- Update to 5.0

- Cleanups

PR:		ports/80372
Submitted by:	maintainer

15 files changed, 851 insertions, 782 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index 95a223dc4cbb..0bc31fead397 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -6,91 +6,72 @@
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.6
+PORTVERSION=	5.0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
-		http://www.scripps.edu/case/ \
+MASTER_SITES=	http://www.scripps.edu/case/ \
 		http://siegfried.utmb.edu/bdodson/
 
 MAINTAINER=	bdodson@scms.utmb.edu
-COMMENT=	\
- "This is nab (nucleic acid builder), a language for macromolecules"
+COMMENT=	A language for macromolecules
 
 BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
 
 ONLY_FOR_ARCHS=	i386
 
-MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH}
+MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \
+		CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
 
 MAN1=		nab.1
-MANCOMPRESSED=	yes
-USE_REINPLACE=	yes
+SUB_FILES=	pkg-message
 
-BINARIES=	matextract      matmul          teLeap          tss_main \
-		matgen          nab             transform       tss_next \
-		matmerge        nab2c           tss_init
+BINARIES=	matextract	matmul		teLeap		tss_main \
+		matgen		nab		transform	tss_next \
+		matmerge	nab2c		tss_init
 
-LIBRARIES=	cifparse.a      libnab.a        libsym.a
+LIBRARIES=	cifparse.a	libnab.a        libsym.a
 
-INCS=	defreal.h       nab.h           nabcode.h       nabtypes.h
+INCS=	defreal.h	nab.h		nabcode.h	nabtypes.h
 
 post-extract:
 	@${CP} ${FILESDIR}/config.h ${WRKSRC}
 
-pre-patch:
-	@${REINPLACE_CMD} -e 's,<malloc.h>,<stdlib.h>,' \
-		${WRKSRC}/cifparse/cifparse.c
-
 post-patch:
-	@${RM} -f ${WRKSRC}/examples/program_7.nab.orig
-	@${RM} -f ${WRKSRC}/examples/program_1.c \
-		${WRKSRC}/examples/program_1.exe
-	@${RM} -f ${WRKSRC}/test/1ubq/a.exe
-	@${RM} -f ${WRKSRC}/test/1ubq/rattle_min.c
-	@${RM} -f ${WRKSRC}/test/1ubq/runleap.c
-	@${RM} -f ${WRKSRC}/test/*.exe
-	@${RM} -f ${WRKSRC}/tleap/utilMakeHelp.exe
-	@${RM} -f ${WRKSRC}/fd_data/abdna.dat.old
+	@${RM} -f ${WRKSRC}/examples/circle.c
 	@${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]' | \
-			${XARGS} ${RM} -f)
 
 pre-install:
 	@cd ${WRKSRC}/src && \
-		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall
+		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} beforerealinstall
 
 do-install:
-	@-${MKDIR} ${PREFIX}/share/nab
-	@-${MKDIR} ${PREFIX}/share/nab/bin
-	@-${MKDIR} ${PREFIX}/share/nab/include
-	@-${MKDIR} ${PREFIX}/share/nab/lib
+	${MKDIR} ${DATADIR}/bin ${DATADIR}/include ${DATADIR}/lib
+	cd ${WRKSRC}/test && ${RM} -f gbrna.pdb.lpdb rembed.out
 .if !defined(NOPORTDOCS)
-	@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
+	cd ${WRKSRC} && (${TAR} cf - benchmarks examples test peptide suppose | \
+		(cd ${DATADIR}; ${TAR} xf -))
+	${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR}
 .endif
-	@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)
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/*     ${PREFIX}/bin
+	cd ${WRKSRC} && (${TAR} cf - dgdb reslib fd_data leap | \
+		(cd ${DATADIR}; ${TAR} xf -))
+	${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${DATADIR}/*
+	cd ${DATADIR} && ${LN} -sf ../NDB coords
+	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${PREFIX}/bin
 .for f in ${INCS}
-	${INSTALL_DATA}    ${WRKSRC}/include/${f} ${PREFIX}/include
-	@-(cd ${PREFIX}/share/nab/include && ${LN} -sf ${PREFIX}/include/${f} .)
+	${INSTALL_DATA} ${WRKSRC}/include/${f} ${PREFIX}/include
+	cd ${DATADIR}/include && ${LN} -sf ${PREFIX}/include/${f} .
 .endfor
-	${INSTALL_DATA} ${WRKSRC}/config.h ${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
+	${INSTALL_DATA} ${WRKSRC}/config.h ${DATADIR}
+	${INSTALL_MAN} ${WRKSRC}/doc/nab.1 ${MAN1PREFIX}/man/man1
 .for f in ${BINARIES}
-	@cd ${PREFIX}/share/nab/bin && ${LN} -sf ../../../bin/${f} .
+	cd ${DATADIR}/bin && ${LN} -sf ${PREFIX}/bin/${f} .
 .endfor
 .for f in ${LIBRARIES}
-	@cd ${PREFIX}/share/nab/lib && ${LN} -sf ../../../lib/${f} .
+	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib
+	cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} .
+.endfor
+.for f in blas.a lapack.a
+	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib
 .endfor
 
 post-install:
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index be2704233758..186fc15e8374 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1,2 +1,2 @@
-MD5 (nab-4.6.tar.gz) = ec1e51b8a9f6d5a46770b952f0e59d26
-SIZE (nab-4.6.tar.gz) = 3794078
+MD5 (nab-5.0.tar.gz) = dfcde2ddaa833f4dc24d53c87b842cf9
+SIZE (nab-5.0.tar.gz) = 5853573
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
index cd5dece57ec8..7dd5649fc85d 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -1,114 +1,70 @@
+#  NAB configuration file, created with: ./configure 
+
 ###############################################################################
-# Configuration section:  look at sections (1) to (4) below, making
-#      changes that seem necessary.  For many UNIX systems, no changes
-#      should be necessary, but check especially the compiler options in
-#      section (4).
-#
-###############################################################################
-#
-# (1)  You need to define the symbols NABHOME and ARCH, either on the
-#    make command line (e.g. "make ARCH=sun4 NABHOME=/thr/eigen/nab5")
-#    or as environment variables.
-#
-#    NABHOME should be an absolute path to this directory.
-#    ARCH is used to distinguish compilations for various architectures.
-#
-#    Files created by "make install" end up in:
-#        $NABHOME/bin/$ARCH
-#        $NABHOME/lib/$ARCH
-#        $NABHOME/include
-#
-#       You can choose ARCH as you wish, but it would generally 
-#       be related to the output of the "uname" command.
-#
+
+# (1)  You need to define the symbol NABHOME in your environment
+
+#    NABHOME should be an absolute path to the top-level NAB directory;
+#    files are installed to the following directories:
+
 BINDIR=$(NABHOME)/bin
 LIBDIR=$(NABHOME)/lib
 INCDIR=$(NABHOME)/include
-#
+
 ###############################################################################
-#
-#
+
+
 #  (2) If you want to search additional libraries by default, add them
 #      to the FLIBS variable here.  (External libraries can also be linked into
 #      NAB programs simply by including them on the command line; libraries
 #      included in FLIBS are always searched.)
-#
-#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a
-#
-#  following for linking in fortran subroutines on Sun4, Solaris 2.x
-#
-#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a -lF77 -lM77 -lsunmath
-#
-#  following for HP-UX
-#
-#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a lapack.a blas.a -lf -lvec
-#
-###############################################################################
-#
-#  (3)  Set AVS to 1 if you want AVS support; if so, set AVSDIR to point to
-#       your AVS distribution.  The directories $AVSDIR/include and $AVSDIR/lib
-#       must exist, and CFLAGS (below) must also be modified for AVS support.
-#
-AVS=		0
-#
-#AVSDIR=	/tsri/avs/$(ARCH)/avs
-#AVSINCDIR=	$(AVSDIR)/include
-#
-#
+
+FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a  -lg2c
+
 ###############################################################################
-#
-#  (4)  Modify any of the following if you need to change, e.g. to use gcc
+
+#  (3)  Modify any of the following if you need to change, e.g. to use gcc
 #        rather than cc, etc.
-#
-#
+
 SHELL=		/bin/sh
-#
+
 #  Set the C compiler, etc. 
-#
-#          For GNU:  cc-->gcc; lex-->flex; yacc-->bison -y -t;
-#          Note: If you lexer is "really" flex, you need to set
+
+#          For GNU:  CC-->gcc; LEX-->flex; YACC-->bison -y -t;
+#          Note: If your lexer is "really" flex, you need to set
 #          LEX=flex below.  For example, on many linux distributions,
 #          /usr/bin/lex is really just a pointer to /usr/bin/flex,
 #          so LEX=flex is necessary.  In general, gcc seems to need
 #          flex.
-#
-#          For 64-bit IRIX, add "-n32" unless 64-bit objects are 
-#          needed; it is also useful to add "-Wl,-dont_warn_unused"
-#          to keep the loader from complaining about libraries that
-#          are not used.
-#
-#          For RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
-#
-#CC=
-LEX=    	flex
-YACC=   	yacc
-AR=		ar
-#
+
+CC?=		cc
+CFLAGS?= 
+OCFLAGS=${CFLAGS}
+NABFLAGS?= 
+
+LEX=    flex
+YACC=   yacc
+AR=	ar
+RANLIB=	ranlib
+
 #  Set the C-preprocessor.  Code for a small preprocessor is in
-#    uccp-0.7;  it gets installed as $(NABHOME)/bin/$(ARCH)/ucpp;
+#    uccp-1.3;  it gets installed as $(NABHOME)/bin/ucpp;
 #    this should generally *not* be changed.
-#  Changed 14 Feb 2003 to use the ucpp port (FreeBSD). MLD
-#
-#  For FreeBSD 4.x, I had problems using the system C-preprocessor. MLD
-#
+
 CPP=    ucpp -l
-#
-#  Use these CFLAGS if AVS = 0
-#
-# Pick up initial CFLAGS from /etc/make.conf instead of here
-# This is a Berkeley make- (pmake-)specific construct
-CFLAGS+=
-OCFLAGS= ${CFLAGS}
-NABFLAGS=
-#
-#  Use these CFLAGS if AVS = 1
-#
-#CFLAGS= 	-g -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR)
-#OCFLAGS= 	-O -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR)
-#
-#
-#  For Win95/98, set SFX to ".exe"; for Unix,NT leave it empty:
-#
-#SFX=.exe
+
+#  If you are going to use the Fortran lapack and blas libraries, you need
+#  to set the compiler information here.  (Also, add the appropriate entries
+#  to the FLIBS variable, above.)
+
+FC?=f77
+FFLAGS?=
+FOPTFLAGS=${FFLAGS}
+FREEFORMAT_FLAG=-ffree-form
+LAPACK=install
+BLAS=install
+
+#  For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty:
+
 SFX=
-#
+
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
index 493b85bcda86..d754d329ca56 100644
--- a/biology/nab/files/patch-Makefile
+++ b/biology/nab/files/patch-Makefile
@@ -1,28 +1,30 @@
---- Makefile.orig	Tue May 18 15:46:55 2004
-+++ Makefile	Thu Jul  1 09:03:32 2004
-@@ -1,16 +1,15 @@
- #   top-level Makefile for the NAB suite of programs
+--- Makefile.orig	Thu Apr  7 20:18:20 2005
++++ Makefile	Mon Apr 25 13:37:39 2005
+@@ -2,42 +2,39 @@
  
