11 files changed, 308 insertions, 236 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index ceac0e54df55..3df071abe00c 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -1,18 +1,16 @@
 # New ports collection Makefile for: nab
 # Date created:         Sept. 10, 2000
-# Whom:                 M. L. Dodson <bdodson@scms.utmb.edu>
+# Whom:                 M. L. Dodson <mldodson@houston.rr.com>
 #
 # $FreeBSD$
 #
 
 PORTNAME=	nab
-PORTVERSION=	5.0
-PORTREVISION=	1
+PORTVERSION=	5.1.2
 CATEGORIES=	biology
-MASTER_SITES=	http://www.scripps.edu/case/ \
-		http://siegfried.utmb.edu/bdodson/
+MASTER_SITES=	http://www.scripps.edu/mb/case/
 
-MAINTAINER=	bdodson@scms.utmb.edu
+MAINTAINER=	mldodson@houston.rr.com
 COMMENT=	A language for macromolecules
 
 BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
@@ -21,35 +19,46 @@ RUN_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
 ONLY_FOR_ARCHS=	i386
 
 MAKE_ENV+=	NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \
-		CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
+		CFLAGS="${CFLAGS}" OCFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}"
 
 MAN1=		nab.1
 SUB_FILES=	pkg-message
 
-BINARIES=	matextract	matmul		teLeap		tss_main \
-		matgen		nab		transform	tss_next \
-		matmerge	nab2c		tss_init
+BINARIES=	matmerge nab2c teLeap tss_main \
+		matextract matmul transform tss_next \
+		matgen nab 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:
+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
 
-pre-install:
+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:
+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 peptide suppose | \
+	cd ${WRKSRC} && (${TAR} cf - benchmarks examples test | \
 		(cd ${DATADIR}; ${TAR} xf -))
 	${MKDIR} ${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR}
@@ -72,11 +81,9 @@ do-install:
 	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib
 	cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} .
 .endfor
-.for f in blas.a lapack.a
+.for f in blas.a lapack.a f2c.a
 	${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib
 .endfor
-
-post-install:
 	@${CAT} ${PKGMESSAGE}
 
 .include <bsd.port.mk>
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index 21d1a03b3167..16cf8d035e82 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1,3 +1,3 @@
-MD5 (nab-5.0.tar.gz) = dfcde2ddaa833f4dc24d53c87b842cf9
-SHA256 (nab-5.0.tar.gz) = e7aaf3a870f22bc6d4125cdee92e7ad19042fbbc7e8fd1dba58528d91d4e7ffe
-SIZE (nab-5.0.tar.gz) = 5853573
+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
index 7dd5649fc85d..a3e4889166b3 100644
--- a/biology/nab/files/config.h
+++ b/biology/nab/files/config.h
@@ -1,4 +1,4 @@
-#  NAB configuration file, created with: ./configure 
+#  NAB configuration file, created with: ./configure -p4 -static gcc
 
 ###############################################################################
 
@@ -19,14 +19,14 @@ INCDIR=$(NABHOME)/include
 #      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  -lg2c
+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
+SHELL=/bin/sh
 
 #  Set the C compiler, etc. 
 
@@ -37,32 +37,36 @@ SHELL=		/bin/sh
 #          so LEX=flex is necessary.  In general, gcc seems to need
 #          flex.
 
-CC?=		cc
-CFLAGS?= 
-OCFLAGS=${CFLAGS}
-NABFLAGS?= 
+NABFLAGS=
 
 LEX=    flex
 YACC=   yacc
-AR=	ar
-RANLIB=	ranlib
+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 should generally *not* be changed.
+#    this can generally be used (maybe not on 64-bit machines like altix).
 
-CPP=    ucpp -l
+CPP=    /usr/local/bin/ucpp -l
 
-#  If you are going to use the Fortran lapack and blas libraries, you need
+#  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?=
-FOPTFLAGS=${FFLAGS}
+#
+#FC=f77
+#FFLAGS?=$(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:
 
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
index d754d329ca56..3fe19a6cd21f 100644
--- a/biology/nab/files/patch-Makefile
+++ b/biology/nab/files/patch-Makefile
@@ -1,29 +1,49 @@
---- Makefile.orig	Thu Apr  7 20:18:20 2005
-+++ Makefile	Mon Apr 25 13:37:39 2005
-@@ -2,42 +2,39 @@
+--- 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 test
++all: install
 +
  install:
  	-mkdir $(BINDIR) $(LIBDIR) $(INCDIR)
--	(cd ucpp-1.3; make install )
+-	(cd ucpp-1.3; make $(UCPP) )
 -	(cd byacc; make install )
--	(cd lapack; make $(LAPACK) )
--	(cd blas; make $(BLAS) )
+-
+-#   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 lapack; env NABHOME=.. make $(LAPACK) )
-+	(cd blas; env NABHOME=.. make $(BLAS) )
++	(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"
++	@echo "completed installation of NAB version 5.1"
  	@echo
  
  clean:
@@ -32,20 +52,13 @@
  	(cd cifparse; make clean )
  	(cd src; make clean )
  	(cd nss; make clean )
- 	(cd tleap; make clean )
- 	(cd lapack; make clean )
- 	(cd blas; make clean )
--	
-+
- 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)
+@@ -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.
diff --git a/biology/nab/files/patch-configure b/biology/nab/files/patch-configure
new file mode 100644
index 000000000000..412974c8fcfa
--- /dev/null
+++ b/biology/nab/files/patch-configure
@@ -0,0 +1,11 @@
+--- 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-examples:program_7.nab b/biology/nab/files/patch-examples:program_7.nab
deleted file mode 100644
index 4e6455533df4..000000000000
--- a/biology/nab/files/patch-examples:program_7.nab
+++ /dev/null
@@ -1,19 +0,0 @@
-*** examples/program_7.nab	Wed Mar 10 18:57:51 1999
---- examples/program_7.nab	Sun Jun  2 13:40:36 2002
-***************
-*** 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 ];
diff --git a/biology/nab/files/patch-src:wc_helix.nab b/biology/nab/files/patch-src:wc_helix.nab
new file mode 100644
index 000000000000..960c76b2341e
--- /dev/null
+++ b/biology/nab/files/patch-src:wc_helix.nab
@@ -0,0 +1,11 @@
+--- 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
index 32a56f228ba4..70f7c1b799f1 100644
--- a/biology/nab/files/patch-src_Makefile
+++ b/biology/nab/files/patch-src_Makefile
@@ -1,6 +1,6 @@
---- src/Makefile.orig	Fri Apr  8 03:17:27 2005
-+++ src/Makefile	Sat Apr 30 00:02:37 2005
-@@ -181,6 +181,14 @@
+--- 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)
  
