- Delete biology/nab port after being marked DEPRECATED for three months

PR:		ports/125891
Submitted by:	M. L. Dodson <mldodson@comcast.net> (maintainer)

15 files changed, 0 insertions, 1093 deletions

diff --git a/biology/Makefile b/biology/Makefile
index cd0e5740f286..1f0088c3235c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -51,7 +51,6 @@
     SUBDIR += mrbayes
     SUBDIR += mummer
     SUBDIR += muscle
-    SUBDIR += nab
     SUBDIR += ncbi-toolkit
     SUBDIR += njplot
     SUBDIR += ortep3
diff --git a/biology/nab/Makefile b/biology/nab/Makefile
deleted file mode 100644
index 4af654a65190..000000000000
--- a/biology/nab/Makefile
+++ /dev/null
@@ -1,91 +0,0 @@
-# New ports collection Makefile for: nab
-# Date created:         Sept. 10, 2000
-# Whom:                 M. L. Dodson <mldodson@comcast.net>
-#
-# $FreeBSD$
-#
-
-PORTNAME=	nab
-PORTVERSION=	5.1.2
-PORTREVISION=	1
-CATEGORIES=	biology
-MASTER_SITES=	http://www.activesitedynamics.com/mldodson/
-
-MAINTAINER=	mldodson@comcast.net
-COMMENT=	A language for macromolecules
-
-BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
-RUN_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
-
-DEPRECATED=	superseded by AmberTools (by same development group)
-
-MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \
-		CFLAGS="${CFLAGS}" OCFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
-
-MAN1=		nab.1
-SUB_FILES=	pkg-message
-
-BINARIES=	matmerge nab2c teLeap tss_main \
-		matextract matmul transform tss_next \
-		matgen nab tss_init
-
-LIBRARIES=	cifparse.a libnab.a libsym.a
-
-INCS=		defreal.h nab.h nabcode.h nabtypes.h
-
-do-configure:
-	@${CP} ${FILESDIR}/config.h ${WRKSRC}
-
-post-patch:
-	@${RM} -f ${WRKSRC}/examples/circle.c
-	@${RM} -f ${WRKSRC}/reslib/conf.lib.orig
-	@${RM} -f ${WRKSRC}/examples/program_7.nab.orig
-
-do-build:
-	@cd ${WRKSRC} && \
-		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} install
-	@cd ${WRKSRC}/test && \
-		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test
-	@cd ${WRKSRC}/nss  && \
-		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test
-
-build-general-version:
-	@cd ${WRKSRC}/src && \
-		${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} beforerealinstall
-
-do-install: build-general-version
-	${MKDIR} ${DATADIR}/bin ${DATADIR}/include ${DATADIR}/lib
-	cd ${WRKSRC}/test && ${RM} -f d01.pdb gbrna.pdb.lpdb rembed.out
-	cd ${WRKSRC}/examples && ${RM} -f gcg10.pdb.save
-	cd ${WRKSRC}/leap/parm && ${RM} -f leap.log
-.if !defined(NOPORTDOCS)
-	cd ${WRKSRC} && (${TAR} cf - benchmarks examples test | \
-		(cd ${DATADIR}; ${TAR} xf -))
-	${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR}
-.endif
-	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 ${DATADIR}/include && ${LN} -sf ${PREFIX}/include/${f} .
-.endfor
-	${INSTALL_DATA} ${WRKSRC}/config.h ${DATADIR}
-	${INSTALL_MAN} ${WRKSRC}/doc/nab.1 ${MAN1PREFIX}/man/man1
-.for f in ${BINARIES}
-	cd ${DATADIR}/bin && ${LN} -sf ${PREFIX}/bin/${f} .
-.endfor
-.for f in ${LIBRARIES}
-	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib
-	cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} .
-.endfor
-.for f in blas.a lapack.a f2c.a
-	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib
-	${LN} ${DATADIR}/lib/${f} ${DATADIR}/lib/lib${f}
-.endfor
-	@${CAT} ${PKGMESSAGE}
-
-.include <bsd.port.mk>
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
deleted file mode 100644
index 16cf8d035e82..000000000000
--- a/biology/nab/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 (nab-5.1.2.tar.gz) = fc87da8a7f19832cfb4e88e6ac2b9a7f
-SHA256 (nab-5.1.2.tar.gz) = 207579b78d08efa3c64796efc56b019ff2a41c035373d35d241af80ee812d625
-SIZE (nab-5.1.2.tar.gz) = 9886440
diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h
deleted file mode 100644
index a3e4889166b3..000000000000
--- a/biology/nab/files/config.h
+++ /dev/null
@@ -1,74 +0,0 @@
-#  NAB configuration file, created with: ./configure -p4 -static gcc
-
-###############################################################################
-
-# (1)  You need to define the symbol NABHOME in your environment
-
-#    NABHOME should be an absolute path to the top-level NAB directory;
-#    files are installed to the following directories:
-
-BINDIR=$(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)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/f2c.a -static   
-
-###############################################################################
-
-#  (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 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.
-
-NABFLAGS=
-
-LEX=    flex
-YACC=   yacc
-AR=     ar
-RANLIB= ranlib
-
-#  Set the C-preprocessor.  Code for a small preprocessor is in
-#    uccp-1.3;  it gets installed as $(NABHOME)/bin/ucpp;
-#    this can generally be used (maybe not on 64-bit machines like altix).
-
-CPP=    /usr/local/bin/ucpp -l
-
-#  If you are going to link in Fortran routines, you need
-#  to set the compiler information here.  (Also, add the appropriate entries
-#  to the FLIBS variable, above.)
-#
-#FC=f77
-#FFLAGS?=$(FFLAGS)
-#FOPTFLAGS?=$(FFLAGS)
-FREEFORMAT_FLAG=-ffree-form
-
-#  These variables control whether we will use compiled versions of BLAS
-#  and LAPACK (which are generally slower), or whether those libraries are
-#  already available (presumably in an optimized form).
-
-LAPACK=install
-BLAS=install
-F2C=install
-UCPP=
-
-#  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
deleted file mode 100644
index 3fe19a6cd21f..000000000000
--- a/biology/nab/files/patch-Makefile
+++ /dev/null
@@ -1,70 +0,0 @@
---- Makefile.orig	Mon Aug 21 11:16:05 2006
-+++ Makefile	Fri Dec 15 16:06:57 2006
-@@ -2,31 +2,32 @@
- 
- include config.h
- 
-+all: install
-+
- install:
- 	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
--	(cd ucpp-1.3; make $(UCPP) )
--	(cd byacc; make install )
--
--#   here are the Fortran versions:
--#	(cd lapack; make $(LAPACK) )
--#	(cd blas; make $(BLAS) )
--
--#   here are the C versions:
--	(cd clapack; make $(LAPACK) )
--	(cd cblas; make $(BLAS) )
--	(cd f2c;  make $(F2C)  )
--
--	(cd cifparse; make install )
--	(cd src; make install )
--	(cd nss; make install )
--	(cd tleap; make install )
-+	(cd clapack; env NABHOME=.. make $(LAPACK) )
-+	(cd cblas; env NABHOME=.. make $(BLAS) )
-+	(cd f2c; env NABHOME=.. make $(F2C) )
-+	(cd cifparse; env NABHOME=.. make install )
-+	(cd src; env NABHOME=.. make install )
-+	(cd nss; env NABHOME=.. make install )
-+	(cd tleap; env NABHOME=.. make install )
-+#	(cd peptide && \
-+#		env NABHOME=.. ../bin/nab $(CFLAGS) -o peptide peptide.nab )
-+#	cp -p peptide/README doc/README-peptide
-+#	mv peptide/peptide bin
-+#	@echo
-+#	@echo "Ignore conflicting types warnings"
-+#	@echo
-+#	(cd suppose; env NABHOME=.. make all )
-+#	cp -p suppose/suppose.1 doc
-+#	mv suppose/suppose suppose/PCA_suppose bin
- 	@echo
--	@echo "completed installation of NAB version 5"
-+	@echo "completed installation of NAB version 5.1"
