man_1 *.1) --install(FILES ${man_1} DESTINATION share/man/man1) -+install(FILES ${man_1} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1) - install(FILES splash.png DESTINATION share/openbabel/${BABEL_VERSION}) - - OPTION(BUILD_DOCS "Build Open Babel documentation" OFF) diff --git a/biology/openbabel/patches/patch-openbabel-3.pc.cmake b/biology/openbabel/patches/patch-openbabel-3.pc.cmake deleted file mode 100644 index f6892cd2256..00000000000 --- a/biology/openbabel/patches/patch-openbabel-3.pc.cmake +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-openbabel-3.pc.cmake,v 1.1 2019/11/20 18:07:55 kamil Exp $ - ---- openbabel-3.pc.cmake.orig 2019-10-07 16:39:17.000000000 +0000 -+++ openbabel-3.pc.cmake -@@ -2,7 +2,7 @@ prefix=@CMAKE_INSTALL_PREFIX@ - exec_prefix=${prefix} - libdir=${exec_prefix}/@LIB_INSTALL_DIR@ - includedir=${prefix}/include --pkgincludedir=${includedir}/openbabel-2.0 -+pkgincludedir=${includedir}/openbabel3/ - - Name: Open Babel library - Description: libopenbabel diff --git a/biology/openbabel/patches/patch-src_conformersearch.cpp b/biology/openbabel/patches/patch-src_conformersearch.cpp deleted file mode 100644 index 221094f548a..00000000000 --- a/biology/openbabel/patches/patch-src_conformersearch.cpp +++ /dev/null @@ -1,12 +0,0 @@ -$NetBSD: patch-src_conformersearch.cpp,v 1.1 2019/11/20 17:02:12 kamil Exp $ - ---- src/conformersearch.cpp.orig 2019-10-07 16:39:17.000000000 +0000 -+++ src/conformersearch.cpp -@@ -23,6 +23,7 @@ GNU General Public License for more deta - #include <openbabel/elements.h> - #include <openbabel/bond.h> - #include "rand.h" -+#include <algorithm> - - #if defined(_MSC_VER) && (_MSC_VER < 1800) - #define OB_ISNAN _isnan diff --git a/biology/openbabel/patches/patch-src_formats_confabreport.cpp b/biology/openbabel/patches/patch-src_formats_confabreport.cpp deleted file mode 100644 index 3945513427a..00000000000 --- a/biology/openbabel/patches/patch-src_formats_confabreport.cpp +++ /dev/null @@ -1,17 +0,0 @@ -$NetBSD: patch-src_formats_confabreport.cpp,v 1.1 2019/11/20 17:02:12 kamil Exp $ - ---- src/formats/confabreport.cpp.orig 2019-10-07 16:39:17.000000000 +0000 -+++ src/formats/confabreport.cpp -@@ -33,6 +33,7 @@ as an example. - #include <openbabel/babelconfig.h> - #include <openbabel/obmolecformat.h> - #include <openbabel/math/align.h> -+#include <algorithm> - - using namespace std; - namespace OpenBabel -@@ -224,4 +225,3 @@ bool ConfabReport::WriteMolecule(OBBase* - } - - } //namespace OpenBabel -- diff --git a/biology/openbabel/patches/patch-test_addhtest.cpp b/biology/openbabel/patches/patch-test_addhtest.cpp deleted file mode 100644 index f42363430de..00000000000 --- a/biology/openbabel/patches/patch-test_addhtest.cpp +++ /dev/null @@ -1,17 +0,0 @@ -$NetBSD: patch-test_addhtest.cpp,v 1.1 2020/05/02 15:05:30 wiedi Exp $ - -Need alloca.h on SunOS - ---- test/addhtest.cpp.orig 2019-10-07 16:39:17.000000000 +0000 -+++ test/addhtest.cpp -@@ -34,6 +34,10 @@ GNU General Public License for more deta - #include <iostream> - #include <fstream> - -+#if defined(__sun) -+#include <alloca.h> -+#endif -+ - using namespace std; - using namespace OpenBabel; - |