@@ -9,7 +9,7 @@
 +		-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 $(PREFIX)/share/nab/lib/blas.a -lg2c"' \
++		-DFLIBS='"$(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
diff --git a/biology/nab/files/patch-suppose_Makefile b/biology/nab/files/patch-suppose_Makefile
new file mode 100644
index 000000000000..9317b951a30c
--- /dev/null
+++ b/biology/nab/files/patch-suppose_Makefile
@@ -0,0 +1,10 @@
+--- 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/pkg-descr b/biology/nab/pkg-descr
index 0d61ae35a96a..2c37138e877a 100644
--- a/biology/nab/pkg-descr
+++ b/biology/nab/pkg-descr
@@ -18,6 +18,5 @@ Please send comments and suggestions to Tom Macke
 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
+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
index 0570ee87a8ee..c7291dd51d1a 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -17,21 +17,47 @@ lib/cifparse.a
 lib/libnab.a
 lib/libsym.a
 %%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%%/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
@@ -43,6 +69,7 @@ lib/libsym.a
 %%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
@@ -249,45 +276,44 @@ lib/libsym.a
 %%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
-%%PORTDOCS%%%%DATADIR%%/examples/program_13.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_14.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_2.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_2.ref
-%%PORTDOCS%%%%DATADIR%%/examples/program_3.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_4.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_4.ref
-%%PORTDOCS%%%%DATADIR%%/examples/program_5.ata.in
-%%PORTDOCS%%%%DATADIR%%/examples/program_5.cgc.in
-%%PORTDOCS%%%%DATADIR%%/examples/program_5.gcg.in
-%%PORTDOCS%%%%DATADIR%%/examples/program_5.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_5.tat.in
-%%PORTDOCS%%%%DATADIR%%/examples/program_6.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_7.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_7.nab.orig
-%%PORTDOCS%%%%DATADIR%%/examples/program_8.nab
-%%PORTDOCS%%%%DATADIR%%/examples/program_9.nab
-%%PORTDOCS%%%%DATADIR%%/examples/rna_pseudoknot.pdb
-%%PORTDOCS%%%%DATADIR%%/examples/spline.nab
-%%PORTDOCS%%%%DATADIR%%/examples/tat.triad.min.pdb
-%%PORTDOCS%%%%DATADIR%%/examples/test.pdb
-%%PORTDOCS%%%%DATADIR%%/examples/test.sup.pdb
-%%PORTDOCS%%%%DATADIR%%/examples/toto.dat
+%%DATADIR%%/examples/ADE.pdb
+%%DATADIR%%/examples/Makefile
+%%DATADIR%%/examples/README
+%%DATADIR%%/examples/THY.pdb
+%%DATADIR%%/examples/acgtacgt.pdb
+%%DATADIR%%/examples/ata.triad.min.pdb
+%%DATADIR%%/examples/aua.triad.min.pdb
+%%DATADIR%%/examples/cgc.triad.min.pdb
+%%DATADIR%%/examples/gcg.triad.min.pdb
+%%DATADIR%%/examples/gcg10.pdb
+%%DATADIR%%/examples/getbase.nab
+%%DATADIR%%/examples/mme_typical_calling_sequence.nab
+%%DATADIR%%/examples/program_1.nab