- 	@echo
- 
- clean:
--	(cd ucpp-1.3; make clean )
--	(cd byacc; make clean )
- 	(cd cifparse; make clean )
- 	(cd src; make clean )
- 	(cd nss; make clean )
-@@ -34,10 +35,12 @@
- 	(cd cblas; make clean )
- 	(cd clapack; make clean )
- 	(cd f2c; make clean )
--	
-+	(cd suppose; make clean )
-+	(cd peptide && rm -f peptide.c peptide )
-+
- #   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-configure b/biology/nab/files/patch-configure
deleted file mode 100644
index 412974c8fcfa..000000000000
--- a/biology/nab/files/patch-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	Mon Aug 21 11:18:10 2006
-+++ configure	Fri Aug 25 22:30:10 2006
-@@ -61,7 +61,7 @@
- p4='no'
- gotolib='no'
- compiler='gcc'
--processor=`/bin/uname -p`
-+processor=`/usr/bin/uname -p`
- static='no'
- 
- while [ $# -gt 0 ]; do
diff --git a/biology/nab/files/patch-reslib:conf.lib b/biology/nab/files/patch-reslib:conf.lib
deleted file mode 100644
index 088afbf29321..000000000000
--- a/biology/nab/files/patch-reslib:conf.lib
+++ /dev/null
@@ -1,14 +0,0 @@
-*** 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/files/patch-src:wc_helix.nab b/biology/nab/files/patch-src:wc_helix.nab
deleted file mode 100644
index 960c76b2341e..000000000000
--- a/biology/nab/files/patch-src:wc_helix.nab
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/wc_helix.nab.orig	Thu Apr  7 20:17:27 2005
-+++ src/wc_helix.nab	Fri Sep 15 09:22:13 2006
-@@ -25,6 +25,8 @@
- 
- 	loup["g"] = "G"; loup["a"] = "A";
- 	loup["t"] = "T"; loup["c"] = "C";
-+	loup["G"] = "G"; loup["A"] = "A";
-+	loup["T"] = "T"; loup["C"] = "C";
- 
- 	has_s = 1; has_a = 1;
- 	if( sreslib == "" ) sreslib_use = "all_nucleic94.lib";
diff --git a/biology/nab/files/patch-src_Makefile b/biology/nab/files/patch-src_Makefile
deleted file mode 100644
index 70f7c1b799f1..000000000000
--- a/biology/nab/files/patch-src_Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
---- src/Makefile.orig	Fri Aug 11 17:38:10 2006
-+++ src/Makefile	Fri Dec 15 17:01:39 2006
-@@ -189,6 +189,14 @@
- 	cp defreal.h $(INCDIR)
- 	cp nab.h $(INCDIR)
- 
-+beforerealinstall:
-+	$(CC) -DBINDIR='"$(PREFIX)/bin"' \
-+		-DINCDIR='"$(PREFIX)/include"' \
-+		-DLIBDIR='"$(PREFIX)/share/nab/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 $(PREFIX)/share/nab/lib/f2c.a"' \
-+		-static -o ../bin/nab${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
deleted file mode 100644
index c6538200406e..000000000000
--- a/biology/nab/files/patch-src_cgen.c
+++ /dev/null
@@ -1,21 +0,0 @@
---- 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
deleted file mode 100644
index 348e3a157d8b..000000000000
--- a/biology/nab/files/patch-src_nabgrm.y
+++ /dev/null
@@ -1,20 +0,0 @@
---- 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-suppose_Makefile b/biology/nab/files/patch-suppose_Makefile
deleted file mode 100644
index 9317b951a30c..000000000000
--- a/biology/nab/files/patch-suppose_Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
---- suppose/Makefile.orig	Thu Apr  7 20:18:34 2005
-+++ suppose/Makefile	Sat Aug 26 08:49:50 2006
-@@ -1,5 +1,7 @@
- include ../config.h
- 
-+all: suppose$(SFX) PCA_suppose$(SFX)
-+
- suppose$(SFX): suppose.nab
- 	nab -o suppose$(SFX) suppose.nab
- 
diff --git a/biology/nab/files/pkg-message.in b/biology/nab/files/pkg-message.in
deleted file mode 100644
index e89f4516b02e..000000000000
--- a/biology/nab/files/pkg-message.in
+++ /dev/null
@@ -1,8 +0,0 @@
--------------------------------------------------------------------------------
-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-descr b/biology/nab/pkg-descr
deleted file mode 100644
index 2c37138e877a..000000000000
--- a/biology/nab/pkg-descr
+++ /dev/null
@@ -1,22 +0,0 @@
-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:
-
-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.
