ports/96444: [NEW PORT] graphics/Raster3D: tools for generating raster images of proteins and molecules

Fri Apr 28 04:10:22 UTC 2006

>Number:         96444
>Category:       ports
>Synopsis:       [NEW PORT] graphics/Raster3D: tools for generating raster images of proteins and molecules
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Fri Apr 28 04:10:18 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator:     Shaun Amott
>Release:        FreeBSD 6.1-PRERELEASE i386
>Organization:
>Environment:

>Description:

This is a port of Raster3D: a set of tools for generating high-quality
raster images of proteins and molecules.

For example:
  http://skuld.bmsc.washington.edu/raster3d/examples/examples.html

This is a very mature program: I'm surprised it hasn't already been
ported.

>How-To-Repeat:

>Fix:

--- Raster3D.shar begins here ---
# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	Raster3D
#	Raster3D/Makefile
#	Raster3D/distinfo
#	Raster3D/pkg-descr
#	Raster3D/files
#	Raster3D/files/patch-Makefile
#	Raster3D/pkg-plist
#
echo c - Raster3D
mkdir -p Raster3D > /dev/null 2>&1
echo x - Raster3D/Makefile
sed 's/^X//' >Raster3D/Makefile << 'END-of-Raster3D/Makefile'
X# New ports collection makefile for:	Raster3D
X# Date Created:				2006-04-28
X# Whom:					Shaun Amott <shaun at inerd.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	Raster3D
XPORTVERSION=	2.7d
XCATEGORIES=	graphics biology
XMASTER_SITES=	http://skuld.bmsc.washington.edu/${PORTNAME:L}/
XDISTNAME=	${PORTNAME}_${PORTVERSION}
X
XMAINTAINER=	shaun at inerd.com
XCOMMENT=	A set of tools for generating raster images of proteins and molecules
X
XBINARIES=	avs2ps balls rastep render ribbon rings3d rods normal3d
X
X.if !defined(WITHOUT_IMAGEMAGICK)
XSCRIPTS=	label3d stereo3d
XPLIST_FILES+=	${SCRIPTS:C/^/bin\//}
X.endif
X
XMANL=		avs2ps.l label3d.l r3d_objects.l rastep.l render.l rods.l  \
X		balls.l normal3d.l r3dtops.l raster3d.l ribbon.l stereo3d.l
X
X.include <bsd.port.pre.mk>
X
Xpost-patch:
X	@cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE} freebsd
X
Xdo-install:
X	cd ${WRKSRC} && ${INSTALL_PROGRAM} ${BINARIES} ${PREFIX}/bin
X.if !defined(WITHOUT_IMAGEMAGICK)
X	cd ${WRKSRC} && ${INSTALL_SCRIPT} ${SCRIPTS} ${PREFIX}/bin
X.endif
X	@${MKDIR} ${DATADIR}/materials
X	cd ${WRKSRC}/materials && ${INSTALL_DATA} * ${DATADIR}/materials
X
X	cd ${WRKSRC}/doc && ${INSTALL_MAN} ${MANL} ${MANLPREFIX}/man/manl
X
Xpost-install:
X.if !defined(NOPORTDOCS)
X	@${MKDIR} ${DOCSDIR}/html
X	cd ${WRKSRC}/doc && ${INSTALL_DATA} R3D_manual.pdf ${DOCSDIR}
X	cd ${WRKSRC}/html && ${INSTALL_DATA} * ${DOCSDIR}/html
X
X	@${MKDIR} ${EXAMPLESDIR}/msms
X	cd ${WRKSRC}/examples && ${INSTALL_DATA} *.* ${EXAMPLESDIR}
X	cd ${WRKSRC}/examples/msms && ${INSTALL_DATA} * ${EXAMPLESDIR}/msms
X.endif
X
X.include <bsd.port.post.mk>
END-of-Raster3D/Makefile
echo x - Raster3D/distinfo
sed 's/^X//' >Raster3D/distinfo << 'END-of-Raster3D/distinfo'
XMD5 (Raster3D_2.7d.tar.gz) = 755445130a4292abf047cd6740b919b2
XSHA256 (Raster3D_2.7d.tar.gz) = 80c2442e38291473b6d66475b7a6511f34868ecfbec7e553b444a0820db50e91
XSIZE (Raster3D_2.7d.tar.gz) = 1724348
END-of-Raster3D/distinfo
echo x - Raster3D/pkg-descr
sed 's/^X//' >Raster3D/pkg-descr << 'END-of-Raster3D/pkg-descr'
XRaster3D is a set of tools for generating high quality raster images of
Xproteins or other molecules.
X
XThe core program renders spheres, triangles, cylinders, and quadric
Xsurfaces with specular highlighting, Phong shading, and shadowing. It
Xuses an efficient software Z-buffer algorithm which is independent of
Xany graphics hardware.
X
XAncillary programs process atomic coordinates from PDB files into
Xrendering descriptions for pictures composed of ribbons, space-filling
Xatoms, bonds, ball+stick, etc.
X
XRaster3D can also be used to render pictures composed in other programs
Xsuch as Molscript in glorious 3D with highlights, shadowing, etc. Output
Xis to pixel image files with 24 bits of color information per pixel.
X
XWWW: http://skuld.bmsc.washington.edu/raster3d/
END-of-Raster3D/pkg-descr
echo c - Raster3D/files
mkdir -p Raster3D/files > /dev/null 2>&1
echo x - Raster3D/files/patch-Makefile
sed 's/^X//' >Raster3D/files/patch-Makefile << 'END-of-Raster3D/files/patch-Makefile'
X--- Makefile.orig	Wed Apr 12 19:46:10 2006
X+++ Makefile	Fri Apr 28 02:48:06 2006
X@@ -156,6 +156,16 @@
X 	@echo FFLAGS = \${CFLAGS}               >> Makefile.incl
X 	@echo RM = /bin/rm -f                 >> Makefile.incl
X 
X+freebsd:	strip-for-g77
X+	@cp Makefile.template Makefile.incl
X+	@echo OS = freebsd                    >> Makefile.incl
X+	@echo CC = ${CC}                      >> Makefile.incl
X+	@echo CFLAGS = ${CFLAGS}              >> Makefile.incl
X+	@echo FC = f77                        >> Makefile.incl
X+	@echo FFLAGS = -g -O -w -malign-double>> Makefile.incl
X+	@echo RM = /bin/rm -f                 >> Makefile.incl
X+	@echo OSDEFS =  -DLINUX -DNETWORKBYTEORDER       >> Makefile.incl
X+	@echo include Makefile.package        >> Makefile.incl
X 
X strip-for-g77: render.f.bak normal3d.f.bak rastep.f.bak
X render.f.bak:
END-of-Raster3D/files/patch-Makefile
echo x - Raster3D/pkg-plist
sed 's/^X//' >Raster3D/pkg-plist << 'END-of-Raster3D/pkg-plist'
Xbin/avs2ps
Xbin/balls
Xbin/rastep
Xbin/render
Xbin/ribbon
Xbin/rings3d
Xbin/rods
Xbin/normal3d
X%%PORTDOCS%%%%DOCSDIR%%/html/README
X%%PORTDOCS%%%%DOCSDIR%%/html/avs2ps.html
X%%PORTDOCS%%%%DOCSDIR%%/html/balls.html
X%%PORTDOCS%%%%DOCSDIR%%/html/index_button.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/label3d.html
X%%PORTDOCS%%%%DOCSDIR%%/html/normal3d.html
X%%PORTDOCS%%%%DOCSDIR%%/html/pdb_anisou.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_animation.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_colorpicker.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_colorpicker.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_colors.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_docbkg.jpg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_docstyle.css
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example1.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example2.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example5.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example6.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example6.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example7.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example8.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_example9.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_examples.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_filters.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_hints.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_icon.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_labels.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_msms.png
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_obj15.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_obj19.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_stereo7.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/r3d_transparent.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3dtops.html
X%%PORTDOCS%%%%DOCSDIR%%/html/r3dtops_tex1.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3dtops_tex2.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/r3dtops_tex3.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/rastep.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rastep_options.gif
X%%PORTDOCS%%%%DOCSDIR%%/html/raster3d.html
X%%PORTDOCS%%%%DOCSDIR%%/html/render.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rgb_black.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/rgb_white.jpeg
X%%PORTDOCS%%%%DOCSDIR%%/html/rgbmap_black.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rgbmap_white.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rgbtext.html
X%%PORTDOCS%%%%DOCSDIR%%/html/ribbon.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rings3d.html
X%%PORTDOCS%%%%DOCSDIR%%/html/rods.html
X%%PORTDOCS%%%%DOCSDIR%%/html/stereo3d.html
X%%PORTDOCS%%%%DOCSDIR%%/R3D_manual.pdf
X%%PORTDOCS%%%%EXAMPLESDIR%%/msms/README
X%%PORTDOCS%%%%EXAMPLESDIR%%/msms/msms2r3d.c
X%%PORTDOCS%%%%EXAMPLESDIR%%/msms/msms_example.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/LT.pdb
X%%PORTDOCS%%%%EXAMPLESDIR%%/README.examples
