From owner-svn-ports-head@freebsd.org Mon Sep 10 05:53:48 2018 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id B70751080077; Mon, 10 Sep 2018 05:53:48 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 527D270C8B; Mon, 10 Sep 2018 05:53:48 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 46E6524546; Mon, 10 Sep 2018 05:53:48 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w8A5rms8014953; Mon, 10 Sep 2018 05:53:48 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w8A5rkoD014943; Mon, 10 Sep 2018 05:53:46 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201809100553.w8A5rkoD014943@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 10 Sep 2018 05:53:46 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r479360 - in head: . science science/msms science/msms/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head: . science science/msms science/msms/files X-SVN-Commit-Revision: 479360 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 10 Sep 2018 05:53:49 -0000 Author: yuri Date: Mon Sep 10 05:53:46 2018 New Revision: 479360 URL: https://svnweb.freebsd.org/changeset/ports/479360 Log: New port: science/msms: Program to efficiently compute molecular surfaces Added: head/science/msms/ head/science/msms/Makefile (contents, props changed) head/science/msms/distinfo-amd64 (contents, props changed) head/science/msms/distinfo-i386 (contents, props changed) head/science/msms/files/ head/science/msms/files/extract-license.awk (contents, props changed) head/science/msms/pkg-descr (contents, props changed) Modified: head/LEGAL head/science/Makefile Modified: head/LEGAL ============================================================================== --- head/LEGAL Mon Sep 10 05:36:10 2018 (r479359) +++ head/LEGAL Mon Sep 10 05:53:46 2018 (r479360) @@ -242,3 +242,4 @@ atom-*.tgz science/atom Redistribution in any form i charm-uiuc-* net/charm No commercial use: commercial use requires a commercial license namd-* science/namd No commercial use: commercial use requires a commercial license vmd-* science/vmd No commercial use: commercial use requires a commercial license +msms-* science/msms No commercial use, only for use by individuals in scientific research Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Mon Sep 10 05:36:10 2018 (r479359) +++ head/science/Makefile Mon Sep 10 05:53:46 2018 (r479360) @@ -137,6 +137,7 @@ SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc + SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += ncs Added: head/science/msms/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/msms/Makefile Mon Sep 10 05:53:46 2018 (r479360) @@ -0,0 +1,41 @@ +# $FreeBSD$ + +PORTNAME= msms +DISTVERSIONPREFIX= v +DISTVERSION= 2.6.1 +CATEGORIES= science +MASTER_SITES= http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL${DISTVERSION}/ +DISTNAME= ${PORTNAME}_${ARCH_MSMS_DIST}Linux2_${DISTVERSION} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Program to efficiently compute molecular surfaces + +LICENSE= MSMS_LICENSE +LICENSE_NAME= MSMS License +LICENSE_FILE= ${WRKSRC}/license.txt +LICENSE_PERMS= no-auto-accept no-dist-mirror no-pkg-mirror # No redistribution is allowed. + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= Binaries available only for ${ONLY_FOR_ARCHS}. + +RESTRICTED= No commercial use, only for use by individuals + +NO_WRKSUBDIR= yes +NO_BUILD= yes + +ARCH_MSMS_DIST= ${ARCH:S/amd64/i86_64/:S/i386/i86/} +ARCH_MSMS_FILE= ${ARCH:S/amd64/x86_64/:S/i386/i86/} + +DISTINFO_FILE= ${MASTERDIR}/distinfo-${ARCH} + +PLIST_FILES= bin/${PORTNAME} \ + man/man1/${PORTNAME}.1.gz + +post-extract: + @${AWK} -f ${FILESDIR}/extract-license.awk < ${WRKSRC}/README > ${LICENSE_FILE} + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}.${ARCH_MSMS_FILE}Linux2.${DISTVERSION}${ARCH:S/amd64/.staticgcc/:S/${ARCH}//} ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 + +.include Added: head/science/msms/distinfo-amd64 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/msms/distinfo-amd64 Mon Sep 10 05:53:46 2018 (r479360) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536557816 +SHA256 (msms_i86_64Linux2_2.6.1.tar.gz) = 5f0ca50360b5938e74c538e0399d582abc4a40ef4cf410e66f31a1f91e6e3e1f +SIZE (msms_i86_64Linux2_2.6.1.tar.gz) = 593147 Added: head/science/msms/distinfo-i386 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/msms/distinfo-i386 Mon Sep 10 05:53:46 2018 (r479360) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536557847 +SHA256 (msms_i86Linux2_2.6.1.tar.gz) = ab4f9e60df6fe18a5ac05550bf074b287792638a818a047697ead049d8737caf +SIZE (msms_i86Linux2_2.6.1.tar.gz) = 112762 Added: head/science/msms/files/extract-license.awk ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/msms/files/extract-license.awk Mon Sep 10 05:53:46 2018 (r479360) @@ -0,0 +1,21 @@ + +BEGIN { in_licence = 0 } + +{ + if (!in_licence && $2 == "LICENSE") { + in_licence = 1 + print prev_line + del_count = 1 + } else if (in_licence) { + if ($1 == "############################################################################") { + del_count = del_count+1 + if (del_count > 2) + in_licence = 0 + } + } + + if (in_licence) + print $0 + + prev_line = $0 +} Added: head/science/msms/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/msms/pkg-descr Mon Sep 10 05:53:46 2018 (r479360) @@ -0,0 +1,8 @@ +MSMS computes, for a given probe radius, the reduced surface of a set of +spheres. An analytical description of the solvent excluded surface is +computed from the reduced surface. Special attention is paid to the proper +handling of self-intersecting parts of the surface called singularities. +This analytical model of the solvent excluded surface can be triangulated +with a user specified vertex density. + +WWW: http://mgltools.scripps.edu/downloads#msms