[67811] trunk/dports/science
jmr at macports.org
jmr at macports.org
Tue May 18 13:48:27 PDT 2010
Revision: 67811
http://trac.macports.org/changeset/67811
Author: jmr at macports.org
Date: 2010-05-18 13:48:25 -0700 (Tue, 18 May 2010)
Log Message:
-----------
New port: molmol, molecular graphics display program (#21835)
Added Paths:
-----------
trunk/dports/science/molmol/
trunk/dports/science/molmol/Portfile
trunk/dports/science/molmol/files/
trunk/dports/science/molmol/files/molmol-build.diff
Added: trunk/dports/science/molmol/Portfile
===================================================================
--- trunk/dports/science/molmol/Portfile (rev 0)
+++ trunk/dports/science/molmol/Portfile 2010-05-18 20:48:25 UTC (rev 67811)
@@ -0,0 +1,51 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem 1.0
+
+name molmol
+version 2k.2.0
+categories science
+maintainers bromo.med.uc.edu:howarth
+description Molecular graphics display program
+long_description MOLMOL is a molecular graphics program for displaying, analyzing, \
+ and manipulating the three-dimensional structure of biological \
+ macromolecules, with special emphasis on the study of protein \
+ or DNA structures determined by NMR. The program runs on UNIX \
+ and Windows NT/95/98/2000 and is freely available. It does not work \
+ properly with RNA.
+homepage http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
+platforms darwin
+master_sites ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip
+distfiles molmol-${version}-src.tar.gz \
+ molmol-${version}-doc.tar.gz
+checksums molmol-${version}-src.tar.gz md5 e1f4416d8041a67fa08cadb03ed91c7c \
+ sha1 09482a1dea601563ca64e773dc0ec47019e22c63 \
+ rmd160 b1de89953631dd9b11928751d7853cb511bf45f0 \
+ molmol-${version}-doc.tar.gz md5 517545b60b0179ab691a679ed29903a7 \
+ sha1 b47551283fa19f57f4d5edcbd52f725055d80b7f \
+ rmd160 08b3e21ab6eb7c9044e59373334181ff91ca8a53
+depends_lib port:openmotif \
+ port:glut \
+ port:glw \
+ port:tiff \
+ port:jpeg \
+ port:libpng
+patchfiles molmol-build.diff
+use_configure no
+use_parallel_build no
+build.target-delete all
+extract.mkdir yes
+post-patch {
+ reinplace "s|@PREFIX@|${prefix}|g" ${worksrcpath}/makedef \
+ ${worksrcpath}/molmol
+}
+destroot {
+ # Install example files not installed by the Makefile
+ file copy ${worksrcpath} \
+ ${destroot}${prefix}/share/${name}
+ ln -s ${prefix}/share/${name}/${name} ${destroot}${prefix}/bin/${name}
+ file mkdir ${destroot}${prefix}/share/doc/${name}
+ ln -s ${prefix}/share/${name}/COPYING ${destroot}${prefix}/share/doc/${name}/COPYING
+ ln -s ${prefix}/share/${name}/man ${destroot}${prefix}/share/doc/${name}/man
+}
Property changes on: trunk/dports/science/molmol/Portfile
___________________________________________________________________
Added: svn:keywords
+ Id
Added: svn:eol-style
+ native
Added: trunk/dports/science/molmol/files/molmol-build.diff
===================================================================
--- trunk/dports/science/molmol/files/molmol-build.diff (rev 0)
+++ trunk/dports/science/molmol/files/molmol-build.diff 2010-05-18 20:48:25 UTC (rev 67811)
@@ -0,0 +1,200 @@
+--- makedef.orig 1969-12-31 16:00:00.000000000 -0800
++++ makedef 2005-05-28 09:44:47.000000000 -0700
+@@ -0,0 +1,60 @@
++ TIFFDIR = @PREFIX@/lib
++ MESADIR =
++ JPEGDIR = @PREFIX@/lib
++
++ PNGDIR = @PREFIX@/lib
++ ZLIBDIR = /usr/lib
++
++# If you configured any of the above three image formats, uncomment
++# the following four lines, and delete the non-relevant parts if
++# necessary, i. e. if you did not configure all three formats.
++#
++ IMGDEF = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT
++ IMGINCL = -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR)
++ IMGLIB = $(TIFFDIR)/libtiff.3.dylib $(JPEGDIR)/libjpeg.dylib \
++ $(PNGDIR)/libpng.dylib $(ZLIBDIR)/libz.dylib
++
++# Some systems do not have the float versions of various math functions,
++# uncomment the following lines if this is the case
++
++ MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log \
++ -Dsinf=sin -Dcosf=cos \
++ -Dfabsf=fabs -DMAXINT=INT_MAX
++
++ # -Dceilf=ceil
++
++CPP = /usr/bin/cpp
++
++MCPPFLAGS = -DMAXINT=INT_MAX -I at PREFIX@/include -bind_at_load -I$(TOP)
++
++CC = gcc
++
++MCFLAGS = -O -bind_at_load -Wall
++
++RANLIB = /usr/bin/ranlib
++
++WAIT = /bin/sleep 2
++
++SHELL = /bin/sh
++
++SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm
++
++SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4
++
++PUDEVDIR = motif tty
++
++PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY
++
++IODEVDIR = motx11 motogl ttyno
++
++IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_MOTIF_OGL -DIO_DEV_TTY_NO
++
++
++MOTIFDEF = -DFUNCPROTO
++
++SYSLIB = -L/usr/lib -L at PREFIX@/lib \
++ -lX11 -lXm -lGLU -lGL /System/Library/Frameworks/OpenGL.framework/Libraries/libGL.dylib @PREFIX@/lib/libGLw.dylib \
++ -lXmu -lXt -lXp -lXpm -lX11 -lXext -lSM -lICE -lm -lc -lmx
++
++TOOLSDIR = $(TOP)/tools
++SGDIR = $(TOP)/sg
+--- molmol.orig 2003-01-20 17:44:58.000000000 -0800
++++ molmol 2005-05-28 09:44:48.000000000 -0700
+@@ -1,9 +1,9 @@
+-#!/bin/ksh
++#!/bin/zsh
+ #
+ # startup script for MOLMOL
+ #
+
+-MOLMOLHOME=/opt/group/MOLMOL
++MOLMOLHOME=@PREFIX@/share/molmol;MOLMOLDEV="Motif/OpenGL"
+ export MOLMOLHOME
+ export MOLMOLDEV
+
+@@ -11,55 +11,8 @@
+ osrel=`uname -r`
+ osmaj=`echo $osrel | awk -F. '{print $1}'`
+ osmin=`echo $osrel | awk -F. '{print $2}'`
+-localdev=
+-glxdev=
+-
+-if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then
+- if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then
+- arch=sgi6
+- localdev=Motif/OpenGL
+- glxdev=Motif/OpenGL
+- elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then
+- arch=sgi5
+- localdev=Motif/OpenGL
+- glxdev=Motif/OpenGL
+- else
+- arch=sgi4
+- localdev=Motif/GL
+- fi
+- MONITOR=72HZ; export MONITOR
+-elif [ $ostype = "AIX" ]; then
+- arch=aix
+- localdev=Motif/OpenGL
+-elif [ $ostype = "HP-UX" ]; then
+- arch=hp
+- localdev=Motif/OpenGL
+- glxdev=Motif/OpenGL
+-elif [ $ostype = "OSF1" ]; then
+- arch=dec
+- localdev=Motif/OpenGL
+-elif [ $ostype = "Linux" ]; then
+- arch=lnx
+- localdev=Motif/OpenGL
+-elif [ $ostype = "SunOS" ]; then
+- if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then
+- arch=sol
+- localdev=Motif/OpenGL
+- else
+- arch=sun
+- fi
+-else
+- arch=unknown
+-fi
+-
+-if [ $ostype = "SunOS" ]; then
+- xdpy=/usr/openwin/bin/xdpyinfo
+-elif [ $ostype = "HP-UX" ]; then
+- xdpy=/usr/contrib/bin/X11/xdpyinfo
+-else
+- xdpy=/usr/bin/X11/xdpyinfo
+-fi
+-
++localdev=Motif/OpenGL
++glxdev=Motif/OpenGL
+ printUsage () {
+ echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files"
+ echo ""
+@@ -209,7 +162,7 @@
+ fi
+
+ if [ "$input" = "-" -o -n "$nograph" ]; then
+- $MOLMOLHOME/molmol.$arch $xopt
++ echo "LineBond solid 1 " >>| $startmacro ; @PREFIX@/share/molmol/src/main/molmol $xopt
+ else
+- $MOLMOLHOME/molmol.$arch $xopt < /dev/null
++ echo "LineBond solid 1 " >>| $startmacro ; @PREFIX@/share/molmol/src/main/molmol $xopt < /dev/null
+ fi
+--- src/iodev/IODev.c.orig 2001-05-27 14:03:30.000000000 -0700
++++ src/iodev/IODev.c 2005-05-28 11:03:09.000000000 -0700
+@@ -44,7 +44,6 @@
+ #endif
+ #ifdef IO_DEV_MOTIF_OGL
+ extern void IOMotifOGLSetDev(void);
+-extern void IOMotifOGLDSetDev(void);
+ #endif
+ #ifdef IO_DEV_MOTIF_XGL
+ extern void IOMotifXGLSetDev(void);
+@@ -76,7 +75,6 @@
+ #endif
+ #ifdef IO_DEV_MOTIF_OGL
+ {"Motif/OpenGL", IOMotifOGLSetDev},
+- {"Motif/OpenGLD", IOMotifOGLDSetDev},
+ #endif
+ #ifdef IO_DEV_MOTIF_XGL
+ {"Motif/XGL", IOMotifXGLSetDev},
+--- src/motogl/MotOGL.c.orig 2000-05-29 09:31:51.000000000 -0700
++++ src/motogl/MotOGL.c 2005-05-28 09:44:50.000000000 -0700
+@@ -31,7 +31,7 @@
+ #include <Xm/XmStrDefs.h>
+
+ #define BOOL MOTIF_BOOL /* hack to avoid naming conflict */
+-#include <X11/GLw/GLwMDrawA.h>
++#include <GL/GLwMDrawA.h>
+ #undef BOOL
+
+ #include <sg.h>
+--- src/os/GFile.c.orig 2001-06-17 11:59:17.000000000 -0700
++++ src/os/GFile.c 2005-05-28 11:04:20.000000000 -0700
+@@ -38,7 +38,6 @@
+ const INT32 GFMagic = 0x3b7a12f9;
+
+ #ifndef __linux__
+-extern char *sys_errlist[];
+ #endif
+ extern int errno;
+
+--- tools/include/values.h.orig 1969-12-31 16:00:00.000000000 -0800
++++ tools/include/values.h 2005-05-28 09:44:52.000000000 -0700
+@@ -0,0 +1,2 @@
++#include <math.h>
++#include <limits.h>
+--- src/data/DataDist.c.org 2009-08-29 14:34:52.000000000 -0400
++++ src/data/DataDist.c 2009-08-29 14:36:50.000000000 -0400
+@@ -89,7 +89,7 @@
+ {
+ TabEntryInter *entryP = p;
+
+- return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size;
++ return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size;
+ }
+
+ static int
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