X%%PORTDOCS%%%%EXAMPLESDIR%%/chaincolours.pdb
X%%PORTDOCS%%%%EXAMPLESDIR%%/clip.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex5.jpeg
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex5_matrix.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex7_header.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex7_helix.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex7_labels.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex7_tex.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/ex7_titles.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example1.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example1.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example2.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example2.sgi
X%%PORTDOCS%%%%EXAMPLESDIR%%/example3.mol
X%%PORTDOCS%%%%EXAMPLESDIR%%/example3.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example3.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example4.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example5.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example5.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example6.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example6.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example7.jpeg
X%%PORTDOCS%%%%EXAMPLESDIR%%/example7.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/example7.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example8.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/example9.script
X%%PORTDOCS%%%%EXAMPLESDIR%%/gal_srf.r3d.gz
X%%PORTDOCS%%%%EXAMPLESDIR%%/header1.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/header2.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/header4.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/header8.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/plane.r3d
X%%PORTDOCS%%%%EXAMPLESDIR%%/sugarG.pdb
X%%PORTDOCS%%%%EXAMPLESDIR%%/sugarcolours.pdb
X%%PORTDOCS%%%%EXAMPLESDIR%%/sugars.pdb
X%%PORTDOCS%%%%EXAMPLESDIR%%/transparent.r3d
X%%DATADIR%%/materials/2-sided.r3d
X%%DATADIR%%/materials/backdrop_1.r3d
X%%DATADIR%%/materials/backdrop_2.r3d
X%%DATADIR%%/materials/backdrop_3.r3d
X%%DATADIR%%/materials/backface.r3d
X%%DATADIR%%/materials/basement.r3d
X%%DATADIR%%/materials/black.r3d
X%%DATADIR%%/materials/blue.r3d
X%%DATADIR%%/materials/bronze.r3d
X%%DATADIR%%/materials/brown.r3d
X%%DATADIR%%/materials/cpk.colours
X%%DATADIR%%/materials/cyan.r3d
X%%DATADIR%%/materials/darkblue.r3d
X%%DATADIR%%/materials/darkgreen.r3d
X%%DATADIR%%/materials/darkgrey.r3d
X%%DATADIR%%/materials/darkred.r3d
X%%DATADIR%%/materials/dna.colours
X%%DATADIR%%/materials/end_material.r3d
X%%DATADIR%%/materials/floor.r3d
X%%DATADIR%%/materials/fog.r3d
X%%DATADIR%%/materials/forestgreen.r3d
X%%DATADIR%%/materials/gold.r3d
X%%DATADIR%%/materials/green.r3d
X%%DATADIR%%/materials/grey.r3d
X%%DATADIR%%/materials/lightblue.r3d
X%%DATADIR%%/materials/lightgreen.r3d
X%%DATADIR%%/materials/lightgrey.r3d
X%%DATADIR%%/materials/lightorange.r3d
X%%DATADIR%%/materials/lightyellow.r3d
X%%DATADIR%%/materials/lilac.r3d
X%%DATADIR%%/materials/matte.r3d
X%%DATADIR%%/materials/moccasin.r3d
X%%DATADIR%%/materials/mycolors.pdb
X%%DATADIR%%/materials/orange.r3d
X%%DATADIR%%/materials/orchid.r3d
X%%DATADIR%%/materials/pearl.r3d
X%%DATADIR%%/materials/pink.r3d
X%%DATADIR%%/materials/purple.r3d
X%%DATADIR%%/materials/red.r3d
X%%DATADIR%%/materials/residue.colours
X%%DATADIR%%/materials/shapely.colours
X%%DATADIR%%/materials/silver.r3d
X%%DATADIR%%/materials/translucent.r3d
X%%DATADIR%%/materials/translucent_30.r3d
X%%DATADIR%%/materials/translucent_60.r3d
X%%DATADIR%%/materials/translucent_90.r3d
X%%DATADIR%%/materials/transparent.r3d
X%%DATADIR%%/materials/transparent0.r3d
X%%DATADIR%%/materials/transparent1.r3d
X%%DATADIR%%/materials/white.r3d
X%%DATADIR%%/materials/yellow.r3d
X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/msms
X%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
X%%PORTDOCS%%@dirrm %%DOCSDIR%%/html
X%%PORTDOCS%%@dirrm %%DOCSDIR%%
X at dirrm %%DATADIR%%/materials
X at dirrm %%DATADIR%%
END-of-Raster3D/pkg-plist
exit
--- Raster3D.shar ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted: