From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Apr 28 04:10:22 2006 Return-Path: X-Original-To: freebsd-ports-bugs@hub.freebsd.org Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 80B8D16A418 for ; Fri, 28 Apr 2006 04:10:22 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by mx1.FreeBSD.org (Postfix) with ESMTP id 35C2743D53 for ; Fri, 28 Apr 2006 04:10:19 +0000 (GMT) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.13.4/8.13.4) with ESMTP id k3S4AJuU011209 for ; Fri, 28 Apr 2006 04:10:19 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.13.4/8.13.4/Submit) id k3S4AIxw011208; Fri, 28 Apr 2006 04:10:19 GMT (envelope-from gnats) Resent-Date: Fri, 28 Apr 2006 04:10:19 GMT Resent-Message-Id: <200604280410.k3S4AIxw011208@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Shaun Amott Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125]) by hub.freebsd.org (Postfix) with ESMTP id 2D37216A401 for ; Fri, 28 Apr 2006 04:03:47 +0000 (UTC) (envelope-from shaun@inerd.com) Received: from dione.picobyte.net (host-212-158-207-124.bulldogdsl.com [212.158.207.124]) by mx1.FreeBSD.org (Postfix) with SMTP id 11E9C43D5A for ; Fri, 28 Apr 2006 04:03:45 +0000 (GMT) (envelope-from shaun@inerd.com) Received: from charon.picobyte.net (charon.picobyte.net [IPv6:2001:4bd0:201e::fe03]) by dione.picobyte.net (Postfix) with ESMTP for ; Fri, 28 Apr 2006 05:03:43 +0100 (BST) Message-Id: <1146197023.94585@charon.picobyte.net> Date: Fri, 28 Apr 2006 05:03:43 +0100 From: Shaun Amott To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/96444: [NEW PORT] graphics/Raster3D: tools for generating raster images of proteins and molecules X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Shaun Amott List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 28 Apr 2006 04:10:22 -0000 >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 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@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 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 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@dirrm %%DATADIR%%/materials X@dirrm %%DATADIR%% END-of-Raster3D/pkg-plist exit --- Raster3D.shar ends here --- >Release-Note: >Audit-Trail: >Unformatted: