Initiail version of nab (4.2)

PR:		21585
Submitted by:	M. L. Dodson <bdodson@scms.utmb.EDU>

biology/nab/Makefile

@@ -0,0 +1,51 @@
+# New ports collection Makefile for: nab
+# Date created:         Sept. 10, 2000
+# Whom:                 M. L. Dodson <bdodson@scms.utmb.edu>
+# $FreeBSD$
+
+PORTNAME=	nab
+PORTVERSION=	4.2
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/
+
+MAINTAINER=	bdodson@scms.utmb.edu
+
+NO_WRKSUBDIR=	yes
+MAKE_ENV+=	WRKSRC=${WRKSRC} PREFIX=${PREFIX} \
+		NABHOME=${PREFIX}/share/nab ARCH= \
+		INSTALL_MAN="${INSTALL_MAN}"
+MAN1=		nab.1
+MANCOMPRESSED=	yes
+
+post-extract:
+	@${CP} ${FILESDIR}/Makefile ${WRKSRC}
+	@${CP} ${FILESDIR}/Makefile.doc ${WRKSRC}/doc/Makefile
+	@${CP} ${FILESDIR}/config.h ${WRKSRC}
+
+pre-install:
+	@-mkdir -p ${PREFIX}/share/nab
+.if !defined(${NOPORTDOCS})
+	@cd ${WRKSRC} && (tar cf - examples test | \
+		(cd ${PREFIX}/share/nab; tar xf -))
+	@-mkdir -p ${PREFIX}/share/doc/nab
+	${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab
+.endif
+	@cd ${WRKSRC} && (tar cf - dgdb reslib | \
+		(cd ${PREFIX}/share/nab; tar xf -))
+	@(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}.${SHAREGRP} nab; \
+		${CHMOD} -R ugo+rX-w nab)
+	@-(cd ${PREFIX}/share/nab; ${RM} -f coords && ${LN} -s ../NDB coords)
+
+post-install:
+	@(cd ${PREFIX}/bin; \
+	${RM} -f nab && ${MV} ${PREFIX}/share/nab/bin/nab . ; \
+	${RM} -f nab2c && ${MV} ${PREFIX}/share/nab/bin/nab2c . ; \
+	${CHOWN} ${BINOWN}:${BINGRP} nab nab2c teLeap ; \
+	strip nab nab2c teLeap ; \
+	${RMDIR} ${PREFIX}/share/nab/bin)
+	@${CAT} ${PKGMESSAGE}
+
+test:	all
+	@cd ${WRKSRC}/src && make test
+
+.include <bsd.port.mk>

biology/nab/distinfo

@@ -0,0 +1 @@
+MD5 (nab-4.2.tar.gz) = 5b703cc9dc514549ea97c751fa68f239

biology/nab/files/Makefile

@@ -0,0 +1,6 @@
+# $FreeBSD$
+#SUBDIR=cccp cifparse src
+SUBDIR=src tleap doc
+MAN1=nab.1
+
+.include <bsd.subdir.mk>

biology/nab/files/Makefile.doc

@@ -0,0 +1,5 @@
+all:
+
+install:
+	gzip -nfc -9 nab.1 > nab.1.gz
+	${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz   ${PREFIX}/man/man1

