diff options
Diffstat (limited to 'biology/nab')
| -rw-r--r-- | biology/nab/Makefile | 11 | ||||
| -rw-r--r-- | biology/nab/distinfo | 4 | ||||
| -rw-r--r-- | biology/nab/files/patch-atom.c | 10 | ||||
| -rw-r--r-- | biology/nab/files/patch-reslib:conf.lib | 14 | ||||
| -rw-r--r-- | biology/nab/pkg-descr | 10 | ||||
| -rw-r--r-- | biology/nab/pkg-plist | 203 |
6 files changed, 235 insertions, 17 deletions
diff --git a/biology/nab/Makefile b/biology/nab/Makefile index 698943ce5c46..45bfd381f1b2 100644 --- a/biology/nab/Makefile +++ b/biology/nab/Makefile @@ -6,7 +6,7 @@ # PORTNAME= nab -PORTVERSION= 4.5.2 +PORTVERSION= 4.5.3 CATEGORIES= biology MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ \ http://www.scripps.edu/case/ \ @@ -18,7 +18,7 @@ COMMENT= \ BUILD_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp -ONLY_FOR_ARCHS= i386 +ONLY_FOR_ARCHS= i386 MAKE_ENV+= NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} @@ -51,6 +51,7 @@ post-patch: @${RM} -f ${WRKSRC}/test/*.exe @${RM} -f ${WRKSRC}/tleap/utilMakeHelp.exe @${RM} -f ${WRKSRC}/fd_data/abdna.dat.old + @${RM} -f ${WRKSRC}/reslib/conf.lib.orig @${RM} -f ${WRKSRC}/reslib/leap/parm94.dat~ @(cd ${WRKSRC}/reslib/leap && \ ${FIND} . -type f -print | ${GREP} -v '\./[a-zA-Z0-9]' | \ @@ -59,6 +60,7 @@ post-patch: pre-install: @cd ${WRKSRC}/src && \ ${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall + @${CP} ${WRKSRC}/config.h ${WRKSRC}/include/ do-install: @-${MKDIR} ${PREFIX}/share/nab @@ -77,7 +79,7 @@ do-install: ${CHMOD} -R ugo+rX-w nab) @-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords) ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin - ${INSTALL_DATA} ${WRKSRC}/include/* ${PREFIX}/include + ${INSTALL_DATA} ${WRKSRC}/include/* ${PREFIX}/share/nab/include ${INSTALL_DATA} ${WRKSRC}/lib/* ${PREFIX}/lib @-cd ${WRKSRC}/doc && ${GZIP_CMD} ${MAN1} ${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1 @@ -87,9 +89,6 @@ do-install: .for f in ${LIBRARIES} @cd ${PREFIX}/share/nab/lib && ${LN} -sf ../../../lib/${f} . .endfor -.for f in ${INCS} - @cd ${PREFIX}/share/nab/include && ${LN} -sf ../../../include/${f} . -.endfor post-install: @${CAT} ${PKGMESSAGE} diff --git a/biology/nab/distinfo b/biology/nab/distinfo index f6c521100cca..6f5ed092a61a 100644 --- a/biology/nab/distinfo +++ b/biology/nab/distinfo @@ -1,2 +1,2 @@ -MD5 (nab-4.5.2.tar.gz) = b5e9053e6ae97f36a55cc2a1317e9ba8 -SIZE (nab-4.5.2.tar.gz) = 3881361 +MD5 (nab-4.5.3.tar.gz) = 844cc6e4dad076edb4773bd06e1fe126 +SIZE (nab-4.5.3.tar.gz) = 4045456 diff --git