Update to 3.6.

PR:		19091
Submitted by:	MAINTAINER

6 files changed, 145 insertions, 114 deletions

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index 0912935e7531..2b919394af2d 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -6,58 +6,67 @@
 #
 
 PORTNAME=	molden
-PORTVERSION=	3.4
+PORTVERSION=	3.6
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.caos.kun.nl/pub/molgraph/molden/
-MASTER_SITES+=	ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/
-DISTFILES=	${PORTNAME}${PORTVERSION}.tar.Z ${PORTNAME}${PORTVERSION}-freebsd
-EXTRACT_ONLY=	molden3.4.tar.Z
+DISTNAME=	${PORTNAME}${PORTVERSION}
+EXTRACT_SUFX=	.tar.Z
+EXTRACT_ONLY=	${PORTNAME}${PORTVERSION}.tar.Z
+
+PATCH_SITES=	ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/
+PATCHFILES=	${PORTNAME}${PORTVERSION}-freebsd
 
 MAINTAINER=	rmiya@cc.hirosaki-u.ac.jp
 
-RESTRICTED=     "free for academic, non profit usage; do not re-distribute source and executable"
+RESTRICTED=	"free for academic, non profit usage;"
+NO_CDROM=	"Do not re-distribute source and executable."
+NO_PACKAGE=	"Though the source codes is accessible, the author is hoping for distribution in an original binary form."
+MAKEFILE=	${WRKSRC}/makefile
 
-WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
+.include <bsd.port.pre.mk>
 
-.if ${MACHINE_ARCH} == "alpha"
-DONOTUSE_ORIGINALBINARY=	yes
-.endif
+post-configure:
+	@${ECHO_MSG} "********************"
+	@${ECHO_MSG} "**  If you want to use a larger MOLDEN,"
+	@${ECHO_MSG} "**  edit change_parameter, change_parameter.sh"
+	@${ECHO_MSG} "**  or utils/*, and run them before building it."
+	@${ECHO_MSG} "********************"
 
 pre-build:
-.if defined(DONOTUSE_ORIGINALBINARY)
-	(cd ${WRKSRC}; ${CP} makefile Makefile)
-	(cd ${WRKSRC}; ./change_parameter)
+.if defined(ORIGINALBINARY)
 	@${ECHO_MSG} "********************"
-	@${ECHO_MSG} "**  re-build with customizations"
-	@${ECHO_MSG} "**  maxorb: 256 -> 1024"
-	@${ECHO_MSG} "**  maxatm: 150 -> 300"
+	@${ECHO_MSG} "**  using original binary"
+	@${ECHO_MSG} "********************"
+.elif defined(MYBINARY)
+	@${ECHO_MSG} "********************"
+	@${ECHO_MSG} "**  re-build your own MOLDEN"
 	@${ECHO_MSG} "********************"
 .else
 	@${ECHO_MSG} "********************"
-	@${ECHO_MSG} "**  using original binary"
+	@${ECHO_MSG} "**  set ORIGINALBINARY=yes or MYBINARY=yes"
 	@${ECHO_MSG} "********************"
 .endif
 
 do-build:
-.if defined(DONOTUSE_ORIGINALBINARY)
-	(cd ${WRKSRC};${MAKE})
+.if defined(ORIGINALBINARY)
+	${CP}  ${DISTDIR}/${PORTNAME}${PORTVERSION}-freebsd ${WRKSRC}/molden
+.elif defined(MYBINARY)
+	(cd ${WRKSRC} && ${MAKE})
 .else
-	${CP} ${DISTDIR}/${PORTNAME}${PORTVERSION}-freebsd ${WRKSRC}/molden
-.endif
-
-pre-install:
-	${RM} -rf ${PREFIX}/share/doc/molden
-.if !defined(NOPORTDOCS)
-	${MKDIR} ${PREFIX}/share/doc/molden
-	${MKDIR} ${PREFIX}/share/doc/molden/doc
-	${MKDIR} ${PREFIX}/share/doc/molden/test
+	@${ECHO_MSG} "********************"
+	@${ECHO_MSG} "**  set ORIGINALBINARY=yes or MYBINARY=yes"
+	@${ECHO_MSG} "********************"
 .endif
 
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/molden ${PREFIX}/bin/
 .if !defined(NOPORTDOCS)
-	${INSTALL_DATA} ${WRKSRC}/doc/* ${PREFIX}/share/doc/molden/doc
-	${INSTALL_DATA} ${WRKSRC}/test/* ${PREFIX}/share/doc/molden/test
+	${MKDIR} ${PREFIX}/share/doc/molden
+	${MKDIR} ${PREFIX}/share/molden/test
+	${MKDIR} ${PREFIX}/share/molden/utils
+	${INSTALL_DATA} ${WRKSRC}/doc/* ${PREFIX}/share/doc/molden
+	${INSTALL_DATA} ${WRKSRC}/test/* ${PREFIX}/share/molden/test
+	${INSTALL_DATA} ${WRKSRC}/utils/* ${PREFIX}/share/molden/utils
 .endif
 