+%%DATADIR%%/examples/program_10.nab
+%%DATADIR%%/examples/program_11.nab
+%%DATADIR%%/examples/program_12.nab
+%%DATADIR%%/examples/program_13.nab
+%%DATADIR%%/examples/program_14.nab
+%%DATADIR%%/examples/program_2.nab
+%%DATADIR%%/examples/program_2.ref
+%%DATADIR%%/examples/program_3.nab
+%%DATADIR%%/examples/program_4.nab
+%%DATADIR%%/examples/program_4.ref
+%%DATADIR%%/examples/program_5.ata.in
+%%DATADIR%%/examples/program_5.cgc.in
+%%DATADIR%%/examples/program_5.gcg.in
+%%DATADIR%%/examples/program_5.nab
+%%DATADIR%%/examples/program_5.tat.in
+%%DATADIR%%/examples/program_6.nab
+%%DATADIR%%/examples/program_7.nab
+%%DATADIR%%/examples/program_8.nab
+%%DATADIR%%/examples/program_9.nab
+%%DATADIR%%/examples/rna_pseudoknot.pdb
+%%DATADIR%%/examples/spline.nab
+%%DATADIR%%/examples/tat.triad.min.pdb
+%%DATADIR%%/examples/test.pdb
+%%DATADIR%%/examples/test.sup.pdb
+%%DATADIR%%/examples/toto.dat
 %%DATADIR%%/fd_data/abdna.dat
 %%DATADIR%%/fd_data/abdna.dat.old
 %%DATADIR%%/fd_data/adna.dat
@@ -303,6 +329,7 @@ lib/libsym.a
 %%DATADIR%%/leap/cmd/leaprc.ff02
 %%DATADIR%%/leap/cmd/leaprc.ff02EP
 %%DATADIR%%/leap/cmd/leaprc.ff03
+%%DATADIR%%/leap/cmd/leaprc.ff03ua
 %%DATADIR%%/leap/cmd/leaprc.ff84
 %%DATADIR%%/leap/cmd/leaprc.ff86
 %%DATADIR%%/leap/cmd/leaprc.ff94
@@ -310,6 +337,9 @@ lib/libsym.a
 %%DATADIR%%/leap/cmd/leaprc.ff96
 %%DATADIR%%/leap/cmd/leaprc.ff98
 %%DATADIR%%/leap/cmd/leaprc.ff99
+%%DATADIR%%/leap/cmd/leaprc.ff99SB
+%%DATADIR%%/leap/cmd/leaprc.ffAM1
+%%DATADIR%%/leap/cmd/leaprc.ffPM3
 %%DATADIR%%/leap/cmd/leaprc.gaff
 %%DATADIR%%/leap/cmd/leaprc.glycam04
 %%DATADIR%%/leap/cmd/leaprc.glycam04EP
@@ -330,6 +360,8 @@ lib/libsym.a
 %%DATADIR%%/leap/lib/all_amino91.lib
 %%DATADIR%%/leap/lib/all_amino94.lib
 %%DATADIR%%/leap/lib/all_amino94.nmr.lib
+%%DATADIR%%/leap/lib/all_aminoAM1.lib
+%%DATADIR%%/leap/lib/all_aminoPM3.lib
 %%DATADIR%%/leap/lib/all_aminoct02.lib
 %%DATADIR%%/leap/lib/all_aminoct02EP.lib
 %%DATADIR%%/leap/lib/all_aminoct91.lib
@@ -350,6 +382,7 @@ lib/libsym.a
 %%DATADIR%%/leap/lib/ff02EP.cmd
 %%DATADIR%%/leap/lib/ff03.cmd
 %%DATADIR%%/leap/lib/ff03.log
+%%DATADIR%%/leap/lib/ff03ua.cmd
 %%DATADIR%%/leap/lib/ff91.cmd
 %%DATADIR%%/leap/lib/ff94.cmd
 %%DATADIR%%/leap/lib/glycam91.cmd
@@ -366,19 +399,28 @@ lib/libsym.a
 %%DATADIR%%/leap/lib/solvents.cmd
 %%DATADIR%%/leap/lib/solvents.lib
 %%DATADIR%%/leap/lib/spcebox.off
+%%DATADIR%%/leap/lib/spcfwbox.off
 %%DATADIR%%/leap/lib/tip3pbox.off
 %%DATADIR%%/leap/lib/tip4pbox.off
 %%DATADIR%%/leap/lib/tip4pewbox.off
+%%DATADIR%%/leap/lib/uni_amino03.lib
+%%DATADIR%%/leap/lib/uni_aminoct03.lib
+%%DATADIR%%/leap/lib/uni_aminont03.lib
 %%DATADIR%%/leap/parm/frcmod.chcl3
 %%DATADIR%%/leap/parm/frcmod.constph
 %%DATADIR%%/leap/parm/frcmod.dc4
 %%DATADIR%%/leap/parm/frcmod.ff03
+%%DATADIR%%/leap/parm/frcmod.ff03ua
+%%DATADIR%%/leap/parm/frcmod.ff99SB
+%%DATADIR%%/leap/parm/frcmod.ff99SP
 %%DATADIR%%/leap/parm/frcmod.meoh
 %%DATADIR%%/leap/parm/frcmod.mod_phipsi.1
 %%DATADIR%%/leap/parm/frcmod.mod_phipsi.2
 %%DATADIR%%/leap/parm/frcmod.nma
 %%DATADIR%%/leap/parm/frcmod.pol3
+%%DATADIR%%/leap/parm/frcmod.qspcfw
 %%DATADIR%%/leap/parm/frcmod.spce
+%%DATADIR%%/leap/parm/frcmod.spcfw
 %%DATADIR%%/leap/parm/frcmod.tip4p
 %%DATADIR%%/leap/parm/frcmod.tip4pew
 %%DATADIR%%/leap/parm/frcmod.tip5p
@@ -386,7 +428,6 @@ lib/libsym.a
 %%DATADIR%%/leap/parm/gaff.dat
 %%DATADIR%%/leap/parm/glycam04.dat
 %%DATADIR%%/leap/parm/glycam04EP.dat
-%%DATADIR%%/leap/parm/leap.log
 %%DATADIR%%/leap/parm/nucgen.dat
 %%DATADIR%%/leap/parm/opls.info
 %%DATADIR%%/leap/parm/opls_parm.dat
@@ -398,6 +439,8 @@ lib/libsym.a
 %%DATADIR%%/leap/parm/parm98.dat
 %%DATADIR%%/leap/parm/parm99.dat
 %%DATADIR%%/leap/parm/parm99EP.dat
+%%DATADIR%%/leap/parm/parmAM1.dat
+%%DATADIR%%/leap/parm/parmPM3.dat
 %%DATADIR%%/leap/parm/toyrna.dat
 %%DATADIR%%/leap/prep/all.in
 %%DATADIR%%/leap/prep/all_amino02.in
@@ -430,15 +473,17 @@ lib/libsym.a
 %%DATADIR%%/leap/prep/protein.amberua.in
 %%DATADIR%%/leap/prep/toyrna.in
 %%DATADIR%%/leap/prep/uni.in
+%%DATADIR%%/leap/prep/uni_amino03.in
+%%DATADIR%%/leap/prep/uni_aminoct03.in
+%%DATADIR%%/leap/prep/uni_aminont03.in
 %%DATADIR%%/leap/prep/unict.in
 %%DATADIR%%/leap/prep/unint.in
 %%DATADIR%%/lib/blas.a
 %%DATADIR%%/lib/cifparse.a
+%%DATADIR%%/lib/f2c.a
 %%DATADIR%%/lib/lapack.a
 %%DATADIR%%/lib/libnab.a
 %%DATADIR%%/lib/libsym.a
-%%PORTDOCS%%%%DATADIR%%/peptide/README
-%%PORTDOCS%%%%DATADIR%%/peptide/peptide.nab
 %%DATADIR%%/reslib/adna.std.rlb
 %%DATADIR%%/reslib/adna.std/adna.std.bnd
 %%DATADIR%%/reslib/adna.std/adna.std.pdb
@@ -559,93 +604,87 @@ lib/libsym.a
 %%DATADIR%%/reslib/rna.amberua/rna.amberua.chi
 %%DATADIR%%/reslib/rna.amberua/rna.amberua.pdb
 %%DATADIR%%/reslib/rna.amberua/rna.amberua.qr
-%%PORTDOCS%%%%DATADIR%%/suppose/Makefile
-%%PORTDOCS%%%%DATADIR%%/suppose/PCA_suppose.nab
-%%PORTDOCS%%%%DATADIR%%/suppose/ccmath.h
-%%PORTDOCS%%%%DATADIR%%/suppose/eigen.c
-%%PORTDOCS%%%%DATADIR%%/suppose/housev.c
-%%PORTDOCS%%%%DATADIR%%/suppose/matutl.h
-%%PORTDOCS%%%%DATADIR%%/suppose/qrevec.c
-%%PORTDOCS%%%%DATADIR%%/suppose/suppose.1
-%%PORTDOCS%%%%DATADIR%%/suppose/suppose.nab
-%%PORTDOCS%%%%DATADIR%%/suppose/trnm.c
-%%PORTDOCS%%%%DATADIR%%/test/2.pdb
-%%PORTDOCS%%%%DATADIR%%/test/5pti.obs
-%%PORTDOCS%%%%DATADIR%%/test/5pti.pdb
-%%PORTDOCS%%%%DATADIR%%/test/5pti.shifts.check
-%%PORTDOCS%%%%DATADIR%%/test/Makefile
-%%PORTDOCS%%%%DATADIR%%/test/asp.nab
-%%PORTDOCS%%%%DATADIR%%/test/asp.out.check
-%%PORTDOCS%%%%DATADIR%%/test/asp.pdb
-%%PORTDOCS%%%%DATADIR%%/test/asp.top
-%%PORTDOCS%%%%DATADIR%%/test/crambin.nab
-%%PORTDOCS%%%%DATADIR%%/test/crambin.out.check
-%%PORTDOCS%%%%DATADIR%%/test/crambin.pdb
-%%PORTDOCS%%%%DATADIR%%/test/crambin.top
-%%PORTDOCS%%%%DATADIR%%/test/crambin.x