a/biology/nab/files/patch-atom.c b/biology/nab/files/patch-atom.c new file mode 100644 index 000000000000..61958e20d134 --- /dev/null +++ b/biology/nab/files/patch-atom.c @@ -0,0 +1,10 @@ +--- tleap/atom.c.orig Sat Apr 20 22:35:09 2002 ++++ tleap/atom.c Sat Mar 6 08:02:25 2004 +@@ -908,6 +908,7 @@ + for ( i=0; i<iBonds; i++ ) { + aBond = aaBond[i]; + VP1(( "Breaking bond: %s - %s\n", ++ sAtom1, + sContainerFullDescriptor( (CONTAINER)aBond, sAtom2 ) )); + AtomRemoveBond( aAtom, aBond ); + } diff --git a/biology/nab/files/patch-reslib:conf.lib b/biology/nab/files/patch-reslib:conf.lib new file mode 100644 index 000000000000..088afbf29321 --- /dev/null +++ b/biology/nab/files/patch-reslib:conf.lib @@ -0,0 +1,14 @@ +*** reslib/conf.lib.orig Wed Mar 10 19:00:11 1999 +--- reslib/conf.lib Tue Dec 23 15:34:07 2003 +*************** +*** 13,18 **** +--- 13,21 ---- + PI 1 pi helix + phi -57.0 psi -70.0 omega 180.0 + ++ PPII 1 polyproline II helix ++ phi -75.0 psi 145.0 omega 180.0 ++ + EXTENDED 1 extended conformation + phi 180.0 psi 180.0 omega 180.0 + diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr index 2d85d2947733..0d61ae35a96a 100644 --- a/biology/nab/pkg-descr +++ b/biology/nab/pkg-descr @@ -1,8 +1,8 @@ -This is version 4.5.2 of nab (nucleic acid builder), a computer -language that is intended for use in creating, describing and -modifying macromolecules, especially nucleic acids. Programs -written in nab are translated into C, which in turn is compiled -into machine code. +This is nab (nucleic acid builder), a computer language that +is intended for use in creating, describing and modifying +macromolecules, especially nucleic acids. Programs written in +nab are translated into C, which in turn is compiled into machine +code. Further general information can be obtained from our web page: diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist index 388373ba5080..f887aca3aab6 100644 --- a/biology/nab/pkg-plist +++ b/biology/nab/pkg-plist @@ -9,10 +9,6 @@ bin/transform bin/tss_init bin/tss_main bin/tss_next -include/defreal.h -include/nab.h -include/nabcode.h -include/nabtypes.h lib/cifparse.a lib/libnab.a lib/libsym.a @@ -46,6 +42,200 @@ share/nab/dgdb/trna.stack.db share/nab/dgdb/zdna.basepair.db share/nab/dgdb/zdna.nucleotide.db share/nab/dgdb/zdna.stack.db +share/nab/dgdb/basepairs/aa.I.pdb +share/nab/dgdb/basepairs/aa.II.pdb +share/nab/dgdb/basepairs/aa.V.pdb +share/nab/dgdb/basepairs/aa.Va.pdb +share/nab/dgdb/basepairs/ac.XXV.pdb +share/nab/dgdb/basepairs/ac.XXVI.pdb +share/nab/dgdb/basepairs/ag.IX.pdb +share/nab/dgdb/basepairs/ag.VIII.pdb +share/nab/dgdb/basepairs/ag.X.pdb +share/nab/dgdb/basepairs/ag.XI.pdb +share/nab/dgdb/basepairs/at.XX.pdb +share/nab/dgdb/basepairs/at.XXI.pdb +share/nab/dgdb/basepairs/at.XXIII.pdb +share/nab/dgdb/basepairs/at.XXIV.pdb +share/nab/dgdb/basepairs/au.XX.pdb +share/nab/dgdb/basepairs/au.XXI.pdb +share/nab/dgdb/basepairs/au.XXIII.pdb +share/nab/dgdb/basepairs/au.XXIV.pdb +share/nab/dgdb/basepairs/ca.XXV.pdb +share/nab/dgdb/basepairs/ca.XXVI.pdb +share/nab/dgdb/basepairs/cc.XIV.pdb +share/nab/dgdb/basepairs/cc.XV.pdb +share/nab/dgdb/basepairs/cg.XIX.pdb +share/nab/dgdb/basepairs/cg.XXII.pdb +share/nab/dgdb/basepairs/ct.XVII.pdb +share/nab/dgdb/basepairs/ct.XVIII.pdb +share/nab/dgdb/basepairs/cu.XVII.pdb +share/nab/dgdb/basepairs/cu.XVIII.pdb +share/nab/dgdb/basepairs/CVS/Entries +share/nab/dgdb/basepairs/CVS/Repository +share/nab/dgdb/basepairs/CVS/Root +share/nab/dgdb/basepairs/ga.IX.pdb +share/nab/dgdb/basepairs/ga.VIII.pdb +share/nab/dgdb/basepairs/ga.X.pdb +share/nab/dgdb/basepairs/ga.XI.pdb +share/nab/dgdb/basepairs/gc.XIX.pdb +share/nab/dgdb/basepairs/gc.XXII.pdb +share/nab/dgdb/basepairs/gg.III.pdb +share/nab/dgdb/basepairs/gg.IV.pdb +share/nab/dgdb/basepairs/gg.VI.pdb +share/nab/dgdb/basepairs/gg.VIa.pdb +share/nab/dgdb/basepairs/gg.VII.pdb +share/nab/dgdb/basepairs/gg.VIIa.pdb +share/nab/dgdb/basepairs/gt.XXVII.pdb +share/nab/dgdb/basepairs/gt.XXVIII.pdb +share/nab/dgdb/basepairs/gu.XXVII.pdb +share/nab/dgdb/basepairs/gu.XXVIII.pdb +share/nab/dgdb/basepairs/ta.XX.pdb +share/nab/dgdb/basepairs/ta.XXI.pdb +share/nab/dgdb/basepairs/ta.XXIII.pdb +share/nab/dgdb/basepairs/ta.XXIV.pdb +share/nab/dgdb/basepairs/tc.XVII.pdb +share/nab/dgdb/basepairs/tc.XVIII.pdb +share/nab/dgdb/basepairs/tg.XXVII.pdb +share/nab/dgdb/basepairs/tg.XXVIII.pdb +share/nab/dgdb/basepairs/tt.XII.pdb +share/nab/dgdb/basepairs/tt.XIII.pdb +share/nab/dgdb/basepairs/tt.XVI.pdb +share/nab/dgdb/basepairs/tt.XVIa.pdb +share/nab/dgdb/basepairs/tu.XII.pdb +share/nab/dgdb/basepairs/tu.XIII.pdb +share/nab/dgdb/basepairs/tu.XVI.pdb +share/nab/dgdb/basepairs/ua.XX.pdb +share/nab/dgdb/basepairs/ua.XXI.pdb +share/nab/dgdb/basepairs/ua.XXIII.pdb +share/nab/dgdb/basepairs/ua.XXIV.pdb +share/nab/dgdb/basepairs/uc.XVII.pdb +share/nab/dgdb/basepairs/uc.XVIII.pdb +share/nab/dgdb/basepairs/ug.XXVII.pdb +share/nab/dgdb/basepairs/ug.XXVIII.pdb +share/nab/dgdb/basepairs/ut.XII.pdb +share/nab/dgdb/basepairs/ut.XIII.pdb +share/nab/dgdb/basepairs/ut.XVI.pdb +share/nab/dgdb/basepairs/uu.XII.pdb +share/nab/dgdb/basepairs/uu.XIII.pdb +share/nab/dgdb/basepairs/uu.XVI.pdb +share/nab/dgdb/basepairs/uu.XVIa.pdb +share/nab/dgdb/stacking/aa.a-rna.pdb +share/nab/dgdb/stacking/aa.adna.pdb +share/nab/dgdb/stacking/aa.arna.pdb +share/nab/dgdb/stacking/aa.bdna.pdb +share/nab/dgdb/stacking/aa.cdna.pdb +share/nab/dgdb/stacking/aa.ddna.pdb +share/nab/dgdb/stacking/aa.tdna.pdb +share/nab/dgdb/stacking/ac.a-rna.pdb +share/nab/dgdb/stacking/ac.adna.pdb +share/nab/dgdb/stacking/ac.arna.pdb +share/nab/dgdb/stacking/ac.bdna.pdb +share/nab/dgdb/stacking/ac.cdna.pdb +share/nab/dgdb/stacking/ac.ddna.pdb +share/nab/dgdb/stacking/ac.tdna.pdb +share/nab/dgdb/stacking/ag.a-rna.pdb +share/nab/dgdb/stacking/ag.adna.pdb +share/nab/dgdb/stacking/ag.arna.pdb +share/nab/dgdb/stacking/ag.bdna.pdb +share/nab/dgdb/stacking/ag.cdna.pdb +share/nab/dgdb/stacking/ag.ddna.pdb +share/nab/dgdb/stacking/ag.tdna.pdb +share/nab/dgdb/stacking/at.adna.pdb +share/nab/dgdb/stacking/at.bdna.pdb +share/nab/dgdb/stacking/CVS/Entries +share/nab/dgdb/stacking/CVS/Repository +share/nab/dgdb/stacking/CVS/Root +share/nab/dgdb/stacking/at.cdna.pdb +share/nab/dgdb/stacking/at.ddna.pdb +share/nab/dgdb/stacking/at.tdna.pdb +share/nab/dgdb/stacking/au.a-rna.pdb +share/nab/dgdb/stacking/au.arna.pdb +share/nab/dgdb/stacking/ca.a-rna.pdb +share/nab/dgdb/stacking/ca.adna.pdb +share/nab/dgdb/stacking/ca.arna.pdb +share/nab/dgdb/stacking/ca.bdna.pdb +share/nab/dgdb/stacking/ca.cdna.pdb +share/nab/dgdb/stacking/ca.ddna.pdb +share/nab/dgdb/stacking/ca.tdna.pdb +share/nab/dgdb/stacking/cc.a-rna.pdb +share/nab/dgdb/stacking/cc.adna.pdb +share/nab/dgdb/stacking/cc.arna.pdb +share/nab/dgdb/stacking/cc.bdna.pdb +share/nab/dgdb/stacking/cc.cdna.pdb +share/nab/dgdb/stacking/cc.ddna.pdb +share/nab/dgdb/stacking/cc.tdna.pdb +share/nab/dgdb/stacking/cg.a-rna.pdb +share/nab/dgdb/stacking/cg.adna.pdb +share/nab/dgdb/stacking/cg.arna.pdb +share/nab/dgdb/stacking/cg.bdna.pdb +share/nab/dgdb/stacking/cg.cdna.pdb +share/nab/dgdb/stacking/cg.ddna.pdb +share/nab/dgdb/stacking/cg.tdna.pdb +share/nab/dgdb/stacking/cg.zdna.pdb +share/nab/dgdb/stacking/ct.adna.pdb +share/nab/dgdb/stacking/ct.bdna.pdb +share/nab/dgdb/stacking/ct.cdna.pdb +share/nab/dgdb/stacking/ct.ddna.pdb +share/nab/dgdb/stacking/ct.tdna.pdb +share/nab/dgdb/stacking/cu.a-rna.pdb +share/nab/dgdb/stacking/cu.arna.pdb +share/nab/dgdb/stacking/ga.a-rna.pdb +share/nab/dgdb/stacking/ga.adna.pdb +share/nab/dgdb/stacking/ga.arna.pdb +share/nab/dgdb/stacking/ga.bdna.pdb +share/nab/dgdb/stacking/ga.cdna.pdb +share/nab/dgdb/stacking/ga.ddna.pdb +share/nab/dgdb/stacking/ga.tdna.pdb +share/nab/dgdb/stacking/gc.a-rna.pdb +share/nab/dgdb/stacking/gc.adna.pdb +share/nab/dgdb/stacking/gc.arna.pdb +share/nab/dgdb/stacking/gc.bdna.pdb +share/nab/dgdb/stacking/gc.cdna.pdb +share/nab/dgdb/stacking/gc.ddna.pdb +share/nab/dgdb/stacking/gc.tdna.pdb +share/nab/dgdb/stacking/gc.zdna.pdb +share/nab/dgdb/stacking/gg.a-rna.pdb +share/nab/dgdb/stacking/gg.adna.pdb +share/nab/dgdb/stacking/gg.arna.pdb +share/nab/dgdb/stacking/gg.bdna.pdb +share/nab/dgdb/stacking/gg.cdna.pdb +share/nab/dgdb/stacking/gg.ddna.pdb +share/nab/dgdb/stacking/gg.tdna.pdb +share/nab/dgdb/stacking/gt.adna.pdb +share/nab/dgdb/stacking/gt.bdna.pdb +share/nab/dgdb/stacking/gt.cdna.pdb +share/nab/dgdb/stacking/gt.ddna.pdb +share/nab/dgdb/stacking/gt.tdna.pdb +share/nab/dgdb/stacking/gu.a-rna.pdb +share/nab/dgdb/stacking/gu.arna.pdb +share/nab/dgdb/stacking/ta.adna.pdb +share/nab/dgdb/stacking/ta.bdna.pdb +share/nab/dgdb/stacking/ta.cdna.pdb +share/nab/dgdb/stacking/ta.ddna.pdb +share/nab/dgdb/stacking/ta.tdna.pdb +share/nab/dgdb/stacking/tc.adna.pdb +share/nab/dgdb/stacking/tc.bdna.pdb +share/nab/dgdb/stacking/tc.cdna.pdb +share/nab/dgdb/stacking/tc.ddna.pdb +share/nab/dgdb/stacking/tc.tdna.pdb +share/nab/dgdb/stacking/tg.adna.pdb +share/nab/dgdb/stacking/tg.bdna.pdb +share/nab/dgdb/stacking/tg.cdna.pdb +share/nab/dgdb/stacking/tg.ddna.pdb +share/nab/dgdb/stacking/tg.tdna.pdb +share/nab/dgdb/stacking/tt.adna.pdb +share/nab/dgdb/stacking/tt.bdna.pdb +share/nab/dgdb/stacking/tt.cdna.pdb +share/nab/dgdb/stacking/tt.ddna.pdb +share/nab/dgdb/stacking/tt.tdna.pdb +share/nab/dgdb/stacking/ua.a-rna.pdb +share/nab/dgdb/stacking/ua.arna.pdb +share/nab/dgdb/stacking/uc.a-rna.pdb +share/nab/dgdb/stacking/uc.arna.pdb +share/nab/dgdb/stacking/ug.a-rna.pdb +share/nab/dgdb/stacking/ug.arna.pdb +share/nab/dgdb/stacking/uu.a-rna.pdb +share/nab/dgdb/stacking/uu.arna.pdb share/nab/examples/ADE.pdb share/nab/examples/Makefile share/nab/examples/README @@ -83,6 +273,7 @@ share/nab/fd_data/aprna.dat share/nab/fd_data/arna.dat share/nab/fd_data/lbdna.dat share/nab/fd_data/sbdna.dat +share/nab/include/config.h share/nab/include/defreal.h share/nab/include/nab.h share/nab/include/nabcode.h @@ -355,6 +546,10 @@ share/nab/test/2strand.pdb @dirrm share/nab/include @dirrm share/nab/fd_data @dirrm share/nab/examples +@dirrm share/nab/dgdb/stacking/CVS +@dirrm share/nab/dgdb/stacking +@dirrm share/nab/dgdb/basepairs/CVS +@dirrm share/nab/dgdb/basepairs @dirrm share/nab/dgdb @dirrm share/nab/bin @dirrm share/nab |