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