biology/nab/files/config.h

@@ -0,0 +1,110 @@
+###############################################################################
+# Configuration section:  look at sections (1) to (4) below, making
+#      changes that seem necessary.  For most UNIX systems, no changes
+#      should be necessary.
+#
+###############################################################################
+#
+# (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 the directory above this one.
+#    ARCH is used to distinguish compilations for various architectures.
+#
+#    Files created by "make install" end up in:
+#        $NABHOME/bin/$ARCH
+#        $NABHOME/lib/$ARCH
+#        $NABHOME/include
+#
+#       You can choose ARCH as you wish, but it would generally 
+#       be related to the output of the "uname" command.
+#
+#BINDIR=$(NABHOME)/bin/$(ARCH)
+#LIBDIR=$(NABHOME)/lib/$(ARCH)
+#NABHOME=/usr/local/share/nab
+#ARCH=
+BINDIR=$(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 $(LIBDIR)/libsym.a
+#FLIBS=../cifparse/cifparse.a
+#
+#  following for Sun4, Solaris 2.x
+#
+#FLIBS=$(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
+#
+#
+###############################################################################
+#
+#  (4)  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
+#                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.)
+#
+CC=		cc
+LEX=    	flex
+YACC=   	yacc
+AR=		ar
+#
+#  Set the C-preprocessor.  Code for the preprocessor from gcc is in
+#    ../cccp;  it gets installed as $(NABHOME)/bin/$(ARCH)/cpp;
+#    this should generally *not* be changed.
+#
+#CPP=    $(NABHOME)/bin/$(ARCH)/cpp -lang-c++
+#CPP=    ../cccp/cpp -lang-c++
+CPP=    cc -E -x c++
+#
+#  Use these CFLAGS if AVS = 0
+#  Notes: for 64-bit IRIX, add "-n32" to both CFLAGS and OCFLAGS
+#         for RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR
+#
+OCFLAGS= -O
+CFLAGS= -DHAVE_STRERROR ${OCFLAGS}
+NABFLAGS=
+#
+#  Use these CFLAGS if AVS = 1
+#
+#CFLAGS= 	-g -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR)
+#OCFLAGS= 	-O -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR)
+#
+#
+#  For Win95, set SFX to ".exe"; for Unix,NT leave it empty:
+#
+#SFX=.exe
+SFX=
+#

biology/nab/files/patch-aa

@@ -0,0 +1,25 @@
+*** src/Makefile.orig	Fri Jan  8 16:06:59 1999
+--- src/Makefile	Thu Jan 14 16:15:53 1999
+***************
+*** 7,15 ****
+  	./nab  -c $(NABFLAGS) $<
+  	@rm -f $*.c
+  
+- .c.o: $<
+- 	$(CC) -c $(CFLAGS) $<
+- 
+  NAB2COBJS=	\
+  	nab2c.o	\
+  	cgen.o	\
+--- 7,12 ----
+***************
+*** 77,82 ****
+--- 74,81 ----
+  	yammp.o
+  
+  #===========================================================================
++ 
++ all: system
+  
+  system:	nab	\
+  	nab2c	\

biology/nab/files/patch-ac

@@ -0,0 +1,13 @@
+*** cccp/Makefile.orig	Thu Jan 14 16:20:38 1999
+--- cccp/Makefile	Thu Jan 14 16:21:08 1999
+***************
+*** 4,9 ****
+--- 4,11 ----
+  ######### no configuration should be needed beyond this line #################
+  ##############################################################################
+  
++ all: cpp$(SFX)
++ 
+  cpp$(SFX): cppmain.o cpplib.o cpphash.o cppalloc.o cpperror.o cppexp.o version.o \
+  		obstack.o alloca.o
+  	$(CC) $(CFLAGS) -o cpp$(SFX) cppmain.o cpplib.o cpphash.o \

biology/nab/files/patch-ad

@@ -0,0 +1,13 @@
+*** cifparse/Makefile.orig	Thu Jan 14 16:21:50 1999
+--- cifparse/Makefile	Thu Jan 14 16:22:08 1999
+***************
+*** 11,16 ****
+--- 11,18 ----
+  	cifp.tab.o \
+  	cifparse.o
+  
++ all: cifparse.a
++ 
+  cifparse.a: $(CIFOBS)
+  	-rm cifparse.a
+  	$(AR) rv cifparse.a $(CIFOBS)

biology/nab/files/patch-ae

@@ -0,0 +1,19 @@
+*** examples/program_7.nab.orig	Thu Jan 14 16:53:07 1999
+--- examples/program_7.nab	Thu Jan 14 16:53:24 1999
+***************
+*** 9,15 ****
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 4.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];
+--- 9,15 ----
+  cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" );
+  
+  m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb",
+!          "dna", 2.25, -4.96, 36.0, 3.38, "" );
+  
+  b = newbounds(m, "");
+  allocate xyz[ 4*m.natoms ];

biology/nab/files/patch-af

@@ -0,0 +1,23 @@
+*** src/reslib.c.orig	Tue Apr 21 14:10:50 1998
+--- src/reslib.c	Mon Feb  1 09:50:35 1999
+***************
+*** 610,618 ****
+  		fclose( cfp );
+  	}
+  
+! 	fclose( pfp );
+  
+! 	fclose( bfp );
+  
+  	return( rlp );
+  }
+--- 610,618 ----
+  		fclose( cfp );
+  	}
+  
+! 	if( pfp ) {fclose( pfp );}
+  
+! 	if( bfp ) {fclose( bfp );}
+  
+  	return( rlp );
+  }

biology/nab/files/patch-ag

@@ -0,0 +1,32 @@
+*** src/database.c.orig	Tue Apr 21 12:17:17 1998
+--- src/database.c	Tue Mar  9 09:09:06 1999
+***************
+*** 73,78 ****
+--- 73,85 ----
+  
+  #include        "database.h"
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  #ifndef	TRUE
+  #define	TRUE	1
+***************
+*** 985,991 ****
+--- 992,1002 ----
+  
+      sDBRemoveLeadingSpaces( sLine );
+      sDBRemoveFirstString( sLine, sHead );
++ #if defined(linux) || defined(BSD)
++     sscanf( sHead, "%lg", dPDbl );
++ #else
+      sscanf( sHead, "%lG", dPDbl );
++ #endif
+  
+  }
+  

biology/nab/files/patch-ah

@@ -0,0 +1,19 @@
+*** semantics/Makefile.orig	Fri Mar 10 20:08:16 2000
+--- semantics/Makefile	Sun Sep 10 18:47:44 2000
+***************
+*** 43,49 ****
+  SYM_UPARROW_ASSIGN.rules
+  
+  checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y
+! 	./parse *.rules
+  
+  parse: parse.c
+  	$(CC) -o parse parse.c
+--- 43,49 ----
+  SYM_UPARROW_ASSIGN.rules
+  
+  checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y
+! 	env NABHOME=.. ./parse *.rules
+  
+  parse: parse.c
+  	$(CC) -o parse parse.c

biology/nab/files/patch-ai

@@ -0,0 +1,41 @@
+*** tleap/Makefile.orig	Tue Jun 20 13:41:55 2000
+--- tleap/Makefile	Sun Sep 10 19:38:24 2000
+***************
+*** 5,13 ****
+  .SUFFIXES:
+  .SUFFIXES:  .c .o
+  
+- .c.o: $<
+- 	$(CC) -c $(CFLAGS) -DSYSV $<
+- 
+  #
+  #  Absolutely necessary routines
+  #
+--- 5,10 ----
+***************
+*** 76,81 ****
+--- 73,79 ----
+  OUL2P= utilLib2Pdb.o
+  
+  TLEAP_OBJ= $(OA) $(OG) $(OO) $(OL) $(OC)
++ all: teLeap$(SFX)
+  teLeap$(SFX): $(TLEAP_OBJ)
+  	$(CC) -o $@ $(TLEAP_OBJ) -lm
+  
+***************
+*** 409,415 ****
+  zMatrix.o: zMatrix.h
+  
+  install:  teLeap$(SFX)
+! 	mv teLeap$(SFX) $(BINDIR)
+  
+  uninstall: clean
+  	-rm $(BINDIR)/teLeap$(SFX)
+--- 407,413 ----
+  zMatrix.o: zMatrix.h
+  
+  install:  teLeap$(SFX)
+! 	mv teLeap$(SFX) $(PREFIX)/bin
+  
+  uninstall: clean
+  	-rm $(BINDIR)/teLeap$(SFX)