-+all:	compiler test
- compiler:
- 	-mkdir bin lib include
+ include config.h
+ 
++all: install test
++
+ install:
+ 	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
 -	(cd ucpp-1.3; make install )
 -	(cd byacc; 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.
-@@ -19,18 +18,15 @@
- 	(cd nss; make test )
+-	(cd lapack; make $(LAPACK) )
+-	(cd blas; make $(BLAS) )
+-	(cd cifparse; make install )
+-	(cd src; make install )
+-	(cd nss; make install )
+-	(cd tleap; make install )
++	(cd lapack; env NABHOME=.. make $(LAPACK) )
++	(cd blas; env NABHOME=.. make $(BLAS) )
++	(cd cifparse; env NABHOME=.. make install )
++	(cd src; env NABHOME=.. make install )
++	(cd nss; env NABHOME=.. make install )
++	(cd tleap; env NABHOME=.. make install )
+ 	@echo
+ 	@echo "completed installation of NAB version 5"
+ 	@echo
  
  clean:
 -	(cd ucpp-1.3; make clean )
@@ -31,14 +33,25 @@
  	(cd src; make clean )
  	(cd nss; make clean )
  	(cd tleap; make clean )
+ 	(cd lapack; make clean )
+ 	(cd blas; make clean )
 -	
 +
- uninstall:
+ uninstall: clean
 -	(cd ucpp-1.3; make uninstall )
  	(cd cifparse; make uninstall )
  	(cd src; make uninstall )
  	(cd nss; make uninstall )
  	(cd tleap; make uninstall )
  	-/bin/rm config.h
+ 	-rm -rf $(BINDIR) $(LIBDIR) $(INCDIR)
 -	
 +
+ #   note:  "make test" needs to follow "make", since it is very hard to
+ #          tell if the compiler is completely "made" or not.
+ 
+ test::
+-	(cd test; make test)
+-	(cd nss; make test)
++	(cd test; env NABHOME=.. make test)
++	(cd nss; env NABHOME=.. make test)
diff --git a/biology/nab/files/patch-ac b/biology/nab/files/patch-ac
deleted file mode 100644
index e3c6e85535de..000000000000
--- a/biology/nab/files/patch-ac
+++ /dev/null
@@ -1,18 +0,0 @@
-*** src/Makefile.orig	Mon Nov 13 13:37:07 2000
---- src/Makefile	Mon Jan 29 12:33:37 2001
-***************
-*** 175,180 ****
---- 175,187 ----
-  	cp defreal.h $(INCDIR)
-  	cp nab.h $(INCDIR)
-  
-+ beforerealinstall: 
-+ 	$(CC) -DBINDIR='"$(PREFIX)/bin"' \
-+ 		-DINCDIR='"$(PREFIX)/include"' \
-+ 		-DLIBDIR='"$(PREFIX)/lib"' \
-+ 		$(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' -DFLIBS='"$(FLIBS)"' \
-+ 		-o ../bin/nab nab.c
-+ 
-  uninstall: clean
-  	-rm -f \
-          $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \
diff --git a/biology/nab/files/patch-src:database.c b/biology/nab/files/patch-src:database.c
deleted file mode 100644
index 14e70c31326a..000000000000
--- a/biology/nab/files/patch-src:database.c
+++ /dev/null
@@ -1,25 +0,0 @@
---- 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
- 
- 
- 
-@@ -71,7 +78,7 @@
- 
- #include	<stdio.h>
- #include	<string.h>
--#include	<malloc.h>
-+#include	<stdlib.h>
- 
- #include        "database.h"
- 
diff --git a/biology/nab/files/patch-src:molio.c b/biology/nab/files/patch-src:molio.c
deleted file mode 100644
index 656042bb2f24..000000000000
--- a/biology/nab/files/patch-src:molio.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- src/molio.c.orig	Mon May 10 16:53:34 2004
-+++ src/molio.c	Fri Jun 18 23:26:01 2004
-@@ -1,7 +1,6 @@
- #include	<stdio.h>
- #include	<ctype.h>
- #include	<string.h>
--#include	<malloc.h>
- #include	<math.h>
- #include	<stdlib.h>
- #include	<assert.h>
diff --git a/biology/nab/files/patch-src_Makefile b/biology/nab/files/patch-src_Makefile
new file mode 100644
index 000000000000..23bce990b0e3
--- /dev/null
+++ b/biology/nab/files/patch-src_Makefile
@@ -0,0 +1,17 @@
+--- src/Makefile.orig	Thu Apr  7 20:17:27 2005
++++ src/Makefile	Tue Apr 26 12:54:15 2005
+@@ -181,6 +181,14 @@
+ 	cp defreal.h $(INCDIR)
+ 	cp nab.h $(INCDIR)
+ 
++beforerealinstall:
++	$(CC) -DBINDIR='"$(PREFIX)/bin"' \
++		-DINCDIR='"$(PREFIX)/include"' \
++		-DLIBDIR='"$(NABHOME)/lib"' \
++		$(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' \
++		-DFLIBS='"$(PREFIX)/share/nab/lib/libsym.a $(PREFIX)/share/nab/lib/lapack.a $(PREFIX)/share/nab/lib/blas.a -lg2c"' \
++		-static -o ../bin/nab${SFX} nab.c
++
+ uninstall: clean
+ 	-rm -f \
+         $(BINDIR)/nab2c$(SFX) $(BINDIR)/nab$(SFX) $(INCDIR)/nabcode.h \
diff --git a/biology/nab/files/patch-src_cgen.c b/biology/nab/files/patch-src_cgen.c
new file mode 100644
index 000000000000..c6538200406e
--- /dev/null
+++ b/biology/nab/files/patch-src_cgen.c
@@ -0,0 +1,21 @@
+--- src/cgen.c.orig	Thu Apr  7 20:17:27 2005
++++ src/cgen.c	Sun Apr 17 20:21:22 2005
+@@ -102,6 +102,7 @@
+ void	CG_genpids( NODE_T * );
+ void	CG_genpdecl( NODE_T * );
+ char	*CG_gentemp( int );
++void	CG_gennull( void );
+ 
+ static	int	getdims( NODE_T *, int, int, int *, NODE_T *[] );
+ static	NODE_T	*mk_arraysize( int, NODE_T *[], int );
+@@ -115,6 +116,10 @@
+ static	void	CG_debug( char [], NODE_T *, int );
+ 
+ FILE	*tmpfile();
++
++void	CG_gennull( )
++{
++}
+ 
+ int	CG_init( char cfname[], int aopt )
+ {
diff --git a/biology/nab/files/patch-src_nabgrm.y b/biology/nab/files/patch-src_nabgrm.y
new file mode 100644
index 000000000000..348e3a157d8b
--- /dev/null
+++ b/biology/nab/files/patch-src_nabgrm.y
@@ -0,0 +1,20 @@
+--- src/nabgrm.y.orig	Thu Apr  7 20:17:27 2005
++++ src/nabgrm.y	Sun Apr 17 20:21:36 2005
+@@ -41,6 +41,8 @@
+ 
+ # define YYSTYPE_IS_DECLARED 1
+ 
++#define YYSTYPE_IS_DECLARED 1
++
+ %}
+ 
+ %token	<ival>	SYM_ADDRESS
+@@ -299,7 +301,7 @@
+ 		  f_stmtpart SYM_RBRACE
+ 				{ CG_genestmts( TRUE );
+ 				  CG_genop( NULL, SYM_RBRACE ); }
+-		  SYM_SEMICOLON ;
++		  SYM_SEMICOLON { CG_gennull ( ); } ;
+ f_defpart	: lv_decls 
+ 		| 		{ $$ = NULL; } ;
+ lv_decls	: var_decl
diff --git a/biology/nab/files/patch-tleap:database.c b/biology/nab/files/patch-tleap:database.c
deleted file mode 100644
index c6004d1d9a24..000000000000
--- a/biology/nab/files/patch-tleap:database.c
+++ /dev/null
@@ -1,16 +0,0 @@
---- 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
deleted file mode 100644
index 8b3048548a01..000000000000
--- a/biology/nab/files/patch-unitio.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- 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/files/pkg-message.in b/biology/nab/files/pkg-message.in
new file mode 100644
index 000000000000..e89f4516b02e
--- /dev/null
+++ b/biology/nab/files/pkg-message.in
@@ -0,0 +1,8 @@
+-------------------------------------------------------------------------------
+You must set the environment variable NABHOME to
+
+  %%DATADIR%%
+
+before nab is used. This is needed so that nab can find its residue and
+structure databases.
+-------------------------------------------------------------------------------
diff --git a/biology/nab/pkg-message b/biology/nab/pkg-message
deleted file mode 100644
index 349abd45952d..000000000000
--- a/biology/nab/pkg-message
+++ /dev/null
@@ -1,6 +0,0 @@
--------------------------------------------------------------------------------
-You must set the environment variable NABHOME before nab is used.  This is
-needed so that nab can find its residue and structure databases. This should be
-NABHOME=${PREFIX}/share/nab, where ${PREFIX} was the value of the PREFIX
-makefile variable when nab was built.
--------------------------------------------------------------------------------
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index 191041c7cab2..7e3d1c88e4e5 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -16,529 +16,667 @@ include/nabtypes.h
 lib/cifparse.a
 lib/libnab.a
 lib/libsym.a
-%%DOCSDIR%%/NAB.pdf
-share/nab/bin/matextract
-share/nab/bin/matgen
-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/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
-share/nab/dgdb/arna.basepair.db
-share/nab/dgdb/arna.nucleotide.db
-share/nab/dgdb/arna.stack.db
-share/nab/dgdb/bdna.basepair.db
-share/nab/dgdb/bdna.nucleotide.db
-share/nab/dgdb/bdna.stack.db
-share/nab/dgdb/dna.basepair.db
-share/nab/dgdb/rna.basepair.db
-share/nab/dgdb/trna.basepair.db
-share/nab/dgdb/trna.nucleotide.db
-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/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/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
-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/mme_typical_calling_sequence.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/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/config.h
-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/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/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/conf.lib
-share/nab/reslib/dna.amber94.3.rlb
-share/nab/reslib/dna.amber94.5.rlb
-share/nab/reslib/dna.amber94.rlb
-share/nab/reslib/dna.amber94/ade.pdb
-share/nab/reslib/dna.amber94/dna.amber94.3.bnd
-share/nab/reslib/dna.amber94/dna.amber94.3.pdb
-share/nab/reslib/dna.amber94/dna.amber94.3.qr
-share/nab/reslib/dna.amber94/dna.amber94.35.chi
-share/nab/reslib/dna.amber94/dna.amber94.5.bnd
-share/nab/reslib/dna.amber94/dna.amber94.5.pdb
-share/nab/reslib/dna.amber94/dna.amber94.5.qr
-share/nab/reslib/dna.amber94/dna.amber94.bnd
-share/nab/reslib/dna.amber94/dna.amber94.chi
-share/nab/reslib/dna.amber94/dna.amber94.pdb
-share/nab/reslib/dna.amber94/dna.amber94.qr
-share/nab/reslib/dna.amber94/dna.amber94_nmr.3.qr
-share/nab/reslib/dna.amber94/dna.amber94_nmr.5.qr
-share/nab/reslib/dna.amber94/dna.amber94_nmr.qr
-share/nab/reslib/dna.amber94_nmr.3.rlb
-share/nab/reslib/dna.amber94_nmr.5.rlb
-share/nab/reslib/dna.amber94_nmr.rlb
-share/nab/reslib/dna.amberua.3.rlb
-share/nab/reslib/dna.amberua.5.rlb
-share/nab/reslib/dna.amberua.rlb
-share/nab/reslib/dna.amberua/dna.amberua.3.bnd
-share/nab/reslib/dna.amberua/dna.amberua.3.pdb
-share/nab/reslib/dna.amberua/dna.amberua.3.qr
-share/nab/reslib/dna.amberua/dna.amberua.5.bnd
-share/nab/reslib/dna.amberua/dna.amberua.5.pdb
-share/nab/reslib/dna.amberua/dna.amberua.5.qr
-share/nab/reslib/dna.amberua/dna.amberua.bnd
-share/nab/reslib/dna.amberua/dna.amberua.chi
-share/nab/reslib/dna.amberua/dna.amberua.pdb
-share/nab/reslib/dna.amberua/dna.amberua.qr
-share/nab/reslib/dna3.rlb
-share/nab/reslib/dna3/dna3.bnd
-share/nab/reslib/dna3/dna3.chi
-share/nab/reslib/dna3/dna3.pdb
-share/nab/reslib/dna3/dna3.qr
-share/nab/reslib/hetatm.amber94.rlb
-share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
-share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
-share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
-share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
-share/nab/reslib/leap/0README
-share/nab/reslib/leap/Notes
-share/nab/reslib/leap/all_amino91.lib
-share/nab/reslib/leap/all_amino94.lib
-share/nab/reslib/leap/all_aminoct91.lib
-share/nab/reslib/leap/all_aminoct94.lib
-share/nab/reslib/leap/all_aminont91.lib
-share/nab/reslib/leap/all_aminont94.lib
-share/nab/reslib/leap/all_nucleic91.lib
-share/nab/reslib/leap/all_nucleic94.lib
-share/nab/reslib/leap/dna.amberua.lib
-share/nab/reslib/leap/dna.amberua.redch.lib
-share/nab/reslib/leap/ions91.lib
-share/nab/reslib/leap/ions94.lib
-share/nab/reslib/leap/leaprc.dna.amberua
-share/nab/reslib/leap/leaprc.dna.amberua.redch
-share/nab/reslib/leap/leaprc.nmr
-share/nab/reslib/leap/leaprc.protein.amberua
-share/nab/reslib/leap/leaprc.ff03
-share/nab/reslib/leap/solvents.lib
-share/nab/reslib/leap/frcmod.ff03
-share/nab/reslib/leap/all_amino03.lib
-share/nab/reslib/leap/parm99.dat
-share/nab/reslib/leap/leaprc.rna
-share/nab/reslib/leap/leaprc.rna.amberua
-share/nab/reslib/leap/leaprc.std
-share/nab/reslib/leap/leaprc.stdX
-share/nab/reslib/leap/na.amberua.prepin
-share/nab/reslib/leap/opls_parm.dat
-share/nab/reslib/leap/parm91.lib
-share/nab/reslib/leap/parm91X.dat
-share/nab/reslib/leap/parm91X.ua.dat
-share/nab/reslib/leap/parm94.dat
-share/nab/reslib/leap/parm94X.dat
-share/nab/reslib/leap/pro-dna91.nmr.lib
-share/nab/reslib/leap/pro-dna91.nmr.prepin
-share/nab/reslib/leap/protein.amberua.C.prepin
-share/nab/reslib/leap/protein.amberua.N.prepin
-share/nab/reslib/leap/protein.amberua.lib
-share/nab/reslib/leap/protein.amberua.prepin
-share/nab/reslib/leap/protein.opls.lib
-share/nab/reslib/leap/rna.amberua.lib
-share/nab/reslib/leap/water.lib
-share/nab/reslib/off2star
-share/nab/reslib/parm94.star
-share/nab/reslib/pep1.off
-share/nab/reslib/pro-dna.nmr/pro-dna.nmr.input
-share/nab/reslib/pro-dna.nmr/pro-dna.nmr.off
-share/nab/reslib/pro-dna.nmr/pro-dna.nmr.star
-share/nab/reslib/protein.amber94.C.rlb
-share/nab/reslib/protein.amber94.N.rlb
-share/nab/reslib/protein.amber94.rlb
-share/nab/reslib/protein.amber94/protein.amber94.C.bnd
-share/nab/reslib/protein.amber94/protein.amber94.C.pdb
-share/nab/reslib/protein.amber94/protein.amber94.C.qr
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-share/nab/reslib/protein.amber94/protein.amber94.bnd
-share/nab/reslib/protein.amber94/protein.amber94.chi
-share/nab/reslib/protein.amber94/protein.amber94.pdb
-share/nab/reslib/protein.amber94/protein.amber94.qr
-share/nab/reslib/protein.amber94/protein.amber94_nmr.qr
-share/nab/reslib/protein.amber94_nmr.rlb
-share/nab/reslib/protein.opls.rlb
-share/nab/reslib/protein.opls/protein.opls.bnd
-share/nab/reslib/protein.opls/protein.opls.chi
-share/nab/reslib/protein.opls/protein.opls.pdb
-share/nab/reslib/protein.opls/protein.opls.qr
-share/nab/reslib/rna.amber94.3.rlb
-share/nab/reslib/rna.amber94.5.rlb
-share/nab/reslib/rna.amber94.rlb
-share/nab/reslib/rna.amber94/rna.amber94.3.bnd
-share/nab/reslib/rna.amber94/rna.amber94.3.pdb
-share/nab/reslib/rna.amber94/rna.amber94.3.qr
-share/nab/reslib/rna.amber94/rna.amber94.5.bnd
-share/nab/reslib/rna.amber94/rna.amber94.5.pdb
-share/nab/reslib/rna.amber94/rna.amber94.5.qr
-share/nab/reslib/rna.amber94/rna.amber94.bnd
-share/nab/reslib/rna.amber94/rna.amber94.chi
-share/nab/reslib/rna.amber94/rna.amber94.pdb
-share/nab/reslib/rna.amber94/rna.amber94.qr
-share/nab/reslib/rna.amber94/rna.amber94_nmr.3.qr
-share/nab/reslib/rna.amber94/rna.amber94_nmr.5.qr
-share/nab/reslib/rna.amber94/rna.amber94_nmr.qr
-share/nab/reslib/rna.amber94_nmr.3.rlb
-share/nab/reslib/rna.amber94_nmr.5.rlb
-share/nab/reslib/rna.amber94_nmr.rlb
-share/nab/reslib/rna.amberua.3.rlb
-share/nab/reslib/rna.amberua.5.rlb
-share/nab/reslib/rna.amberua.rlb
-share/nab/reslib/rna.amberua/rna.amberua.3.bnd
-share/nab/reslib/rna.amberua/rna.amberua.3.pdb
-share/nab/reslib/rna.amberua/rna.amberua.3.qr
-share/nab/reslib/rna.amberua/rna.amberua.5.bnd
-share/nab/reslib/rna.amberua/rna.amberua.5.pdb
-share/nab/reslib/rna.amberua/rna.amberua.5.qr
-share/nab/reslib/rna.amberua/rna.amberua.bnd
-share/nab/reslib/rna.amberua/rna.amberua.chi
-share/nab/reslib/rna.amberua/rna.amberua.pdb
-share/nab/reslib/rna.amberua/rna.amberua.qr
-share/nab/suppose/Makefile
-share/nab/suppose/PCA_suppose.nab
-share/nab/suppose/ccmath.h
-share/nab/suppose/eigen.c
-share/nab/suppose/housev.c
-share/nab/suppose/matutl.h
-share/nab/suppose/qrevec.c
-share/nab/suppose/suppose.1
-share/nab/suppose/suppose.nab
-share/nab/suppose/trnm.c
-share/nab/test/2.pdb
-share/nab/test/5pti.obs
-share/nab/test/5pti.pdb
-share/nab/test/5pti.shifts.check
-share/nab/test/d01.lin.check
-share/nab/test/d01.pdb.check
-share/nab/test/dhfrndpmtx.prmtop
-share/nab/test/dg_gyrate.nab
-share/nab/test/dg_gyrate.out.check
-share/nab/test/dg_gyrate2.nab
-share/nab/test/dhfrndpmtx.ambpdb
-share/nab/test/dhfrndpmtx.nab
-share/nab/test/dhfrndpmtx.out.check
-share/nab/test/dna.circle.nab
-share/nab/test/duplex.in
-share/nab/test/duplex.nab
-share/nab/test/fd.nab
-share/nab/test/fd.pdb.check
-share/nab/test/gbrna.nab
-share/nab/test/gbrna.out.check
-share/nab/test/gbrna.pdb
-share/nab/test/gbrna.prmtop
-share/nab/test/gbrna_long.nab
-share/nab/test/gbtrx.nab
-share/nab/test/gbtrx.out.check
-share/nab/test/get_pep_info.nab
-share/nab/test/get_ring_info.nab
-share/nab/test/get_sugar_info.nab
-share/nab/test/getresid_from_pdb.nab
-share/nab/test/hash.in
-share/nab/test/hash.nab
-share/nab/test/hash.out.check
-share/nab/test/ico.sym
-share/nab/test/ico.sym.out.check
-share/nab/test/ltest.nab
-share/nab/test/ltest.out.check
-share/nab/test/mm_plus_dg.nab
-share/nab/test/pointplane.nab
-share/nab/test/prmtop
-share/nab/test/prmtop.gb2
-share/nab/test/pseudoknot.nab
-share/nab/test/rattle_md.nab
-share/nab/test/rattle_md.out.check
-share/nab/test/rattle_min.nab
-share/nab/test/rattle_min.out.check
-share/nab/test/read_obs_shifts.nab
-share/nab/test/reflexive.nab
-share/nab/test/reflexive.out
-share/nab/test/rembed.nab
-share/nab/test/rembed.out.check
-share/nab/test/sbcoil.nab
-share/nab/test/shifts.h
-share/nab/test/shifts.nab
-share/nab/test/swap_shifts.nab
-share/nab/test/tbv.60.com.pdb.check
-share/nab/test/tbv.com.pdb
-share/nab/test/trxox.2.4ns.pdb
-share/nab/test/trxox.2.4ns.x
-share/nab/test/write_sander_inp.nab
-@dirrm share/nab/test
-@dirrm share/nab/suppose
-@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/dna3
-@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
-@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/stacking
-@dirrm share/nab/dgdb/basepairs
-@dirrm share/nab/dgdb
-@dirrm share/nab/bin
-@dirrm share/nab
-@dirrm %%DOCSDIR%%
+%%PORTDOCS%%%%DOCSDIR%%/NAB.pdf
+%%PORTDOCS%%%%DATADIR%%/benchmarks/gbrna.nab
+%%PORTDOCS%%%%DATADIR%%/benchmarks/gbrna.out.check
+%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4_md.nab
+%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4_nr.nab
+%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4p1.mc.pdb
+%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.inpcrd
+%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.nab
+%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.out.check
+%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.pdb
+%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.prmtop
+%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.md1.x
+%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.nab
+%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.out.check
+%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.pdb
+%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.prmtop
+%%DATADIR%%/bin/matextract
+%%DATADIR%%/bin/matgen
+%%DATADIR%%/bin/matmerge
+%%DATADIR%%/bin/matmul
+%%DATADIR%%/bin/nab
+%%DATADIR%%/bin/nab2c
+%%DATADIR%%/bin/teLeap
+%%DATADIR%%/bin/transform
+%%DATADIR%%/bin/tss_init
+%%DATADIR%%/bin/tss_main
+%%DATADIR%%/bin/tss_next
+%%DATADIR%%/coords
+%%DATADIR%%/dgdb/adna.basepair.db
+%%DATADIR%%/dgdb/adna.nucleotide.db
+%%DATADIR%%/dgdb/adna.stack.db
+%%DATADIR%%/dgdb/arna.basepair.db
+%%DATADIR%%/dgdb/arna.nucleotide.db
+%%DATADIR%%/dgdb/arna.stack.db
+%%DATADIR%%/dgdb/basepairs/aa.I.pdb
+%%DATADIR%%/dgdb/basepairs/aa.II.pdb
+%%DATADIR%%/dgdb/basepairs/aa.V.pdb
+%%DATADIR%%/dgdb/basepairs/aa.Va.pdb
+%%DATADIR%%/dgdb/basepairs/ac.XXV.pdb
+%%DATADIR%%/dgdb/basepairs/ac.XXVI.pdb
+%%DATADIR%%/dgdb/basepairs/ag.IX.pdb
+%%DATADIR%%/dgdb/basepairs/ag.VIII.pdb
+%%DATADIR%%/dgdb/basepairs/ag.X.pdb
+%%DATADIR%%/dgdb/basepairs/ag.XI.pdb
+%%DATADIR%%/dgdb/basepairs/at.XX.pdb
+%%DATADIR%%/dgdb/basepairs/at.XXI.pdb
+%%DATADIR%%/dgdb/basepairs/at.XXIII.pdb
+%%DATADIR%%/dgdb/basepairs/at.XXIV.pdb
+%%DATADIR%%/dgdb/basepairs/au.XX.pdb
+%%DATADIR%%/dgdb/basepairs/au.XXI.pdb
+%%DATADIR%%/dgdb/basepairs/au.XXIII.pdb
+%%DATADIR%%/dgdb/basepairs/au.XXIV.pdb
+%%DATADIR%%/dgdb/basepairs/ca.XXV.pdb
+%%DATADIR%%/dgdb/basepairs/ca.XXVI.pdb
+%%DATADIR%%/dgdb/basepairs/cc.XIV.pdb
+%%DATADIR%%/dgdb/basepairs/cc.XV.pdb
+%%DATADIR%%/dgdb/basepairs/cg.XIX.pdb
+%%DATADIR%%/dgdb/basepairs/cg.XXII.pdb
+%%DATADIR%%/dgdb/basepairs/ct.XVII.pdb
+%%DATADIR%%/dgdb/basepairs/ct.XVIII.pdb
+%%DATADIR%%/dgdb/basepairs/cu.XVII.pdb
+%%DATADIR%%/dgdb/basepairs/cu.XVIII.pdb
+%%DATADIR%%/dgdb/basepairs/ga.IX.pdb
+%%DATADIR%%/dgdb/basepairs/ga.VIII.pdb
+%%DATADIR%%/dgdb/basepairs/ga.X.pdb
+%%DATADIR%%/dgdb/basepairs/ga.XI.pdb
+%%DATADIR%%/dgdb/basepairs/gc.XIX.pdb
+%%DATADIR%%/dgdb/basepairs/gc.XXII.pdb
+%%DATADIR%%/dgdb/basepairs/gg.III.pdb
+%%DATADIR%%/dgdb/basepairs/gg.IV.pdb
+%%DATADIR%%/dgdb/basepairs/gg.VI.pdb
+%%DATADIR%%/dgdb/basepairs/gg.VII.pdb
+%%DATADIR%%/dgdb/basepairs/gg.VIIa.pdb
+%%DATADIR%%/dgdb/basepairs/gg.VIa.pdb
+%%DATADIR%%/dgdb/basepairs/gt.XXVII.pdb
+%%DATADIR%%/dgdb/basepairs/gt.XXVIII.pdb
+%%DATADIR%%/dgdb/basepairs/gu.XXVII.pdb
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+%%DATADIR%%/dgdb/basepairs/ta.XX.pdb
+%%DATADIR%%/dgdb/basepairs/ta.XXI.pdb
+%%DATADIR%%/dgdb/basepairs/ta.XXIII.pdb
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+%%DATADIR%%/dgdb/basepairs/tc.XVII.pdb
+%%DATADIR%%/dgdb/basepairs/tc.XVIII.pdb
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+%%DATADIR%%/dgdb/basepairs/tt.XVIa.pdb
+%%DATADIR%%/dgdb/basepairs/tu.XII.pdb
+%%DATADIR%%/dgdb/basepairs/tu.XIII.pdb
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+%%DATADIR%%/dgdb/basepairs/ua.XX.pdb
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+%%DATADIR%%/dgdb/basepairs/ua.XXIII.pdb
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+%%DATADIR%%/dgdb/basepairs/uc.XVII.pdb
+%%DATADIR%%/dgdb/basepairs/uc.XVIII.pdb
+%%DATADIR%%/dgdb/basepairs/ug.XXVII.pdb
+%%DATADIR%%/dgdb/basepairs/ug.XXVIII.pdb
+%%DATADIR%%/dgdb/basepairs/ut.XII.pdb
+%%DATADIR%%/dgdb/basepairs/ut.XIII.pdb
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+%%DATADIR%%/dgdb/basepairs/uu.XII.pdb
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+%%DATADIR%%/dgdb/rna.basepair.db
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+%%DATADIR%%/dgdb/stacking/aa.adna.pdb
+%%DATADIR%%/dgdb/stacking/aa.arna.pdb
+%%DATADIR%%/dgdb/stacking/aa.bdna.pdb
+%%DATADIR%%/dgdb/stacking/aa.cdna.pdb
+%%DATADIR%%/dgdb/stacking/aa.ddna.pdb
+%%DATADIR%%/dgdb/stacking/aa.tdna.pdb
+%%DATADIR%%/dgdb/stacking/ac.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/ac.adna.pdb
+%%DATADIR%%/dgdb/stacking/ac.arna.pdb
+%%DATADIR%%/dgdb/stacking/ac.bdna.pdb
+%%DATADIR%%/dgdb/stacking/ac.cdna.pdb
+%%DATADIR%%/dgdb/stacking/ac.ddna.pdb
+%%DATADIR%%/dgdb/stacking/ac.tdna.pdb
+%%DATADIR%%/dgdb/stacking/ag.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/ag.adna.pdb
+%%DATADIR%%/dgdb/stacking/ag.arna.pdb
+%%DATADIR%%/dgdb/stacking/ag.bdna.pdb
+%%DATADIR%%/dgdb/stacking/ag.cdna.pdb
+%%DATADIR%%/dgdb/stacking/ag.ddna.pdb
+%%DATADIR%%/dgdb/stacking/ag.tdna.pdb
+%%DATADIR%%/dgdb/stacking/at.adna.pdb
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+%%DATADIR%%/dgdb/stacking/at.cdna.pdb
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+%%DATADIR%%/dgdb/stacking/ct.cdna.pdb
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+%%DATADIR%%/dgdb/stacking/ct.tdna.pdb
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+%%DATADIR%%/dgdb/stacking/cu.arna.pdb
+%%DATADIR%%/dgdb/stacking/ga.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/ga.adna.pdb
+%%DATADIR%%/dgdb/stacking/ga.arna.pdb
+%%DATADIR%%/dgdb/stacking/ga.bdna.pdb
+%%DATADIR%%/dgdb/stacking/ga.cdna.pdb
+%%DATADIR%%/dgdb/stacking/ga.ddna.pdb
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+%%DATADIR%%/dgdb/stacking/gc.adna.pdb
