Update to 4.7

PR:		ports/128476
Submitted by:	fulvio ciriaco <oivulf@gmail.com>

8 files changed, 309 insertions, 140 deletions

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index 137ecf323acb..8f480a9a211e 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -6,30 +6,24 @@
 #
 
 PORTNAME=	molden
-PORTVERSION=	4.5
-PORTREVISION=	2
+PORTVERSION=	4.7
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/
 DISTNAME=	${PORTNAME}${PORTVERSION}
-EXTRACT_SUFX=	.tar.Z
 DIST_SUBDIR=	${PKGNAME}
-EXTRACT_ONLY=	${PORTNAME}${PORTVERSION}.tar.Z
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	oivulf@gmail.com
 COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
 
 USE_XORG=	x11 xmu
 USE_GL=		glut
+USE_FORTRAN=	yes
 
 RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable.
 MAKEFILE=	${WRKSRC}/makefile
 
-.include <bsd.port.pre.mk>
-
-USE_FORTRAN=	yes
-
 post-patch:
-	${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/xwin.c
+	@${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/xwin.c
 
 post-configure:
 	@${ECHO_MSG} "********************"
@@ -40,7 +34,9 @@ post-configure:
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/molden ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/moldenogl ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/gmolden ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/surf/surf ${PREFIX}/bin
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${PREFIX}/share/doc/molden
 	${MKDIR} ${PREFIX}/share/molden/test
@@ -50,4 +46,4 @@ do-install:
 	${INSTALL_DATA} ${WRKSRC}/utils/* ${PREFIX}/share/molden/utils
 .endif
 
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index 3a06d430cc7c..a66df4280cde 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-MD5 (molden-4.5_2/molden4.5.tar.Z) = 2706a205de011f2dca042f8c7fe95834
-SHA256 (molden-4.5_2/molden4.5.tar.Z) = 84b6905ec786bde9af8bfa6439b0c066b65a98028ffaf1ebc543e58b31fe2ca7
-SIZE (molden-4.5_2/molden4.5.tar.Z) = 3605279
+MD5 (molden-4.7/molden4.7.tar.gz) = 94baf00d545224d328767bfacb8ec194
+SHA256 (molden-4.7/molden4.7.tar.gz) = a5f5eb207894c7cb2e437ad14bed6b52d3845cd78599c89be8de55692ae1cddf
+SIZE (molden-4.7/molden4.7.tar.gz) = 2813532
diff --git a/biology/molden/files/patch-ambfor-makefile b/biology/molden/files/patch-ambfor-makefile
new file mode 100644
index 000000000000..f846b79cbd18
--- /dev/null
+++ b/biology/molden/files/patch-ambfor-makefile
@@ -0,0 +1,17 @@
+--- ambfor/makefile.orig	2008-10-30 10:06:37.000000000 +0100
++++ ambfor/makefile	2008-10-30 10:07:19.000000000 +0100
+@@ -14,11 +14,11 @@
+ #
+ #CC = cc
+ 
+-CFLAGS = -c
+-FC = g77
++CFLAGS += -DFREEBSD=1
++#FC = g77
+ FFLAGS = -c -O3 -ffast-math
+ LIBS =  -lm
+-LDR = g77 
++LDR = $(FC) 
+ 
+ OBJS = ambfor.o angle.o bond.o charge.o conn.o enegrd.o getinp.o \
+ 	param.o tors.o vdwlj.o math.o optimise.o wrtout.o
diff --git a/biology/molden/files/patch-aa b/biology/molden/files/patch-makefile
index 82a56ab159df..ac9cc36e67b1 100644
--- a/biology/molden/files/patch-aa
+++ b/biology/molden/files/patch-makefile
@@ -1,6 +1,6 @@
---- makefile.orig	Thu Sep  7 19:55:00 2006
-+++ makefile	Tue Apr 24 16:40:19 2007
-@@ -12,9 +12,27 @@
+--- makefile.orig	2008-08-25 19:55:57.000000000 +0200
++++ makefile	2008-11-01 21:48:37.000000000 +0100
+@@ -12,9 +12,23 @@
  #
  #	Disregard compiler warnings on rdmolf.f
  #
@@ -15,10 +15,6 @@
 +#CC = gcc
 +CFLAGS += -c -DDOBACK -DHASTIMER -I${LOCALBASE}/include
 +#FC = f77
-+.if ${MACHINE_ARCH} == i386
-+FFLAGS += -malign-double
-+CFLAGS += -malign-double
-+.endif
 +.if ${OSVERSION} < 400005
 +FFLAGS += -Nn802 -Nx400
 +.else
@@ -30,9 +26,9 @@
  
  # Silicon Graphics
  #CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-@@ -46,11 +64,11 @@
- # when using gfortran, replace g77 with gfortran and comment out the line
- # 'external iargc' in molden.f
+@@ -52,11 +66,11 @@
+ # with GCC4.0 or higher replace the line with:
+ # 'external gfortran_iargc'
  #
 -CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
 -FC = g77
@@ -47,8 +43,8 @@
  # 64 bit machines:
  #LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
  #
-@@ -178,7 +196,7 @@
- # and the full opengl version of molden 'gmolden'
+@@ -191,7 +205,7 @@
+ # and the full opengl version of molden 'gmolden', (does not need glut)
  # (make gmolden)
  #
 -LIBSOGL = -lglut -lGLU -lGL -lXmu -lX11 -lm
@@ -56,12 +52,12 @@
  #
  # on linux :
  #
-@@ -201,7 +219,7 @@
- #
- #LIBSG = -L/usr/X11R6/lib -Wl,-framework -Wl,GLUT -Wl,-framework -Wl,OpenGL -Wl,-framework -Wl,Cocoa -lGLU -lGL -lXmu -lX11 -lm
+@@ -227,7 +241,7 @@
+ 	$(MAKE) -C ambfor
  
--
-+all: molden moldenogl
+ surf/surf:	surf/*.h surf/*.c
+-	$(MAKE) -C surf depend
++#	$(MAKE) -C surf depend
+ 	$(MAKE) -C surf
  
- molden:	$(OBJS) mpdum.o xwin.o 
- 	$(LDR) -o molden $(OBJS) $(SOBJ) mpdum.o xwin.o $(LIBS)
+ # noxwin will not work as long as the old ocglbck calls arent in dummys
diff --git a/biology/molden/files/patch-molden.f b/biology/molden/files/patch-molden.f
deleted file mode 100644
index 49d552255b72..000000000000
--- a/biology/molden/files/patch-molden.f
+++ /dev/null
@@ -1,10 +0,0 @@
---- molden.f~	Mon Jul 10 20:46:06 2006
-+++ molden.f	Tue Jan  9 10:43:24 2007
-@@ -255,7 +255,6 @@
-       common /vrmlhl/ spcdfil
-       common /pmflvl/ ipmfm,ipmfh,pmflev(mxpmfl),levcol(mxpmfl)
-       common /comsrf/ vo(3), rt(3),v1t(3),v2t(3),v3t(3)
--      external iargc
-       dimension fcnt(mxcntr)
-       character title*80, keywrd*160, keyhlp*80, keyori*160
-       character tmpstr*80,movfil*80,vrmlfil*80,povfil*80,oglfil*80
diff --git a/biology/molden/files/patch-surf-makefile b/biology/molden/files/patch-surf-makefile
new file mode 100644
index 000000000000..5107bc4637d9
--- /dev/null
+++ b/biology/molden/files/patch-surf-makefile
@@ -0,0 +1,165 @@
+--- surf/Makefile.orig	2008-10-30 10:12:27.000000000 +0100
++++ surf/Makefile	2008-10-30 10:08:43.000000000 +0100
+@@ -63,46 +63,120 @@
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
+   
+  
+-# DO NOT DELETE THIS LINE -- make depend depends on it.
++# DO NOT DELETE
+ 
+-surf.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
+-surf.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
+-surf.o: linalg.h
+-io.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
+-io.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
+-io.o: linalg.h
+-compute.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-compute.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
+-compute.o: /usr/include/sys/time.h linalg.h chull.h dual.h
+-dual.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
+-dual.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
+-dual.o: linalg.h dual.h chull.h
+-utils.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-utils.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
+-utils.o: /usr/include/sys/time.h linalg.h
+-lp.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
+-lp.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
+-lp.o: linalg.h
+-chull.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-chull.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
+-chull.o: /usr/include/sys/time.h linalg.h chull.h
+-tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-tessel_cases.o: /usr/include/stdlib.h /usr/include/sgidefs.h
+-tessel_cases.o: /usr/include/string.h /usr/include/sys/time.h linalg.h dual.h
+-tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-tessel_patches.o: /usr/include/stdlib.h /usr/include/sgidefs.h
+-tessel_patches.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
+-tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-tessel_convex.o: /usr/include/stdlib.h /usr/include/sgidefs.h
+-tessel_convex.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
+-tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-tessel_concave.o: /usr/include/stdlib.h /usr/include/sgidefs.h
+-tessel_concave.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
+-tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/math.h
+-tessel_torus.o: /usr/include/stdlib.h /usr/include/sgidefs.h
+-tessel_torus.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
+-  
+-# DEPENDENCIES MUST END AT END OF FILE
+-# IF YOU PUT STUFF HERE IT WILL GO AWAY
+-# see make depend above
+-  
++surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++surf.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++surf.o: /usr/include/machine/_types.h /usr/include/math.h
++surf.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++surf.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++surf.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++surf.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++surf.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++surf.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
++io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++io.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++io.o: /usr/include/machine/_types.h /usr/include/math.h
++io.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++io.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++io.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++io.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++io.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++io.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
++compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++compute.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++compute.o: /usr/include/machine/_types.h /usr/include/math.h
++compute.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++compute.o: /usr/include/string.h /usr/include/strings.h
++compute.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++compute.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++compute.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++compute.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++compute.o: /usr/include/time.h linalg.h chull.h dual.h
++dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++dual.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++dual.o: /usr/include/machine/_types.h /usr/include/math.h
++dual.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++dual.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++dual.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++dual.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++dual.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++dual.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h dual.h
++dual.o: chull.h
++utils.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++utils.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++utils.o: /usr/include/machine/_types.h /usr/include/math.h
++utils.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++utils.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++utils.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++utils.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++utils.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++utils.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
++lp.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++lp.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++lp.o: /usr/include/machine/_types.h /usr/include/math.h
++lp.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++lp.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++lp.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++lp.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++lp.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++lp.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
++chull.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++chull.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++chull.o: /usr/include/machine/_types.h /usr/include/math.h
++chull.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++chull.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
++chull.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
++chull.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
++chull.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
++chull.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h chull.h
++tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++tessel_cases.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++tessel_cases.o: /usr/include/machine/_types.h /usr/include/math.h
++tessel_cases.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++tessel_cases.o: /usr/include/string.h /usr/include/strings.h
++tessel_cases.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++tessel_cases.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++tessel_cases.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++tessel_cases.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++tessel_cases.o: /usr/include/time.h linalg.h dual.h
++tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++tessel_patches.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++tessel_patches.o: /usr/include/machine/_types.h /usr/include/math.h
++tessel_patches.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++tessel_patches.o: /usr/include/string.h /usr/include/strings.h
++tessel_patches.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++tessel_patches.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++tessel_patches.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++tessel_patches.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++tessel_patches.o: /usr/include/time.h linalg.h
++tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++tessel_convex.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++tessel_convex.o: /usr/include/machine/_types.h /usr/include/math.h
++tessel_convex.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++tessel_convex.o: /usr/include/string.h /usr/include/strings.h
++tessel_convex.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++tessel_convex.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++tessel_convex.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++tessel_convex.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++tessel_convex.o: /usr/include/time.h linalg.h
++tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++tessel_concave.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++tessel_concave.o: /usr/include/machine/_types.h /usr/include/math.h
++tessel_concave.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++tessel_concave.o: /usr/include/string.h /usr/include/strings.h
++tessel_concave.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++tessel_concave.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++tessel_concave.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++tessel_concave.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++tessel_concave.o: /usr/include/time.h linalg.h
++tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
++tessel_torus.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
++tessel_torus.o: /usr/include/machine/_types.h /usr/include/math.h
++tessel_torus.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
++tessel_torus.o: /usr/include/string.h /usr/include/strings.h
++tessel_torus.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
++tessel_torus.o: /usr/include/sys/types.h /usr/include/machine/endian.h
++tessel_torus.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
++tessel_torus.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
++tessel_torus.o: /usr/include/time.h linalg.h
diff --git a/biology/molden/files/patch-xwin.c b/biology/molden/files/patch-xwin.c
index ccb07152e869..bb8017792ddf 100644
--- a/biology/molden/files/patch-xwin.c
+++ b/biology/molden/files/patch-xwin.c
@@ -1,15 +1,15 @@
---- xwin.c~   Mon Jul 10 20:46:06 2006
-+++ xwin.c    Tue Jan  9 10:43:24 2007
-@@ -3177,7 +3177,7 @@
- static int *icopth;
- static int *icoptl;
- static int *icoptm;
+--- xwin.c.orig	2008-11-03 09:37:45.707629185 -0500
++++ xwin.c	2008-11-03 09:37:55.118628907 -0500
+@@ -3747,7 +3747,7 @@
+ static int ibopth = 0;
+ static int iboptl = 0;
+ static int iboptm = 0;
 -static int linkat = 0;
 +static int link_at = 0;
  
  static QBOXSTRU IANZboxes[MAXAT];
  static QBOXSTRU IZboxes[MAXAT][4];
-@@ -11622,7 +11622,7 @@
+@@ -19086,7 +19086,7 @@
  		if (ioniom == 1) {
  		  int ism, isl;
  
@@ -18,20 +18,20 @@
  
  		  /* Counting the number of Link atoms between H and lower 
  		     levels*/
-@@ -11635,10 +11635,10 @@
+@@ -19099,10 +19099,10 @@
  		     if (ionij != 0) continue;
- 		     nconn = atomptr->iconn[j][0];
+ 		     nconn = xyzp->iconn[j*(MXCON+1)];
  		     for (k=1;k<=nconn;k++) {
--		       if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) linkat++;
-+		       if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) link_at++;
+-		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
++		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
  		     }
  		  }
 -		  linkat += 20000;
 +		  link_at += 20000;
- 		  *itotc = *icopth;
- 		  *imult = *ispopth;
+ 		  jobcom->itotc = jobcom->icopth;
+ 		  jobcom->imult = jobcom->ispopth;
  		  if (CheckChargeMult()) {
-@@ -11659,7 +11659,7 @@
+@@ -19123,7 +19123,7 @@
  
  		}  else if (ioniom == 2) {
  
@@ -40,20 +40,20 @@
  
  		  /* Counting the number of Link atoms between H and 
  		       lower levels*/
-@@ -11669,10 +11669,10 @@
+@@ -19133,10 +19133,10 @@
  			 if(ionij != 0) continue;
- 		         nconn = atomptr->iconn[j][0];
+ 		         nconn = xyzp->iconn[j*(MXCON+1)];
  		         for (k=1;k<=nconn;k++) {
--		           if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) linkat++;
-+		           if (ityp[atomptr->iconn[j][k]-1]/10000 > 0) link_at++;
+-		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
++		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
  		         }
  		  }
 -		  linkat += 20000;
 +		  link_at += 20000;
- 		  *itotc = *icopth;
- 		  *imult = *ispopth;
+ 		  jobcom->itotc = jobcom->icopth;
+ 		  jobcom->imult = jobcom->ispopth;
  		  if (CheckChargeMult()) {
-@@ -11684,7 +11684,7 @@
+@@ -19148,7 +19148,7 @@
  	               break;
  */
  		  }
@@ -62,29 +62,29 @@
  
  		  /* Counting the number of Link atoms between H+M and 
  		     lower levels*/
-@@ -11694,10 +11694,10 @@
+@@ -19158,10 +19158,10 @@
  			if (ionij == 2) continue;
- 			nconn = atomptr->iconn[j][0];
+ 			nconn = xyzp->iconn[j*(MXCON+1)];
  			for (k=1;k<=nconn;k++) {
--			   if (ityp[atomptr->iconn[j][k]-1]/10000 == 2) linkat++;
-+			   if (ityp[atomptr->iconn[j][k]-1]/10000 == 2) link_at++;
+-			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
++			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) link_at++;
  			}
  		  }
 -		  linkat += 20000;
 +		  link_at += 20000;
- 		  *itotc = *icoptm;
- 		  *imult = *ispoptm;
+ 		  jobcom->itotc = jobcom->icoptm;
+ 		  jobcom->imult = jobcom->ispoptm;
  		  if (CheckChargeMult()) {
-@@ -11712,7 +11712,7 @@
- 		  icopt = *icoptl+3;
- 		  ispopt = *ispoptl-1;
+@@ -19176,7 +19176,7 @@
+ 		  icopt = jobcom->icoptl+3;
+ 		  ispopt = jobcom->ispoptl-1;
  		}
 -		linkat = 0;
 +		link_at = 0;
- 		*itotc = icopt - 3;
- 		*imult = ispopt + 1;
- 		*ito = itopt[jmode] + 1;
-@@ -11964,10 +11964,10 @@
+ 		jobcom->itotc = icopt - 3;
+ 		jobcom->imult = ispopt + 1;
+ 		jobcom->ito = itopt[jmode] + 1;
+@@ -19428,10 +19428,10 @@
     ionil = 0;
  