-.include <bsd.port.mk>
+.include <bsd.port.post.mk>
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index 389918d465da..b642afeaaae4 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,2 +1,2 @@
-MD5 (molden3.4.tar.Z) = 42a0a001378aac46a84a53c7cbf90500
-MD5 (molden3.4-freebsd) = e31c3ad49d4bf73edf05682faf3e8a3a
+MD5 (molden3.6.tar.Z) = 637c1359c5dbdaeea688084d2bf0f6d0
+MD5 (molden3.6-freebsd) = c27c7e0b7e4ca0dca533ad1c1455f9cb
diff --git a/biology/molden/files/patch-aa b/biology/molden/files/patch-aa
index f0308a8bf6ee..6abea58e5ef3 100644
--- a/biology/molden/files/patch-aa
+++ b/biology/molden/files/patch-aa
@@ -1,63 +1,71 @@
-*** makefile.orig	Fri Dec 20 02:17:40 1996
---- makefile	Wed Apr 30 23:24:13 1997
+*** makefile.orig	Mon Jan 24 23:28:24 2000
+--- makefile	Wed Jun  7 04:25:36 2000
 ***************
-*** 4,11 ****
-  #	of the shaded plots, this can vary over X-servers
-  #       (You can always override it with the command line flag -c0.25)
+*** 12,19 ****
+  #
+  #	Disregard compiler warnings on rdmolf.f
   #
 ! CC = cc
 ! LIBS =  -lX11 -lm
   
   # Ultrix, Dec Alpha, Linux ( and best start for Unix other than below )
-  #CFLAGS = -c -DDOBACK -DHASTIMER 
---- 4,21 ----
-  #	of the shaded plots, this can vary over X-servers
-  #       (You can always override it with the command line flag -c0.25)
+  #
+--- 12,37 ----
+  #
+  #	Disregard compiler warnings on rdmolf.f
   #
 ! #CC = cc
 ! #LIBS =  -lX11 -lm
 ! 
 ! ###
 ! # FreeBSD
-! CC = gcc
-! CFLAGS = -c -O2 -DDOBACK -DHASTIMER -I/usr/X11R6/include
+! #CC = gcc
+! CFLAGS += -c -DDOBACK -DHASTIMER -I/usr/X11R6/include
 ! #FC = f77
-! FFLAGS = -O2 -Nn802 -Nx400
+! .if ${MACHINE_ARCH} == i386
+! FFLAGS += -malign-double
+! CFLAGS += -malign-double
+! .endif
+! .if ${OSVERSION} < 400005
+! FFLAGS += -Nn802 -Nx400
+! .else
+! FFLAGS += -Wno-globals -fno-globals
+! .endif
 ! LIBS =  -L/usr/X11R6/lib -lX11 -lm
 ! LDR = f77
 ! ###
   
   # Ultrix, Dec Alpha, Linux ( and best start for Unix other than below )
-  #CFLAGS = -c -DDOBACK -DHASTIMER 
+  #
 ***************
-*** 20,28 ****
-  #LDR = fort77   
+*** 49,57 ****
+  
   
   # Silicon Graphics
 ! CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-! FFLAGS = 
-! LDR = f77
+! FFLAGS =   
+! LDR = f77 
   
   # AIX
   #
---- 30,38 ----
-  #LDR = fort77   
+--- 67,75 ----
+  
   
   # Silicon Graphics
 ! #CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-! #FFLAGS = 
-! #LDR = f77
+! #FFLAGS =   
+! #LDR = f77 
   
   # AIX
   #
 ***************
-*** 104,109 ****
---- 114,121 ----
-  
-  #If Silicon Graphics Graphics library version needed (You can do without )
-  #SOBJ =	silly.o
+*** 138,143 ****
+--- 156,163 ----
+  # on linux with older Mesa installations try:
+  #LIBSG = -L/usr/X11R6/lib -lglut -lMesaGLU -lMesaGL -lXmu -lXi -lX11 -lm
+  #
 + 
-+ all:	molden
++ all: molden
   