-
-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, Active Site Dynamics
-mldodson@houston.rr.com
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
deleted file mode 100644
index 004d7a59058e..000000000000
--- a/biology/nab/pkg-plist
+++ /dev/null
@@ -1,720 +0,0 @@
-bin/matextract
-bin/matgen
-bin/matmerge
-bin/matmul
-bin/nab
-bin/nab2c
-bin/teLeap
-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
-%%PORTDOCS%%%%DOCSDIR%%/NAB.pdf
-%%DATADIR%%/benchmarks/1akd.mc.pdb
-%%DATADIR%%/benchmarks/1akd.mc.x
-%%DATADIR%%/benchmarks/1akd.top
-%%DATADIR%%/benchmarks/README
-%%DATADIR%%/benchmarks/bench_amber
-%%DATADIR%%/benchmarks/bench_cg.nab
-%%DATADIR%%/benchmarks/bench_md.nab
-%%DATADIR%%/benchmarks/bench_nr.nab
-%%DATADIR%%/benchmarks/cox2.inpcrd
-%%DATADIR%%/benchmarks/cox2.nab
-%%DATADIR%%/benchmarks/cox2.pdb
-%%DATADIR%%/benchmarks/cox2.prmtop
-%%DATADIR%%/benchmarks/gact3.mc.pdb
-%%DATADIR%%/benchmarks/gact3.mc.x
-%%DATADIR%%/benchmarks/gact3.top
-%%DATADIR%%/benchmarks/gact4.mc.pdb
-%%DATADIR%%/benchmarks/gact4.mc.x
-%%DATADIR%%/benchmarks/gact4.top
-%%DATADIR%%/benchmarks/gbrna.nab
-%%DATADIR%%/benchmarks/gbrna.out.check
-%%DATADIR%%/benchmarks/gcn4_md.nab
-%%DATADIR%%/benchmarks/gcn4_nr.nab
-%%DATADIR%%/benchmarks/gcn4dna.mc.pdb
-%%DATADIR%%/benchmarks/gcn4dna.mc.x
-%%DATADIR%%/benchmarks/gcn4dna.top
-%%DATADIR%%/benchmarks/gcn4p1.mc.pdb
-%%DATADIR%%/benchmarks/gcn4p1.mc.x
-%%DATADIR%%/benchmarks/gcn4p1.top
-%%DATADIR%%/benchmarks/halfam0.mc.pdb
-%%DATADIR%%/benchmarks/halfam0.mc.x
-%%DATADIR%%/benchmarks/halfam0.top
-%%DATADIR%%/benchmarks/mb.inpcrd
-%%DATADIR%%/benchmarks/mb.nab
-%%DATADIR%%/benchmarks/mb.out.check
-%%DATADIR%%/benchmarks/mb.pdb
-%%DATADIR%%/benchmarks/mb.prmtop
-%%DATADIR%%/benchmarks/p450.mc.pdb
-%%DATADIR%%/benchmarks/p450.mc.x
-%%DATADIR%%/benchmarks/p450.nab
-%%DATADIR%%/benchmarks/p450.out.check
-%%DATADIR%%/benchmarks/p450.top
-%%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%%/config.h
-%%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
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-@dirrm %%DATADIR%%/reslib/protein.opls
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-@dirrm %%DATADIR%%/reslib/pro-dna.nmr
-@dirrm %%DATADIR%%/reslib/hetatm.amber94
-@dirrm %%DATADIR%%/reslib/dna3
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-@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%%/examples
-@dirrm %%DATADIR%%/dgdb/stacking
-@dirrm %%DATADIR%%/dgdb/basepairs
-@dirrm %%DATADIR%%/dgdb
-@dirrm %%DATADIR%%/bin
-@dirrm %%DATADIR%%/benchmarks
-@dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%