     if (ioniom) {
@@ -97,18 +97,18 @@
 +     link_at = 0;
     }
  
-    if (*zmptr.ihaszm) {
-@@ -11990,10 +11990,10 @@
+    if (*zmptrp->ihaszm) {
+@@ -19454,10 +19454,10 @@
        }
     }
  /*
 -   fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
--                   ionil,ne,*itotc,linkat,*imult);
+-                   ionil,ne,jobcom->itotc,linkat,jobcom->imult);
 +   fprintf(stderr,"ionil %d ne %d itotc %d link_at %d mult %d\n",
-+                   ionil,ne,*itotc,link_at,*imult);
++                   ionil,ne,jobcom->itotc,link_at,jobcom->imult);
  */
--   ne = ne - *itotc + linkat;
-+   ne = ne - *itotc + link_at;
-    if (ne % 2 == *imult % 2) return(1);
+-   ne = ne - jobcom->itotc + linkat;
++   ne = ne - jobcom->itotc + link_at;
+    if (ne % 2 == jobcom->imult % 2) return(1);
     return(0);
  }
diff --git a/biology/molden/pkg-plist b/biology/molden/pkg-plist
index a3cc3029413a..16e660df4a88 100644
--- a/biology/molden/pkg-plist
+++ b/biology/molden/pkg-plist
@@ -1,56 +1,61 @@
+bin/ambfor
+bin/gmolden
 bin/molden
-bin/moldenogl
-%%PORTDOCS%%%%DOCSDIR%%/figures.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/manual.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/manual.txt.Z
-%%PORTDOCS%%share/molden/test/adf.molf
-%%PORTDOCS%%share/molden/test/ampac.arc
-%%PORTDOCS%%share/molden/test/ampac.test
-%%PORTDOCS%%share/molden/test/bucky.xyz
-%%PORTDOCS%%share/molden/test/chemx.test
-%%PORTDOCS%%share/molden/test/complex2.out
-%%PORTDOCS%%share/molden/test/cpeptide.gro
-%%PORTDOCS%%share/molden/test/esp.test
-%%PORTDOCS%%share/molden/test/esp.txt
-%%PORTDOCS%%share/molden/test/esp.xyz
-%%PORTDOCS%%share/molden/test/fragment
-%%PORTDOCS%%share/molden/test/gamess_uk.freq
-%%PORTDOCS%%share/molden/test/gamess_uk.input
-%%PORTDOCS%%share/molden/test/gamess_uk.test1
-%%PORTDOCS%%share/molden/test/gamess_uk.test2
-%%PORTDOCS%%share/molden/test/gamess_us.h2o_631g_opt.out
-%%PORTDOCS%%share/molden/test/gamess_us.irc
-%%PORTDOCS%%share/molden/test/gamess_us_uhf_opt
-%%PORTDOCS%%share/molden/test/gaussian.freq
-%%PORTDOCS%%share/molden/test/gaussian.input
-%%PORTDOCS%%share/molden/test/gaussian.test
-%%PORTDOCS%%share/molden/test/jaguar.cube
-%%PORTDOCS%%share/molden/test/molden.ogl
-%%PORTDOCS%%share/molden/test/mopac.freq
-%%PORTDOCS%%share/molden/test/mopac.test
-%%PORTDOCS%%share/molden/test/pdb.test
-%%PORTDOCS%%share/molden/test/qchem.test
-%%PORTDOCS%%share/molden/test/reacpth.xyz
-%%PORTDOCS%%share/molden/test/shelx.ins
-%%PORTDOCS%%share/molden/test/surface.molf
-%%PORTDOCS%%share/molden/test/test.fdat
-%%PORTDOCS%%share/molden/test/test.mol2
-%%PORTDOCS%%share/molden/test/test_homo.cube
-%%PORTDOCS%%share/molden/test/tinker_charmm.xyz
-%%PORTDOCS%%share/molden/test/tinker_mm3.xyz
-%%PORTDOCS%%share/molden/test/uracil.fdat
-%%PORTDOCS%%share/molden/test/uracil_gauss.out
-%%PORTDOCS%%share/molden/test/vamp.test
-%%PORTDOCS%%share/molden/utils/INFO
-%%PORTDOCS%%share/molden/utils/ch_backspace
-%%PORTDOCS%%share/molden/utils/ch_mxcon
-%%PORTDOCS%%share/molden/utils/ch_par
-%%PORTDOCS%%share/molden/utils/colors
-%%PORTDOCS%%share/molden/utils/ircextract.awk
-%%PORTDOCS%%share/molden/utils/molden
-%%PORTDOCS%%share/molden/utils/multi_vrml.csh
-%%PORTDOCS%%share/molden/utils/multi_vrml_orbitals.csh
-%%PORTDOCS%%@dirrm share/molden/test
-%%PORTDOCS%%@dirrm share/molden/utils
-%%PORTDOCS%%@dirrm share/molden
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
+bin/surf
+share/doc/molden/figures.ps.Z
+share/doc/molden/manual.ps.Z
+share/doc/molden/manual.txt.Z
+share/molden/test/adf.molf
+share/molden/test/ambfor_amber.xyz
+share/molden/test/ambfor_gaff.xyz
+share/molden/test/ampac.arc
+share/molden/test/ampac.test
+share/molden/test/bucky.xyz
+share/molden/test/chemx.test
+share/molden/test/complex2.out
+share/molden/test/cpeptide.gro
+share/molden/test/esp.test
+share/molden/test/esp.txt
+share/molden/test/esp.xyz
+share/molden/test/fragment
+share/molden/test/gamess_uk.freq
+share/molden/test/gamess_uk.input
+share/molden/test/gamess_uk.test1
+share/molden/test/gamess_uk.test2
+share/molden/test/gamess_us.h2o_631g_opt.out
+share/molden/test/gamess_us.irc
+share/molden/test/gamess_us_uhf_opt
+share/molden/test/gaussian.freq
+share/molden/test/gaussian.input
+share/molden/test/gaussian.test
+share/molden/test/jaguar.cube
+share/molden/test/molden.ogl
+share/molden/test/mopac.freq
+share/molden/test/mopac.test
+share/molden/test/pdb.test
+share/molden/test/pdb.test.omap
+share/molden/test/qchem.test
+share/molden/test/reacpth.xyz
+share/molden/test/shelx.ins
+share/molden/test/surface.molf
+share/molden/test/test.fdat
+share/molden/test/test.mol2
+share/molden/test/test_homo.cube
+share/molden/test/tinker_charmm.xyz
+share/molden/test/tinker_mm3.xyz
+share/molden/test/uracil.fdat
+share/molden/test/uracil_gauss.out
+share/molden/test/vamp.test
+share/molden/utils/INFO
+share/molden/utils/ch_backspace
+share/molden/utils/ch_mxcon
+share/molden/utils/ch_par
+share/molden/utils/colors
+share/molden/utils/ircextract.awk
+share/molden/utils/molden
+share/molden/utils/multi_vrml.csh
+share/molden/utils/multi_vrml_orbitals.csh
+@dirrm share/molden/utils
+@dirrm share/molden/test
+@dirrm share/molden
+@dirrm share/doc/molden