display molecular orbitals and electron densities in 2D and 3D

Submitted by:	rmiya@cc.hirosaki-u.ac.jp (Ryo MIYAMOTO)

7 files changed, 201 insertions, 0 deletions

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
new file mode 100644
index 0000000..5359f08
--- /dev/null
+++ b/biology/molden/Makefile
@@ -0,0 +1,59 @@
+# New ports collection makefile for:	molden
+# Version required:	3.4
+# Date created:		1998-11-14
+# Whom:			rmiya
+#
+# $Id$
+#
+
+DISTNAME=	molden3.4
+PKGNAME=	molden-3.4
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp.caos.kun.nl/pub/molgraph/molden/
+MASTER_SITES+=	ftp://ftp.caos.kun.nl/pub/molgraph/molden/bin/
+DISTFILES=	molden3.4.tar.Z molden3.4-freebsd
+
+MAINTAINER=	rmiya@cc.hirosaki-u.ac.jp
+
+EXTRACT_ONLY=	molden3.4.tar.Z
+RESTRICTED=     "free for academic, non profit usage; do not re-distribute source and executable"
+
+pre-build:
+.if defined(DONOTUSE_ORIGINALBINARY)
+	(cd ${WRKSRC}; ${CP} makefile Makefile)
+	(cd ${WRKSRC}; ./change_parameter)
+	@echo "********************"
+	@echo "**  re-build with customizations"
+	@echo "**  maxorb: 256 -> 1024"
+	@echo "**  maxatm: 150 -> 300"
+	@echo "********************"
+.else
+	@echo "********************"
+	@echo "**  using original binary"
+	@echo "********************"
+.endif
+
+do-build:
+.if defined(DONOTUSE_ORIGINALBINARY)
+	(cd ${WRKSRC};${MAKE})
+.else
+	${CP} ${DISTDIR}/${DISTNAME}-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
+.endif
+
+do-install:
+	strip  ${WRKSRC}/molden
+	${INSTALL_PROGRAM} ${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
+.endif
+
+.include <bsd.port.mk>
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
new file mode 100644
index 0000000..389918d
--- /dev/null
+++ b/biology/molden/distinfo
@@ -0,0 +1,2 @@
+MD5 (molden3.4.tar.Z) = 42a0a001378aac46a84a53c7cbf90500
+MD5 (molden3.4-freebsd) = e31c3ad49d4bf73edf05682faf3e8a3a
diff --git a/biology/molden/files/patch-aa b/biology/molden/files/patch-aa
new file mode 100644
index 0000000..f0308a8
--- /dev/null
+++ b/biology/molden/files/patch-aa
@@ -0,0 +1,63 @@
+*** makefile.orig	Fri Dec 20 02:17:40 1996
+--- makefile	Wed Apr 30 23:24:13 1997
+***************
+*** 4,11 ****
+  #	of the shaded plots, this can vary over X-servers
+  #       (You can always override it with the command line flag -c0.25)
+  #
+! 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)
+  #
+! #CC = cc
+! #LIBS =  -lX11 -lm
+! 
+! ###
+! # FreeBSD
+! CC = gcc
+! CFLAGS = -c -O2 -DDOBACK -DHASTIMER -I/usr/X11R6/include
+! #FC = f77
+! FFLAGS = -O2 -Nn802 -Nx400
+! 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   
+  
+  # Silicon Graphics
+! CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+! FFLAGS = 
+! LDR = f77
+  
+  # AIX
+  #
+--- 30,38 ----
+  #LDR = fort77   
+  
+  # Silicon Graphics
+! #CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+! #FFLAGS = 
+! #LDR = f77
+  
+  # AIX
+  #
+***************
+*** 104,109 ****
+--- 114,121 ----
+  
+  #If Silicon Graphics Graphics library version needed (You can do without )
+  #SOBJ =	silly.o
++ 
++ all:	molden
+  
+  molden:	$(OBJS) $(SOBJ) xwin.o 
+  	$(LDR) -o molden $(OBJS) $(SOBJ) xwin.o $(LIBS)
diff --git a/biology/molden/files/patch-ab b/biology/molden/files/patch-ab
new file mode 100644
index 0000000..2e14276
--- /dev/null
+++ b/biology/molden/files/patch-ab
@@ -0,0 +1,19 @@
+*** xwin.c.orig	Mon Nov  9 03:06:06 1998
+--- xwin.c	Sat Nov 14 21:07:52 1998
+***************
+*** 13,19 ****
+  #include <X11/Xos.h>
+  #include <X11/keysym.h>
+  #include <X11/cursorfont.h>
+! #include <malloc.h>
+  #endif
+  
+  #include <stdio.h>
+--- 13,19 ----
+  #include <X11/Xos.h>
+  #include <X11/keysym.h>
+  #include <X11/cursorfont.h>
+! /* #include <malloc.h> */
+  #endif
+  
+  #include <stdio.h>
diff --git a/biology/molden/pkg-comment b/biology/molden/pkg-comment
new file mode 100644
index 0000000..5e6bf76
--- /dev/null
+++ b/biology/molden/pkg-comment
@@ -0,0 +1 @@
+display molecular orbitals and electron densities in 2D and 3D
diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr
new file mode 100644
index 0000000..0335dd6
--- /dev/null
+++ b/biology/molden/pkg-descr
@@ -0,0 +1,18 @@
+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
+
+Everything what you want about MO calculation can be seen.
+
+Please check out, for more detail, the following web site.
+  http://www.caos.kun.nl/~schaft/molden/molden.html
+
+--
+rmiya
diff --git a/biology/molden/pkg-plist b/biology/molden/pkg-plist
new file mode 100644
index 0000000..1d01e32
--- /dev/null
+++ b/biology/molden/pkg-plist
@@ -0,0 +1,39 @@
+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
+@dirrm share/doc/molden