update biology/nab: 4.4 -> 4.5.1

PR:		52786
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU> (maintainer)

12 files changed, 393 insertions, 403 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index ac14470a54fb..fbed8dabae40 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -6,24 +6,28 @@
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.4
+PORTVERSION=	4.5.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
 		http://www.scripps.edu/case/
 
 MAINTAINER=	bdodson@scms.utmb.edu
-COMMENT=	This is nab (nucleic acid builder), a language for macromolecules
+COMMENT=	\
+ "This is nab (nucleic acid builder), a language for macromolecules"
+
+BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
+
+ONLY_FOR_ARCHS= i386
 
 MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH}
 
-USE_BISON=	yes
 MAN1=		nab.1
 MANCOMPRESSED=	yes
 USE_REINPLACE=	yes
 
 BINARIES=	matextract      matmul          teLeap          tss_main \
 		matgen          nab             transform       tss_next \
-		matmerge        nab2c           tss_init        ucpp
+		matmerge        nab2c           tss_init
 
 LIBRARIES=	cifparse.a      libnab.a        libsym.a
 
@@ -44,18 +48,18 @@ pre-install:
 		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
 
 do-install:
-	@-mkdir -p ${PREFIX}/share/nab
-	@-mkdir -p ${PREFIX}/share/nab/bin
-	@-mkdir -p ${PREFIX}/share/nab/include
-	@-mkdir -p ${PREFIX}/share/nab/lib
+	@-${MKDIR} ${PREFIX}/share/nab
+	@-${MKDIR} ${PREFIX}/share/nab/bin
+	@-${MKDIR} ${PREFIX}/share/nab/include
+	@-${MKDIR} ${PREFIX}/share/nab/lib
 .if !defined(NOPORTDOCS)
-	@cd ${WRKSRC} && (tar cf - examples test peptide suppose | \
-		(cd ${PREFIX}/share/nab; tar xf -))
-	@-mkdir -p ${PREFIX}/share/doc/nab
+	@cd ${WRKSRC} && (${TAR} cf - examples test peptide suppose | \
+		(cd ${PREFIX}/share/nab; ${TAR} xf -))
+	@-${MKDIR} ${PREFIX}/share/doc/nab
 	${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab
 .endif
-	@cd ${WRKSRC} && (tar cf - dgdb reslib fd_data | \
-		(cd ${PREFIX}/share/nab; tar xf -))
+	@cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data | \
+		(cd ${PREFIX}/share/nab; ${TAR} xf -))
 	@(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} nab; \
 		${CHMOD} -R ugo+rX-w nab)
 	@-(cd ${PREFIX}/share/nab && ${LN} -sf ../NDB coords)
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index 00bddf409b0e..9b854a4b868a 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1 +1 @@
-MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474
+MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index 1d2f9ebab0a8..51a3556506c5 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -79,26 +79,26 @@ SHELL=		/bin/sh
 #
 #          For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
 #
-#	   For FreeBSD 4.2-STABLE, there seems to be a dependency
-#	   on bison.  Berkeley yacc was very problematic.
-CC=		cc
+#CC=
 LEX=    	flex
-YACC=   	bison -y -t
+YACC=   	yacc
 AR=		ar
 #
 #  Set the C-preprocessor.  Code for a small preprocessor is in
 #    uccp-0.7;  it gets installed as $(NABHOME)/bin/$(ARCH)/ucpp;
 #    this should generally *not* be changed.
+#  Changed 14 Feb 2003 to use the ucpp port (FreeBSD). MLD
 #
-#  Again, for FreeBSD 4.2-STABLE, I had problems using the system
-#    C-preprocessor.
+#  For FreeBSD 4.x, I had problems using the system C-preprocessor. MLD
 #
 CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= -O -pipe
-OCFLAGS= -O -pipe
+# Pick up initial CFLAGS from /etc/make.conf instead of here
+# This is a Berkeley make- (pmake-)specific construct
+CFLAGS+=
+OCFLAGS= ${CFLAGS}
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
new file mode 100644
index 000000000000..039c7d0abffb
--- /dev/null
+++ b/biology/nab/files/patch-Makefile
@@ -0,0 +1,40 @@
+--- Makefile.orig	Mon Oct 23 20:33:23 2000
++++ Makefile	Wed Feb 12 16:33:42 2003
+@@ -1,15 +1,15 @@
+ #   top-level Makefile for the NAB suite of programs
+ 
++all: compiler test
+ compiler:
+ 	-mkdir bin lib include
+-	(cd ucpp-0.7; make install )
+ 	(cd cifparse; make install )
+ 	(cd src; make install )
+ 	(cd nss; make install )
+ 	(cd tleap; make install )
+-	@echo
+-	@echo "completed installation of NAB version 4"
+-	@echo
++#	@echo
++#	@echo "completed installation of NAB version 4"
++#	@echo
+ 
+ #   note:  "make test" needs to follow "make", since it is very hard to
+ #          tell if the compiler is completely "made" or not.
+@@ -18,17 +18,14 @@
+ 	(cd nss; make test )
+ 
+ clean:
+-	(cd ucpp-0.7; make clean )
+ 	(cd cifparse; make clean )
+ 	(cd src; make clean )
+ 	(cd nss; make clean )
+ 	(cd tleap; make clean )
+ 	
+ uninstall:
+-	(cd ucpp-0.7; make uninstall )
+ 	(cd cifparse; make uninstall )
+ 	(cd src; make uninstall )
+ 	(cd nss; make uninstall )
+ 	(cd tleap; make uninstall )
+ 	-/bin/rm config.h
+-	
diff --git a/biology/nab/files/patch-aa b/biology/nab/files/patch-aa
deleted file mode 100644
index a04b27361f18..000000000000
--- a/biology/nab/files/patch-aa
+++ /dev/null
@@ -1,32 +0,0 @@
-*** Makefile.orig	Mon Oct 23 20:01:09 2000
---- Makefile	Sun Jan 28 13:36:22 2001
-***************
-*** 1,5 ****
---- 1,6 ----
-  #   top-level Makefile for the NAB suite of programs
-  
-+ all: compiler test
-  compiler:
-  	-mkdir bin lib include
-  	(cd ucpp-0.7; make install )
-***************
-*** 7,15 ****
-  	(cd src; make install )
-  	(cd nss; make install )
-  	(cd tleap; make install )
-! 	@echo
-! 	@echo "completed installation of NAB version 4"
-! 	@echo
-  
-  #   note:  "make test" needs to follow "make", since it is very hard to
-  #          tell if the compiler is completely "made" or not.
---- 8,16 ----
-  	(cd src; make install )
-  	(cd nss; make install )
-  	(cd tleap; make install )
-! #	@echo
-! #	@echo "completed installation of NAB version 4"
-! #	@echo
-  
-  #   note:  "make test" needs to follow "make", since it is very hard to
-  #          tell if the compiler is completely "made" or not.
diff --git a/biology/nab/files/patch-nabgrm.y b/biology/nab/files/patch-nabgrm.y
deleted file mode 100644
index 78ff31d21884..000000000000
--- a/biology/nab/files/patch-nabgrm.y
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/nabgrm.y.orig	Tue Oct 29 13:04:56 2002
-+++ src/nabgrm.y	Tue Oct 29 13:40:29 2002
-@@ -244,7 +244,7 @@
- expr_stmt	: expr SYM_SEMICOLON
- 				{ CG_genmain(); CG_genexpr( $1 );
- 				  CG_genop( NULL, SYM_SEMICOLON ); } ;
--if_stmt		: if_hdr stmt ;
-+if_stmt		: if_hdr stmt
- 		| if_hdr stmt SYM_ELSE
- 				{ CG_genrword( SYM_ELSE ); } stmt ;
- for_stmt	: for_hdr stmt ;
diff --git a/biology/nab/files/patch-parser.y b/biology/nab/files/patch-parser.y
deleted file mode 100644
index bdf23a785552..000000000000
--- a/biology/nab/files/patch-parser.y
+++ /dev/null
@@ -1,10 +0,0 @@
---- tleap/parser.y.orig	Tue Oct 29 13:46:35 2002
-+++ tleap/parser.y	Tue Oct 29 13:48:18 2002
-@@ -220,6 +220,7 @@
- 		{
- 			return;
- 		}
-+	;
- 
- line    :       LENDOFCOMMAND
- 	|	instruct
diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c
index fc36828b3bfd..34b3f2851083 100644
--- a/biology/nab/files/patch-src:database.c
+++ b/biology/nab/files/patch-src:database.c
@@ -1,32 +1,16 @@
-*** src/database.c.orig	Wed Nov 15 19:46:50 2000
---- src/database.c	Sun Jun  2 12:57:50 2002
-***************
-*** 67,72 ****
---- 67,79 ----
-  
-  
-  
-+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
-+ #include <sys/param.h>
-+ #endif
-+ 
-+ #if defined(BSD)
-+ #include <math.h>
-+ #endif
-  
-  
-  #include	"stdio.h"
-***************
-*** 979,985 ****
---- 986,996 ----
-  
-      sDBRemoveLeadingSpaces( sLine );
-      sDBRemoveFirstString( sLine, sHead );
-+ #if defined (linux) || defined(BSD)
-+     sscanf( sHead, "%lg", dPDbl );
-+ #else
-      sscanf( sHead, "%lG", dPDbl );
-+ #endif
-  
-  }
-  
+--- src/database.c.orig	Thu Nov 16 15:37:11 2000
++++ src/database.c	Fri Feb 14 12:15:53 2003
+@@ -64,6 +64,13 @@
+  *              The TOTAL database name MUST NEVER be longer than
+  *              can be contained in the String object.
+  */
++#if (defined(__unix__) || defined(unix)) && !defined(USG)
++#include <sys/param.h>
++#endif
++
++#if defined(BSD)
++#include <math.h>
++#endif
+ 
+ 
+ 
diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c
index bdb35b202fa7..c6004d1d9a24 100644
--- a/biology/nab/files/patch-tleap:database.c
+++ b/biology/nab/files/patch-tleap:database.c
@@ -1,35 +1,16 @@
-*** tleap/database.c.orig	Wed Mar 27 15:41:01 2002
---- tleap/database.c	Sun Jun  2 12:59:14 2002
-***************
-*** 97,102 ****
---- 97,109 ----
-  
-  
-  
-+ #if (defined(__unix__) || defined(unix)) && !defined(USG)
-+ #include <sys/param.h>
-+ #endif
-+ 
-+ #if defined(BSD)
-+ #include <math.h>
-+ #endif
-  
-  
-  #include	"basics.h"
-***************
-*** 563,569 ****
-  
-      sRemoveLeadingSpaces( sLine );
-      sRemoveFirstString( sLine, sHead );
-! #ifdef linux
-      sscanf( sHead, "%lg", dPDbl );
-  #else
-      sscanf( sHead, "%lG", dPDbl );
---- 570,576 ----
-  
-      sRemoveLeadingSpaces( sLine );
-      sRemoveFirstString( sLine, sHead );
-! #if defined(linux) || defined(BSD)
-      sscanf( sHead, "%lg", dPDbl );
-  #else
-      sscanf( sHead, "%lG", dPDbl );
+--- tleap/database.c.orig	Sat Nov  9 18:36:58 2002
++++ tleap/database.c	Wed Jan 29 09:56:46 2003
+@@ -185,6 +185,13 @@
+ }
+ 
+ 
++#if (defined(__unix__) || defined(unix)) && !defined(USG)
++#include <sys/param.h>
++#endif
++
++#if defined(BSD)
++#include <math.h>
++#endif
+ 
+ 
+ 
diff --git a/biology/nab/files/patch-unitio.c b/biology/nab/files/patch-unitio.c
new file mode 100644
index 000000000000..8b3048548a01
--- /dev/null
+++ b/biology/nab/files/patch-unitio.c
@@ -0,0 +1,10 @@
+--- tleap/unitio.c.orig	Sat Nov  9 18:37:02 2002
++++ tleap/unitio.c	Fri Feb 14 12:20:38 2003
+@@ -5958,6 +5958,7 @@
+  *TODO: Add CAP information
+  */
+ #define AMBERINDEX(i)   3*(i-1)
++#undef  INTFORMAT
+ #define INTFORMAT       "%6d"
+ #define DBLFORMAT       "%16.8lE"
+ #define LBLFORMAT       "%-4s"
diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr
index 6b5bb0463a4b..b4fcfcb34f6a 100644
--- a/biology/nab/pkg-descr
+++ b/biology/nab/pkg-descr
@@ -1,20 +1,23 @@
-This is version 4.4 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 version 4.5 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.
 
 Further general information can be obtained from our web page:
 
 WWW: http://www.scripps.edu/case/
 
-Although we have been using this code for some time now, users should be
-aware that bugs may still exist.  Please see the file COPYING for the usual
-disclaimer of liability.  Further enhancements are planned, and will be
-announced on the web page.
+Although we have been using this code for some time now, users
+should be aware that bugs may still exist.  Please see the file
+COPYING for the usual disclaimer of liability.  Further
+enhancements are planned, and will be announced on the web page.
 
-Please send comments and suggestions to Tom Macke (macke@scripps.edu) and/or
-to Dave Case (case@scripps.edu).  If you find the program useful, please
-send us a note outlining your applications.
+Please send comments and suggestions to Tom Macke
+(macke@scripps.edu) and/or to Dave Case (case@scripps.edu).  If
+you find the program useful, please send us a note outlining your
+applications.
 
-This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical Branch, Galveston
+This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical
+Branch, Galveston
 bdodson@scms.utmb.edu
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index ba96f8b296ca..1d3ca0851424 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -9,7 +9,6 @@ bin/transform
 bin/tss_init
 bin/tss_main
 bin/tss_next
-bin/ucpp
 include/defreal.h
 include/nab.h
 include/nabcode.h
@@ -19,90 +18,17 @@ lib/libnab.a
 lib/libsym.a
 share/doc/nab/NAB.pdf
 share/nab/bin/matextract
-share/nab/bin/matmul
-share/nab/bin/teLeap
-share/nab/bin/tss_main
 share/nab/bin/matgen
-share/nab/bin/nab
-share/nab/bin/transform
-share/nab/bin/tss_next
 share/nab/bin/matmerge
+share/nab/bin/matmul
+share/nab/bin/nab
 share/nab/bin/nab2c
+share/nab/bin/teLeap
+share/nab/bin/transform
 share/nab/bin/tss_init
-share/nab/bin/ucpp
-share/nab/examples/test.pdb
-share/nab/examples/ADE.pdb
-share/nab/examples/README
-share/nab/examples/Makefile
-share/nab/examples/program_9.nab
-share/nab/examples/gcg10.pdb
-share/nab/examples/program_8.nab
-share/nab/examples/program_7.nab
-share/nab/examples/program_6.nab
-share/nab/examples/rna_pseudoknot.pdb
-share/nab/examples/THY.pdb
-share/nab/examples/program_5.gcg.in
-share/nab/examples/program_5.nab
-share/nab/examples/getbase.nab
-share/nab/examples/program_14.nab
-share/nab/examples/program_4.ref
-share/nab/examples/program_4.nab
-share/nab/examples/acgtacgt.pdb
-share/nab/examples/program_5.tat.in
-share/nab/examples/program_3.nab
-share/nab/examples/program_12.nab
-share/nab/examples/program_2.ref
-share/nab/examples/program_2.nab
-share/nab/examples/program_13.nab
-share/nab/examples/program_5.cgc.in
-share/nab/examples/program_1.nab
-share/nab/examples/program_10.nab
-share/nab/examples/program_5.ata.in
-share/nab/examples/test.sup.pdb
-share/nab/examples/program_11.nab
-share/nab/examples/gcg10.pdb.save
-share/nab/test/get_sugar_info.nab
-share/nab/test/get_pep_info.nab
-share/nab/test/read_obs_shifts.nab
-share/nab/test/hash.out.check
-share/nab/test/ico.sym.out.check
-share/nab/test/2.pdb
-share/nab/test/sbcoil.nab
-share/nab/test/ltest.nab
-share/nab/test/prmtop
-share/nab/test/reflexive.nab
-share/nab/test/reflexive.out
-share/nab/test/duplex.in
-share/nab/test/hash.in
-share/nab/test/gbrna.prmtop
-share/nab/test/fd.nab
-share/nab/test/gbrna.out.check
-share/nab/test/d01.pdb.check
-share/nab/test/fd.pdb.check
-share/nab/test/d01.lin.check
-share/nab/test/swap_shifts.nab
-share/nab/test/shifts.h
-share/nab/test/ico.sym
-share/nab/test/gbrna.pdb
-share/nab/test/gbrna.nab
-share/nab/test/tbv.60.com.pdb.check
-share/nab/test/hash.nab
-share/nab/test/5pti.shifts.check
-share/nab/test/5pti.obs
-share/nab/test/5pti.pdb
-share/nab/test/dna.circle.nab
-share/nab/test/tbv.com.pdb
-share/nab/test/pointplane.nab
-share/nab/test/dg_gyrate.nab
-share/nab/test/getresid_from_pdb.nab
-share/nab/test/get_ring_info.nab
-share/nab/test/shifts.nab