-  molden:	$(OBJS) $(SOBJ) xwin.o 
-  	$(LDR) -o molden $(OBJS) $(SOBJ) xwin.o $(LIBS)
+  molden:	$(OBJS) $(SOBJ) mpdum.o xwin.o 
+  	$(LDR) -o molden $(OBJS) $(SOBJ) mpdum.o xwin.o $(LIBS)
diff --git a/biology/molden/files/patch-ab b/biology/molden/files/patch-ab
index 2e14276a7af4..dc5d187e6a32 100644
--- a/biology/molden/files/patch-ab
+++ b/biology/molden/files/patch-ab
@@ -1,18 +1,18 @@
-*** xwin.c.orig	Mon Nov  9 03:06:06 1998
---- xwin.c	Sat Nov 14 21:07:52 1998
+*** xwin.c.orig	Wed May 31 20:27:01 2000
+--- xwin.c	Wed Jun  7 02:34:50 2000
 ***************
-*** 13,19 ****
-  #include <X11/Xos.h>
+*** 15,21 ****
   #include <X11/keysym.h>
   #include <X11/cursorfont.h>
+  #include <X11/Xatom.h>
 ! #include <malloc.h>
   #endif
   
   #include <stdio.h>
---- 13,19 ----
-  #include <X11/Xos.h>
+--- 15,21 ----
   #include <X11/keysym.h>
   #include <X11/cursorfont.h>
+  #include <X11/Xatom.h>
 ! /* #include <malloc.h> */
   #endif
   
diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr
index 2eabe40f9e9f..4c46dd9c8cb0 100644
--- a/biology/molden/pkg-descr
+++ b/biology/molden/pkg-descr
@@ -1,17 +1,19 @@
-If you want to re-build with your own customization, 
-define `DONOTUSE_ORIGINALBINARY', such as:
-  % make DONOTUSE_ORIGINALBINARY=yes
-
 Visualizing the results of molecular orbital calculations
-  MO program:  gaussian, gamess, mopac
-  display molecule in 3D:  geo-opt, single-point, 
-      nomal mode ... animation
-  density:  contour plot, 3D view
-      electron density, MO coefficient
-
+ 1) MO program:  gaussian, gamess, mopac, etc.
+ 2) display molecule in 3D:  geo-opt, single-point, nomal mode (animation)
+ 3) density:  contour plot or 3D view for electron density and MO coefficient
 Everything what you want about MO calculation can be seen.
 
 WWW: http://www.caos.kun.nl/~schaft/molden/molden.html
 
+You must set the environmental variable ether ORIGINALBINARY=yes or 
+MYBINARY=yes. The latter will be used for building up your own binary, 
+which is specially customized.
+web site, shown above.
+
+Acknowledgement:  Porting to 4.0-CURRENT (__FreeBSD_version == 400005) 
+and later versions have been assisted greatly by Glenn Johnson 
+<gjohnson@nola.srrc.usda.gov>, thanks a lot !
+
 --
 rmiya
diff --git a/biology/molden/pkg-plist b/biology/molden/pkg-plist
index 1d01e32a498e..5f8c465338f1 100644
--- a/biology/molden/pkg-plist
+++ b/biology/molden/pkg-plist
@@ -1,39 +1,51 @@
 bin/molden
-share/doc/molden/doc/figures.ps.Z
-share/doc/molden/doc/manual.ps.Z
-share/doc/molden/doc/manual.txt.Z
-share/doc/molden/test/adf.molf
-share/doc/molden/test/ampac.arc
-share/doc/molden/test/ampac.test
-share/doc/molden/test/bucky.xyz
-share/doc/molden/test/chemx.test
-share/doc/molden/test/complex2.out
-share/doc/molden/test/esp.test
-share/doc/molden/test/esp.txt
-share/doc/molden/test/fragment
-share/doc/molden/test/gamess_uk.freq
-share/doc/molden/test/gamess_uk.input
-share/doc/molden/test/gamess_uk.test1
-share/doc/molden/test/gamess_uk.test2
-share/doc/molden/test/gamess_us.h2o_631g_opt.out
-share/doc/molden/test/gamess_us.irc
-share/doc/molden/test/gamess_us_uhf_opt
-share/doc/molden/test/gaussian.freq
-share/doc/molden/test/gaussian.input
-share/doc/molden/test/gaussian.test
-share/doc/molden/test/mopac.freq
-share/doc/molden/test/mopac.test
-share/doc/molden/test/pdb.test
-share/doc/molden/test/reacpth.xyz
-share/doc/molden/test/shelx.ins
-share/doc/molden/test/surface.molf
-share/doc/molden/test/test.fdat
-share/doc/molden/test/test.mol2
-share/doc/molden/test/tinker_charmm.xyz
-share/doc/molden/test/tinker_mm3.xyz
-share/doc/molden/test/uracil.fdat
-share/doc/molden/test/uracil_gauss.out
-share/doc/molden/test/vamp.test
-@dirrm share/doc/molden/test
-@dirrm share/doc/molden/doc
+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/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/esp.test
+share/molden/test/esp.txt
+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/mopac.freq
+share/molden/test/mopac.test
+share/molden/test/pdb.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/test
+@dirrm share/molden/utils
+@dirrm share/molden
 @dirrm share/doc/molden