-%%PORTDOCS%%%%DATADIR%%/test/d01.lin.check
-%%PORTDOCS%%%%DATADIR%%/test/d01.pdb.check
-%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate.nab
-%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate.out.check
-%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate2.nab
-%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.ambpdb
-%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.nab
-%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.out.check
-%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.prmtop
-%%PORTDOCS%%%%DATADIR%%/test/dna.circle.nab
-%%PORTDOCS%%%%DATADIR%%/test/duplex.in
-%%PORTDOCS%%%%DATADIR%%/test/duplex.nab
-%%PORTDOCS%%%%DATADIR%%/test/fd.nab
-%%PORTDOCS%%%%DATADIR%%/test/fd.pdb.check
-%%PORTDOCS%%%%DATADIR%%/test/gbrna.nab
-%%PORTDOCS%%%%DATADIR%%/test/gbrna.out.check
-%%PORTDOCS%%%%DATADIR%%/test/gbrna.pdb
-%%PORTDOCS%%%%DATADIR%%/test/gbrna.prmtop
-%%PORTDOCS%%%%DATADIR%%/test/gbrna_long.nab
-%%PORTDOCS%%%%DATADIR%%/test/gbrna_long.out.check
-%%PORTDOCS%%%%DATADIR%%/test/gbtrx.nab
-%%PORTDOCS%%%%DATADIR%%/test/gbtrx.out.check
-%%PORTDOCS%%%%DATADIR%%/test/get_pep_info.nab
-%%PORTDOCS%%%%DATADIR%%/test/get_ring_info.nab
-%%PORTDOCS%%%%DATADIR%%/test/get_sugar_info.nab
-%%PORTDOCS%%%%DATADIR%%/test/getresid_from_pdb.nab
-%%PORTDOCS%%%%DATADIR%%/test/hash.in
-%%PORTDOCS%%%%DATADIR%%/test/hash.nab
-%%PORTDOCS%%%%DATADIR%%/test/hash.out.check
-%%PORTDOCS%%%%DATADIR%%/test/ico.sym
-%%PORTDOCS%%%%DATADIR%%/test/ico.sym.out.check
-%%PORTDOCS%%%%DATADIR%%/test/ltest.nab
-%%PORTDOCS%%%%DATADIR%%/test/ltest.out.check
-%%PORTDOCS%%%%DATADIR%%/test/mm_plus_dg.nab
-%%PORTDOCS%%%%DATADIR%%/test/pointplane.nab
-%%PORTDOCS%%%%DATADIR%%/test/prm.nab
-%%PORTDOCS%%%%DATADIR%%/test/prm.out.check
-%%PORTDOCS%%%%DATADIR%%/test/prmtop
-%%PORTDOCS%%%%DATADIR%%/test/prmtop.gb2
-%%PORTDOCS%%%%DATADIR%%/test/pseudoknot.nab
-%%PORTDOCS%%%%DATADIR%%/test/rattle_md.nab
-%%PORTDOCS%%%%DATADIR%%/test/rattle_md.out.check
-%%PORTDOCS%%%%DATADIR%%/test/rattle_min.nab
-%%PORTDOCS%%%%DATADIR%%/test/rattle_min.out.check
-%%PORTDOCS%%%%DATADIR%%/test/read_obs_shifts.nab
-%%PORTDOCS%%%%DATADIR%%/test/ref.out.check
-%%PORTDOCS%%%%DATADIR%%/test/reflexive.nab
-%%PORTDOCS%%%%DATADIR%%/test/rembed.nab
-%%PORTDOCS%%%%DATADIR%%/test/rembed.out.check
-%%PORTDOCS%%%%DATADIR%%/test/sbcoil.nab
-%%PORTDOCS%%%%DATADIR%%/test/shifts.h
-%%PORTDOCS%%%%DATADIR%%/test/shifts.nab
-%%PORTDOCS%%%%DATADIR%%/test/swap_shifts.nab
-%%PORTDOCS%%%%DATADIR%%/test/tbv.60.com.pdb.check
-%%PORTDOCS%%%%DATADIR%%/test/tbv.com.pdb
-%%PORTDOCS%%%%DATADIR%%/test/tprmtop.check
-%%PORTDOCS%%%%DATADIR%%/test/trxox.2.4ns.pdb
-%%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
+%%DATADIR%%/test/2.pdb
+%%DATADIR%%/test/5pti.obs
+%%DATADIR%%/test/5pti.pdb
+%%DATADIR%%/test/5pti.shifts.check
+%%DATADIR%%/test/Makefile
+%%DATADIR%%/test/asp.nab
+%%DATADIR%%/test/asp.out.check
+%%DATADIR%%/test/asp.pdb
+%%DATADIR%%/test/asp.top
+%%DATADIR%%/test/aspnb.nab
+%%DATADIR%%/test/aspnb.out.check
+%%DATADIR%%/test/cif.nab
+%%DATADIR%%/test/crambin.nab
+%%DATADIR%%/test/crambin.out.check
+%%DATADIR%%/test/crambin.pdb
+%%DATADIR%%/test/crambin.top
+%%DATADIR%%/test/crambin.x
+%%DATADIR%%/test/d01.lin.check
+%%DATADIR%%/test/d01.pdb.check
+%%DATADIR%%/test/dg_gyrate.nab
+%%DATADIR%%/test/dg_gyrate.out.check
+%%DATADIR%%/test/dg_gyrate2.nab
+%%DATADIR%%/test/dhfrndpmtx.ambpdb
+%%DATADIR%%/test/dhfrndpmtx.nab
+%%DATADIR%%/test/dhfrndpmtx.out.check
+%%DATADIR%%/test/dhfrndpmtx.prmtop
+%%DATADIR%%/test/dna.circle.nab
+%%DATADIR%%/test/duplex.in
+%%DATADIR%%/test/duplex.nab
+%%DATADIR%%/test/fd.nab
+%%DATADIR%%/test/fd.pdb.check
+%%DATADIR%%/test/gbrna.cif.check
+%%DATADIR%%/test/gbrna.nab
+%%DATADIR%%/test/gbrna.out.check
+%%DATADIR%%/test/gbrna.pdb
+%%DATADIR%%/test/gbrna.prmtop
+%%DATADIR%%/test/gbrna_long.nab
+%%DATADIR%%/test/gbrna_long.out.check
+%%DATADIR%%/test/gbtrx.nab
+%%DATADIR%%/test/gbtrx.out.check
+%%DATADIR%%/test/get_pep_info.nab
+%%DATADIR%%/test/get_ring_info.nab
+%%DATADIR%%/test/get_sugar_info.nab
+%%DATADIR%%/test/getresid_from_pdb.nab
+%%DATADIR%%/test/hash.in
+%%DATADIR%%/test/hash.nab
+%%DATADIR%%/test/hash.out.check
+%%DATADIR%%/test/ico.sym
+%%DATADIR%%/test/ico.sym.out.check
+%%DATADIR%%/test/ltest.nab
+%%DATADIR%%/test/ltest.out.check
+%%DATADIR%%/test/mm_plus_dg.nab
+%%DATADIR%%/test/pointplane.nab
+%%DATADIR%%/test/prm.nab
+%%DATADIR%%/test/prm.out.check
+%%DATADIR%%/test/prmtop
+%%DATADIR%%/test/prmtop.gb2
+%%DATADIR%%/test/pseudoknot.nab
+%%DATADIR%%/test/rattle_md.nab
+%%DATADIR%%/test/rattle_md.out.check
+%%DATADIR%%/test/rattle_min.nab
+%%DATADIR%%/test/rattle_min.out.check
+%%DATADIR%%/test/read_obs_shifts.nab
+%%DATADIR%%/test/ref.out.check
+%%DATADIR%%/test/reflexive.nab
+%%DATADIR%%/test/rembed.nab
+%%DATADIR%%/test/rembed.out.check
+%%DATADIR%%/test/sbcoil.nab
+%%DATADIR%%/test/shifts.h
+%%DATADIR%%/test/shifts.nab
+%%DATADIR%%/test/swap_shifts.nab
+%%DATADIR%%/test/tbv.60.com.pdb.check
+%%DATADIR%%/test/tbv.com.pdb
+%%DATADIR%%/test/tprmtop.check
+%%DATADIR%%/test/trxox.2.4ns.pdb
+%%DATADIR%%/test/trxox.2.4ns.x
+%%DATADIR%%/test/vizgrad.nab
+%%DATADIR%%/test/vizgrad.pdb
+%%DATADIR%%/test/vizgrad.prm
+%%DATADIR%%/test/write_sander_inp.nab
+@dirrm %%DATADIR%%/test
 @dirrm %%DATADIR%%/reslib/rna.amberua
 @dirrm %%DATADIR%%/reslib/rna.amber94
 @dirrm %%DATADIR%%/reslib/protein.opls
@@ -668,14 +707,11 @@ lib/libsym.a
 @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
-%%PORTDOCS%%@dirrm %%DATADIR%%/benchmarks
-%%PORTDOCS%%@dirrm %%DATADIR%%/examples
-%%PORTDOCS%%@dirrm %%DATADIR%%/peptide
-%%PORTDOCS%%@dirrm %%DATADIR%%/suppose
-%%PORTDOCS%%@dirrm %%DATADIR%%/test
+@dirrm %%DATADIR%%/benchmarks
 @dirrm %%DATADIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%