-share/nab/test/write_sander_inp.nab
-share/nab/test/duplex.nab
-share/nab/test/ltest.out.check
-share/nab/test/dg_gyrate.out.check
-share/nab/suppose/suppose.1
-share/nab/suppose/suppose.nab
+share/nab/bin/tss_main
+share/nab/bin/tss_next
+share/nab/coords
 share/nab/dgdb/adna.basepair.db
 share/nab/dgdb/adna.nucleotide.db
 share/nab/dgdb/adna.stack.db
@@ -120,210 +46,305 @@ 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/peptide/peptide.nab
+share/nab/examples/ADE.pdb
+share/nab/examples/Makefile
+share/nab/examples/README
+share/nab/examples/THY.pdb
+share/nab/examples/acgtacgt.pdb
+share/nab/examples/gcg10.pdb
+share/nab/examples/gcg10.pdb.save
+share/nab/examples/getbase.nab
+share/nab/examples/program_1.nab
+share/nab/examples/program_10.nab
+share/nab/examples/program_11.nab
+share/nab/examples/program_12.nab
+share/nab/examples/program_13.nab
+share/nab/examples/program_14.nab
+share/nab/examples/program_2.nab
+share/nab/examples/program_2.ref
+share/nab/examples/program_3.nab
+share/nab/examples/program_4.nab
+share/nab/examples/program_4.ref
+share/nab/examples/program_5.ata.in
+share/nab/examples/program_5.cgc.in
+share/nab/examples/program_5.gcg.in
+share/nab/examples/program_5.nab
+share/nab/examples/program_5.tat.in
+share/nab/examples/program_6.nab
+share/nab/examples/program_7.nab
+share/nab/examples/program_8.nab
+share/nab/examples/program_9.nab
+share/nab/examples/rna_pseudoknot.pdb
+share/nab/examples/test.pdb
+share/nab/examples/test.sup.pdb
+share/nab/fd_data/abdna.dat
+share/nab/fd_data/abdna.dat.old
+share/nab/fd_data/adna.dat
+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/defreal.h
+share/nab/include/nab.h
+share/nab/include/nabcode.h
+share/nab/include/nabtypes.h
+share/nab/lib/cifparse.a
+share/nab/lib/libnab.a
+share/nab/lib/libsym.a
 share/nab/peptide/README
-share/nab/reslib/leap.log
-share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
-share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
-share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
-share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
-share/nab/reslib/charlie.star.note
+share/nab/peptide/peptide.nab
+share/nab/reslib/adna.std.rlb
+share/nab/reslib/adna.std/adna.std.bnd
+share/nab/reslib/adna.std/adna.std.pdb
+share/nab/reslib/ala.off
+share/nab/reslib/arna.std.rlb
+share/nab/reslib/arna.std/arna.std.bnd
+share/nab/reslib/arna.std/arna.std.pdb
+share/nab/reslib/axes.rlb
 share/nab/reslib/axes/Axes.bnd
 share/nab/reslib/axes/XYZ.axes
-share/nab/reslib/dna3/dna3.qr
+share/nab/reslib/bdna.std.rlb
+share/nab/reslib/bdna.std/bdna.std.bnd
+share/nab/reslib/bdna.std/bdna.std.chi
+share/nab/reslib/bdna.std/bdna.std.pdb
+share/nab/reslib/bdna.std/dna.qr
+share/nab/reslib/bounds.db
+share/nab/reslib/cdd.mol2
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 @dirrm share/nab/test
-@dirrm share/nab/peptide
 @dirrm share/nab/suppose
-@dirrm share/nab/dgdb
+@dirrm share/nab/reslib/rna.amberua
+@dirrm share/nab/reslib/rna.amber94
+@dirrm share/nab/reslib/protein.opls
+@dirrm share/nab/reslib/protein.amber94
+@dirrm share/nab/reslib/pro-dna.nmr
+@dirrm share/nab/reslib/leap
 @dirrm share/nab/reslib/hetatm.amber94
-@dirrm share/nab/reslib/axes
 @dirrm share/nab/reslib/dna3
-@dirrm share/nab/reslib/leap
+@dirrm share/nab/reslib/dna.amberua
+@dirrm share/nab/reslib/dna.amber94
 @dirrm share/nab/reslib/bdna.std
+@dirrm share/nab/reslib/axes
 @dirrm share/nab/reslib/arna.std
 @dirrm share/nab/reslib/adna.std
-@dirrm share/nab/reslib/protein.opls
-@dirrm share/nab/reslib/dna.amber94
-@dirrm share/nab/reslib/rna.amber94
-@dirrm share/nab/reslib/rna.amberua
-@dirrm share/nab/reslib/dna.amberua
-@dirrm share/nab/reslib/protein.amber94
-@dirrm share/nab/reslib/pro-dna.nmr
 @dirrm share/nab/reslib
+@dirrm share/nab/peptide
+@dirrm share/nab/lib
+@dirrm share/nab/include
 @dirrm share/nab/fd_data
+@dirrm share/nab/examples
+@dirrm share/nab/dgdb
+@dirrm share/nab/bin
 @dirrm share/nab
+@dirrm share/doc/nab