biology/nab/pkg-comment

@@ -0,0 +1 @@
+This is nab (nucleic acid builder), a language for macromolecules

biology/nab/pkg-descr

@@ -0,0 +1,20 @@
+This is version 4.2 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.
+
+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, Univ. of Texas Medical Branch, Galveston
+bdodson@scms.utmb.edu

biology/nab/pkg-message

@@ -0,0 +1,6 @@
+-------------------------------------------------------------------------------
+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.
+-------------------------------------------------------------------------------

biology/nab/pkg-plist

@@ -0,0 +1,281 @@
+bin/nab
+bin/nab2c
+bin/teLeap
+share/doc/nab/NAB.pdf
+share/nab/lib/libnab.a
+share/nab/include/nabcode.h
+share/nab/include/nab.h
+share/nab/include/defreal.h
+share/nab/include/nabtypes.h
+share/nab/examples/program_1.nab
+share/nab/examples/program_2.nab
+share/nab/examples/program_3.nab
+share/nab/examples/program_4.nab
+share/nab/examples/program_5.nab
+share/nab/examples/program_6.nab
+share/nab/examples/program_7.nab
+share/nab/examples/program_7.nab.orig
+share/nab/examples/README
+share/nab/examples/program_9.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_8.nab
+share/nab/examples/test.pdb
+share/nab/examples/ADE.pdb
+share/nab/examples/Makefile
+share/nab/examples/gcg10.pdb
+share/nab/examples/rna_pseudoknot.pdb
+share/nab/examples/THY.pdb
+share/nab/examples/program_5.gcg.in
+share/nab/examples/getbase.nab
+share/nab/examples/program_4.ref
+share/nab/examples/acgtacgt.pdb
+share/nab/examples/program_5.tat.in
+share/nab/examples/program_2.ref
+share/nab/examples/program_5.cgc.in
+share/nab/examples/program_5.ata.in
+share/nab/examples/test.sup.pdb
+share/nab/examples/gcg10.pdb.save
+share/nab/dgdb/bdna.basepair.db
+share/nab/dgdb/bdna.nucleotide.db
+share/nab/dgdb/bdna.stack.db
+share/nab/dgdb/trna.stack.db
+share/nab/dgdb/arna.basepair.db
+share/nab/dgdb/trna.basepair.db
+share/nab/dgdb/zdna.nucleotide.db
+share/nab/dgdb/adna.nucleotide.db
+share/nab/dgdb/adna.basepair.db
+share/nab/dgdb/adna.stack.db
+share/nab/dgdb/zdna.basepair.db
+share/nab/dgdb/zdna.stack.db
+share/nab/dgdb/trna.nucleotide.db
+share/nab/dgdb/dna.basepair.db
+share/nab/dgdb/arna.nucleotide.db
+share/nab/dgdb/rna.basepair.db
+share/nab/dgdb/arna.stack.db
+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/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/arna.std/arna.std.bnd
+share/nab/reslib/arna.std/arna.std.pdb
+share/nab/reslib/adna.std.rlb
+share/nab/reslib/axes/Axes.bnd
+share/nab/reslib/axes/XYZ.axes
+share/nab/reslib/rna.amber94/rna.amber94.3.bnd
+share/nab/reslib/rna.amber94/rna.amber94.3.pdb
+share/nab/reslib/rna.amber94/rna.amber94.5.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.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.amber94.3.qr
+share/nab/reslib/rna.amber94/rna.amber94_nmr.3.qr
+share/nab/reslib/rna.amber94/rna.amber94_nmr.qr
+share/nab/reslib/rna.amber94/rna.amber94_nmr.5.qr
