update biology/nab: 4.5.1 -> 4.5.2

PR:		57970
Submitted by:	M. L. Dodson <bdodson@scms.utmb.edu> (maintainer)

5 files changed, 38 insertions, 20 deletions

diff --git a/biology/nab/Makefile b/biology/nab/Makefile
index e2d701f241a4..406e1323c629 100644
--- a/biology/nab/Makefile
+++ b/biology/nab/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	nab
-PORTVERSION=	4.5.1
+PORTVERSION=	4.5.2
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/ \
 		http://www.scripps.edu/case/
@@ -15,8 +15,6 @@ MAINTAINER=	bdodson@scms.utmb.edu
 COMMENT=	\
  "This is nab (nucleic acid builder), a language for macromolecules"
 
-BROKEN=		Does not fetch
-
 BUILD_DEPENDS=	ucpp:${PORTSDIR}/devel/ucpp
 
 ONLY_FOR_ARCHS= i386
@@ -43,7 +41,19 @@ pre-patch:
 		${WRKSRC}/cifparse/cifparse.c
 
 post-patch:
-	@rm -f ${WRKSRC}/examples/program_7.nab.orig
+	@${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}/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 && \
diff --git a/biology/nab/distinfo b/biology/nab/distinfo
index 9b854a4b868a..e8a2891bb7c0 100644
--- a/biology/nab/distinfo
+++ b/biology/nab/distinfo
@@ -1 +1 @@
-MD5 (nab-4.5.1.tar.gz) = 650be5581dfe5af1b7edb6da44a221d4
+MD5 (nab-4.5.2.tar.gz) = b5e9053e6ae97f36a55cc2a1317e9ba8
diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile
index 039c7d0abffb..9c258367476c 100644
--- a/biology/nab/files/patch-Makefile
+++ b/biology/nab/files/patch-Makefile
@@ -1,12 +1,12 @@
---- Makefile.orig	Mon Oct 23 20:33:23 2000
-+++ Makefile	Wed Feb 12 16:33:42 2003
+--- Makefile.orig	Tue Jul 15 21:11:15 2003
++++ Makefile	Sat Aug  9 13:50:34 2003
 @@ -1,15 +1,15 @@
  #   top-level Makefile for the NAB suite of programs
  
 +all: compiler test
  compiler:
  	-mkdir bin lib include
--	(cd ucpp-0.7; make install )
+-	(cd ucpp-1.3; make install )
  	(cd cifparse; make install )
  	(cd src; make install )
  	(cd nss; make install )
@@ -20,21 +20,18 @@
  
  #   note:  "make test" needs to follow "make", since it is very hard to
  #          tell if the compiler is completely "made" or not.
-@@ -18,17 +18,14 @@
+@@ -18,14 +18,12 @@
  	(cd nss; make test )
  
  clean:
--	(cd ucpp-0.7; make clean )
+-	(cd ucpp-1.3; make clean )
  	(cd cifparse; make clean )
  	(cd src; make clean )
  	(cd nss; make clean )
  	(cd tleap; make clean )
  	
  uninstall:
--	(cd ucpp-0.7; make uninstall )
+-	(cd 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
--	
diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr
index b4fcfcb34f6a..2d85d2947733 100644
--- a/biology/nab/pkg-descr
+++ b/biology/nab/pkg-descr
@@ -1,4 +1,4 @@
-This is version 4.5 of nab (nucleic acid builder), a computer
+This is version 4.5.2 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
diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist
index 1d3ca0851424..27719e7d3fcc 100644
--- a/biology/nab/pkg-plist
+++ b/biology/nab/pkg-plist
@@ -78,7 +78,6 @@ share/nab/examples/rna_pseudoknot.pdb
 share/nab/examples/test.pdb
 share/nab/examples/test.sup.pdb
 share/nab/fd_data/abdna.dat
-share/nab/fd_data/abdna.dat.old
 share/nab/fd_data/adna.dat
 share/nab/fd_data/aprna.dat
 share/nab/fd_data/arna.dat
@@ -171,6 +170,7 @@ 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/parm94.dat.istvan
 share/nab/reslib/leap/leap.log
 share/nab/reslib/leap/leaprc.dna.amberua
 share/nab/reslib/leap/leaprc.dna.amberua.redch
@@ -270,13 +270,11 @@ share/nab/test/2.pdb
 share/nab/test/5pti.obs
 share/nab/test/5pti.pdb
 share/nab/test/5pti.shifts.check
-share/nab/test/a.exe
 share/nab/test/d01.lin.check
 share/nab/test/d01.pdb.check
 share/nab/test/dg_gyrate.nab
 share/nab/test/dg_gyrate.out.check
 share/nab/test/dna.circle.nab
-share/nab/test/duplex.exe
 share/nab/test/duplex.in
 share/nab/test/duplex.nab
 share/nab/test/fd.nab
@@ -285,9 +283,8 @@ 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.exe
 share/nab/test/gbrna_long.nab
-share/nab/test/gbrna_long.out
+share/nab/test/gbrna_sa.nab
 share/nab/test/gbtrx.nab
 share/nab/test/gbtrx.out.check
 share/nab/test/get_pep_info.nab
@@ -301,9 +298,11 @@ 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/msurf.nab
 share/nab/test/pointplane.nab
 share/nab/test/prmtop
 share/nab/test/prmtop.gb2
+share/nab/test/prmtop.new
 share/nab/test/rattle_md.nab
 share/nab/test/rattle_md.out.check
 share/nab/test/rattle_min.nab
@@ -322,6 +321,18 @@ 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
+share/nab/test/lCmd
+share/nab/test/1ubq/1ubq.pdb
+share/nab/test/1ubq/5pti.pdb
+share/nab/test/1ubq/leap.log
+share/nab/test/1ubq/out.1
+share/nab/test/1ubq/prmtop
+share/nab/test/1ubq/prmtop.1
+share/nab/test/1ubq/rattle_min.nab
+share/nab/test/1ubq/runleap.nab
+share/nab/test/2strand.nab
+share/nab/test/2strand.pdb
+@dirrm share/nab/test/1ubq
 @dirrm share/nab/test
 @dirrm share/nab/suppose
 @dirrm share/nab/reslib/rna.amberua