upgrade to 4.4

PR:		40612
Submitted by:	maintainer

biology/nab/Makefile

@@ -4,7 +4,7 @@
 # $FreeBSD$
 
 PORTNAME=	nab
-PORTVERSION=	4.3.2
+PORTVERSION=	4.4
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.scripps.edu/pub/case/
 
@@ -31,6 +31,9 @@ pre-patch:
 	@${PERL} -pi -e 's,<malloc.h>,<stdlib.h>,' \
 		${WRKSRC}/cifparse/cifparse.c
 
+post-patch:
+	@rm -f ${WRKSRC}/examples/program_7.nab.orig
+
 pre-install:
 	@cd ${WRKSRC}/src && \
 		${SETENV} PREFIX=${PREFIX} ${MAKE} beforerealinstall

biology/nab/distinfo

@@ -1 +1 @@
-MD5 (nab-4.3.2.tar.gz) = 35a706bd124a212cc8310ca1327be227
+MD5 (nab-4.4.tar.gz) = c1fe516ab9aebff74fcadd61f874d474

biology/nab/files/config.h

@@ -97,8 +97,8 @@ CPP=    ucpp -l
 #
 #  Use these CFLAGS if AVS = 0
 #
-CFLAGS= 
-OCFLAGS= -O
+CFLAGS= -O -pipe
+OCFLAGS= -O -pipe
 NABFLAGS=
 #
 #  Use these CFLAGS if AVS = 1

biology/nab/files/patch-examples:program_7.nab

@@ -0,0 +1,19 @@
+*** 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 ];

biology/nab/files/patch-src:database.c

@@ -0,0 +1,32 @@
+*** src/database.c.orig	Wed Nov 15 19:46:50 2000
+--- src/database.c	Sun Jun  2 12:57:50 2002
+***************
+*** 67,72 ****
+--- 67,79 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"stdio.h"
+***************
+*** 979,985 ****
+--- 986,996 ----
+  
+      sDBRemoveLeadingSpaces( sLine );
+      sDBRemoveFirstString( sLine, sHead );
++ #if defined (linux) || defined(BSD)
++     sscanf( sHead, "%lg", dPDbl );
++ #else
+      sscanf( sHead, "%lG", dPDbl );
++ #endif
+  
+  }
+  

biology/nab/files/patch-tleap:database.c

@@ -0,0 +1,35 @@
+*** tleap/database.c.orig	Wed Mar 27 15:41:01 2002
+--- tleap/database.c	Sun Jun  2 12:59:14 2002
+***************
+*** 97,102 ****
+--- 97,109 ----
+  
+  
+  
++ #if (defined(__unix__) || defined(unix)) && !defined(USG)
++ #include <sys/param.h>
++ #endif
++ 
++ #if defined(BSD)
++ #include <math.h>
++ #endif
+  
+  
+  #include	"basics.h"
+***************
+*** 563,569 ****
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #ifdef linux
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );
+--- 570,576 ----
+  
+      sRemoveLeadingSpaces( sLine );
+      sRemoveFirstString( sLine, sHead );
+! #if defined(linux) || defined(BSD)
+      sscanf( sHead, "%lg", dPDbl );
+  #else
+      sscanf( sHead, "%lG", dPDbl );

biology/nab/pkg-descr

@@ -1,4 +1,4 @@
-This is version 4.2 of nab (nucleic acid builder), a computer language that
+This is version 4.4 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.

biology/nab/pkg-plist

@@ -101,17 +101,6 @@ share/nab/test/write_sander_inp.nab
 share/nab/test/duplex.nab
 share/nab/test/ltest.out.check
 share/nab/test/dg_gyrate.out.check
-share/nab/peptide/COPYING
-share/nab/peptide/aaaa.pdb
-share/nab/peptide/lprot.nab
-share/nab/peptide/write_pdb.nab
-share/nab/peptide/README
-share/nab/peptide/Makefile
-share/nab/peptide/conf.lib
-share/nab/peptide/peptide.nab
-share/nab/peptide/match_template.nab
-share/nab/peptide/peptide.c
-share/nab/peptide/fix_angles.nab
 share/nab/suppose/suppose.1
 share/nab/suppose/suppose.nab
 share/nab/dgdb/adna.basepair.db
@@ -131,6 +120,8 @@ 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/peptide/peptide.nab
+share/nab/peptide/README
 share/nab/reslib/leap.log
 share/nab/reslib/hetatm.amber94/hetatm.amber94.chi
 share/nab/reslib/hetatm.amber94/hetatm.amber94.bnd
@@ -301,6 +292,7 @@ share/nab/fd_data/sbdna.dat
 share/nab/fd_data/abdna.dat
 share/nab/fd_data/aprna.dat
 share/nab/fd_data/lbdna.dat
+share/nab/fd_data/abdna.dat.old
 share/nab/coords
 share/nab/lib/cifparse.a
 share/nab/lib/libnab.a