+share/nab/reslib/arna.std.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
+share/nab/reslib/protein.amber94/protein.amber94.N.bnd
+share/nab/reslib/protein.amber94/protein.amber94.N.pdb
+share/nab/reslib/protein.amber94/protein.amber94.N.qr
+share/nab/reslib/protein.amber94/protein.amber94.NC.chi
+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/bdna.std.rlb
+share/nab/reslib/dna.amber94_nmr.5.rlb
+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.amber94.5.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/ade.pdb
+share/nab/reslib/dna.amber94/dna.amber94.35.chi
+share/nab/reslib/adna.std/adna.std.bnd
+share/nab/reslib/adna.std/adna.std.pdb
+share/nab/reslib/dna.amber94.3.rlb
+share/nab/reslib/dna.amber94.5.rlb
+share/nab/reslib/dna.amber94_nmr.rlb
+share/nab/reslib/dna.amber94.rlb
+share/nab/reslib/dna.amber94_nmr.3.rlb
+share/nab/reslib/rna.amber94.rlb
+share/nab/reslib/leap/all_amino94.lib
+share/nab/reslib/leap/all_aminoct94.lib
+share/nab/reslib/leap/all_aminont94.lib
+share/nab/reslib/leap/all_nucleic94.lib
+share/nab/reslib/leap/ions94.lib
+share/nab/reslib/leap/leaprc.std
+share/nab/reslib/leap/parm91X.dat
+share/nab/reslib/leap/parm94.dat
+share/nab/reslib/leap/leaprc.nmr
+share/nab/reslib/leap/na.amberua.prepin
+share/nab/reslib/leap/ions91.lib
+share/nab/reslib/leap/water.lib
+share/nab/reslib/leap/protein.opls.lib
+share/nab/reslib/leap/opls_parm.dat
+share/nab/reslib/leap/leaprc.dna.amberua
+share/nab/reslib/leap/rna.amberua.lib
+share/nab/reslib/leap/dna.amberua.lib
+share/nab/reslib/leap/parm91X.ua.dat
+share/nab/reslib/leap/pro-dna91.nmr.db4
+share/nab/reslib/leap/Notes
+share/nab/reslib/leap/0README
+share/nab/reslib/leap/parm91.lib
+share/nab/reslib/leap/pro-dna91.nmr.lib
+share/nab/reslib/leap/protein.amberua.C.prepin
+share/nab/reslib/leap/protein.amberua.N.prepin
+share/nab/reslib/leap/protein.amberua.prepin
+share/nab/reslib/leap/pro-dna91.nmr.prepin
+share/nab/reslib/leap/leaprc.rna.amberua
+share/nab/reslib/leap/dna.amberua.redch.lib
+share/nab/reslib/leap/leaprc.dna.amberua.redch
+share/nab/reslib/leap/leaprc.rna
+share/nab/reslib/leap/protein.amberua.lib
+share/nab/reslib/leap/leaprc.protein.amberua
+share/nab/reslib/leap/leap.log
+share/nab/reslib/leap/all_amino91.lib
+share/nab/reslib/leap/all_aminoct91.lib
+share/nab/reslib/leap/all_aminont91.lib
+share/nab/reslib/leap/all_nucleic91.lib
+share/nab/reslib/protein.amber94.C.rlb
+share/nab/reslib/protein.amber94.N.rlb
+share/nab/reslib/protein.amber94.rlb
+share/nab/reslib/protein.opls.rlb
+share/nab/reslib/axes.rlb
+share/nab/reslib/hetatm.amber94/hetatm.amber94.qr
+share/nab/reslib/hetatm.amber94/hetatm.amber94.pdb
+share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
+share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
+share/nab/reslib/dna.amberua/dna.amberua.bnd
+share/nab/reslib/dna.amberua/dna.amberua.pdb
+share/nab/reslib/dna.amberua/dna.amberua.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.3.qr
+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.chi
+share/nab/reslib/dna.amberua/dna.amberua.5.qr
+share/nab/reslib/hetatm.amber94.rlb
+share/nab/reslib/dna.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.5.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.qr
+share/nab/reslib/rna.amberua/rna.amberua.bnd
+share/nab/reslib/rna.amberua/rna.amberua.pdb
+share/nab/reslib/rna.amberua/rna.amberua.chi
+share/nab/reslib/rna.amberua/rna.amberua.3.qr
+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/dna.amberua.5.rlb
+share/nab/reslib/dna.amberua.3.rlb
+share/nab/reslib/rna.amberua.rlb
+share/nab/reslib/rna.amberua.3.rlb
+share/nab/reslib/rna.amberua.5.rlb
+share/nab/reslib/rna.amber94.5.rlb
+share/nab/reslib/rna.amber94.3.rlb
+share/nab/reslib/rna.amber94_nmr.3.rlb
+share/nab/reslib/ala.off
+share/nab/reslib/rna.amber94_nmr.5.rlb
+share/nab/reslib/rna.amber94_nmr.rlb
+share/nab/reslib/protein.amber94_nmr.rlb
+share/nab/reslib/leap.log
+share/nab/reslib/off2star
+share/nab/reslib/pep1.off
+share/nab/reslib/cdd.mol2
+share/nab/reslib/syblCDD.lib
+share/nab/reslib/parm94.star
+share/nab/reslib/charlie.star.note
+share/nab/reslib/conf.lib
+share/nab/reslib/dna3/dna3.qr
+share/nab/reslib/dna3/dna3.bnd
+share/nab/reslib/dna3/dna3.chi
+share/nab/reslib/dna3/dna3.pdb
+share/nab/reslib/dna3.rlb
+share/nab/test/duplex.in
+share/nab/test/5pti.obs
+share/nab/test/5pti.pdb
+share/nab/test/prmtop
+share/nab/test/2.pdb
+share/nab/test/d01.lin.check
+share/nab/test/ltest.nab
+share/nab/test/d01.pdb.check
+share/nab/test/dna.circle.nab
+share/nab/test/duplex.nab
+share/nab/test/hash.in
+share/nab/test/hash.nab
+share/nab/test/hash.out.check
+share/nab/test/ltest.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/ico.sym
+share/nab/test/read_obs_shifts.nab
+share/nab/test/sbcoil.nab
+share/nab/test/shifts.nab
+share/nab/test/swap_shifts.nab
+share/nab/test/write_sander_inp.nab
+share/nab/test/shifts.h
+share/nab/test/reflexive.nab
+share/nab/test/reflexive.out
+share/nab/test/dg_gyrate.nab
+share/nab/test/5pti.shifts.check
+share/nab/test/ico.sym.out.check
+share/nab/test/tbv.com.pdb
+share/nab/test/dg_gyrate.out.check
+share/nab/test/tbv.60.com.pdb.check
+share/nab/test/gbrna.prmtop
+share/nab/test/gbrna.out.check
+share/nab/test/gbrna.pdb
+share/nab/test/gbrna.nab
+share/nab/test/pointplane.nab
+share/nab/coords
+@dirrm share/nab/reslib/pro-dna.nmr
+@dirrm share/nab/reslib/bdna.std
+@dirrm share/nab/reslib/protein.opls
+@dirrm share/nab/reslib/arna.std
+@dirrm share/nab/reslib/axes
+@dirrm share/nab/reslib/rna.amber94
+@dirrm share/nab/reslib/protein.amber94
+@dirrm share/nab/reslib/dna.amber94
+@dirrm share/nab/reslib/adna.std
+@dirrm share/nab/reslib/hetatm.amber94
+@dirrm share/nab/reslib/dna.amberua
+@dirrm share/nab/reslib/rna.amberua
+@dirrm share/nab/reslib/dna3
+@dirrm share/nab/reslib/leap
+@dirrm share/nab/reslib
+@dirrm share/nab/test
+@dirrm share/nab/examples
+@dirrm share/nab/lib
+@dirrm share/nab/include
+@dirrm share/nab/dgdb
+@dirrm share/nab
+@dirrm share/doc/nab