+%%DATADIR%%/dgdb/stacking/gc.arna.pdb
+%%DATADIR%%/dgdb/stacking/gc.bdna.pdb
+%%DATADIR%%/dgdb/stacking/gc.cdna.pdb
+%%DATADIR%%/dgdb/stacking/gc.ddna.pdb
+%%DATADIR%%/dgdb/stacking/gc.tdna.pdb
+%%DATADIR%%/dgdb/stacking/gc.zdna.pdb
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+%%DATADIR%%/dgdb/stacking/gg.adna.pdb
+%%DATADIR%%/dgdb/stacking/gg.arna.pdb
+%%DATADIR%%/dgdb/stacking/gg.bdna.pdb
+%%DATADIR%%/dgdb/stacking/gg.cdna.pdb
+%%DATADIR%%/dgdb/stacking/gg.ddna.pdb
+%%DATADIR%%/dgdb/stacking/gg.tdna.pdb
+%%DATADIR%%/dgdb/stacking/gt.adna.pdb
+%%DATADIR%%/dgdb/stacking/gt.bdna.pdb
+%%DATADIR%%/dgdb/stacking/gt.cdna.pdb
+%%DATADIR%%/dgdb/stacking/gt.ddna.pdb
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+%%DATADIR%%/dgdb/stacking/gu.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/gu.arna.pdb
+%%DATADIR%%/dgdb/stacking/ta.adna.pdb
+%%DATADIR%%/dgdb/stacking/ta.bdna.pdb
+%%DATADIR%%/dgdb/stacking/ta.cdna.pdb
+%%DATADIR%%/dgdb/stacking/ta.ddna.pdb
+%%DATADIR%%/dgdb/stacking/ta.tdna.pdb
+%%DATADIR%%/dgdb/stacking/tc.adna.pdb
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+%%DATADIR%%/dgdb/stacking/tc.ddna.pdb
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+%%DATADIR%%/dgdb/stacking/tg.adna.pdb
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+%%DATADIR%%/dgdb/stacking/tg.cdna.pdb
+%%DATADIR%%/dgdb/stacking/tg.ddna.pdb
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+%%DATADIR%%/dgdb/stacking/tt.adna.pdb
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+%%DATADIR%%/dgdb/stacking/tt.cdna.pdb
+%%DATADIR%%/dgdb/stacking/tt.ddna.pdb
+%%DATADIR%%/dgdb/stacking/tt.tdna.pdb
+%%DATADIR%%/dgdb/stacking/ua.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/ua.arna.pdb
+%%DATADIR%%/dgdb/stacking/uc.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/uc.arna.pdb
+%%DATADIR%%/dgdb/stacking/ug.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/ug.arna.pdb
+%%DATADIR%%/dgdb/stacking/uu.a-rna.pdb
+%%DATADIR%%/dgdb/stacking/uu.arna.pdb
+%%DATADIR%%/dgdb/trna.basepair.db
+%%DATADIR%%/dgdb/trna.nucleotide.db
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+%%DATADIR%%/dgdb/zdna.basepair.db
+%%DATADIR%%/dgdb/zdna.nucleotide.db
+%%DATADIR%%/dgdb/zdna.stack.db
+%%PORTDOCS%%%%DATADIR%%/examples/ADE.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/Makefile
+%%PORTDOCS%%%%DATADIR%%/examples/README
+%%PORTDOCS%%%%DATADIR%%/examples/THY.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/acgtacgt.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/aua.triad.min.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/cgc.triad.min.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/gcg.triad.min.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/gcg10.pdb
+%%PORTDOCS%%%%DATADIR%%/examples/gcg10.pdb.save
+%%PORTDOCS%%%%DATADIR%%/examples/getbase.nab
+%%PORTDOCS%%%%DATADIR%%/examples/mme_typical_calling_sequence.nab
+%%PORTDOCS%%%%DATADIR%%/examples/program_1.nab
+%%PORTDOCS%%%%DATADIR%%/examples/program_10.nab
+%%PORTDOCS%%%%DATADIR%%/examples/program_11.nab
+%%PORTDOCS%%%%DATADIR%%/examples/program_12.nab
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+%%PORTDOCS%%%%DATADIR%%/test/trxox.2.4ns.x
+%%PORTDOCS%%%%DATADIR%%/test/vizgrad.nab
+%%PORTDOCS%%%%DATADIR%%/test/vizgrad.pdb
+%%PORTDOCS%%%%DATADIR%%/test/vizgrad.prm
+%%PORTDOCS%%%%DATADIR%%/test/write_sander_inp.nab
+%%DATADIR%%/config.h
+@dirrm %%DATADIR%%/reslib/rna.amberua
+@dirrm %%DATADIR%%/reslib/rna.amber94
+@dirrm %%DATADIR%%/reslib/protein.opls
+@dirrm %%DATADIR%%/reslib/protein.amber94
+@dirrm %%DATADIR%%/reslib/pro-dna.nmr
+@dirrm %%DATADIR%%/reslib/hetatm.amber94
+@dirrm %%DATADIR%%/reslib/dna3
+@dirrm %%DATADIR%%/reslib/dna.amberua
+@dirrm %%DATADIR%%/reslib/dna.amber94
+@dirrm %%DATADIR%%/reslib/bdna.std
+@dirrm %%DATADIR%%/reslib/axes
+@dirrm %%DATADIR%%/reslib/arna.std
+@dirrm %%DATADIR%%/reslib/adna.std
+@dirrm %%DATADIR%%/reslib
+@dirrm %%DATADIR%%/lib
+@dirrm %%DATADIR%%/leap/prep
+@dirrm %%DATADIR%%/leap/parm
+@dirrm %%DATADIR%%/leap/lib
+@dirrm %%DATADIR%%/leap/cmd
+@dirrm %%DATADIR%%/leap
+@dirrm %%DATADIR%%/include
+@dirrm %%DATADIR%%/fd_data
+@dirrm %%DATADIR%%/dgdb/stacking
+@dirrm %%DATADIR%%/dgdb/basepairs
+@dirrm %%DATADIR%%/dgdb
+@dirrm %%DATADIR%%/bin
+%%PORTDOCS%%@dirrm %%DATADIR%%/benchmarks
+%%PORTDOCS%%@dirrm %%DATADIR%%/examples
+%%PORTDOCS%%@dirrm %%DATADIR%%/peptide
+%%PORTDOCS%%@dirrm %%DATADIR%%/suppose
+%%PORTDOCS%%@dirrm %%DATADIR%%/test
+@dirrm %%DATADIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%