From patchwork Fri Oct 7 15:21:48 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 43200 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 8098327BBEA; Fri, 7 Oct 2022 17:15:49 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id DA4FC27BBE9 for ; Fri, 7 Oct 2022 17:15:48 +0100 (BST) Received: from localhost ([::1]:49538 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ogq0p-0000qg-Vn for patchwork@mira.cbaines.net; Fri, 07 Oct 2022 12:15:48 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:57158) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ogpBq-0002dL-IN for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:06 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38117) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ogpBq-0005qx-9Z for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ogpBq-0005p4-5Y for guix-patches@gnu.org; Fri, 07 Oct 2022 11:23:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58261] [PATCH v2 11/13] gnu: Add avalontoolkit. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 07 Oct 2022 15:23:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 58261 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 58261@debbugs.gnu.org Cc: David Elsing Received: via spool by 58261-submit@debbugs.gnu.org id=B58261.166515615722230 (code B ref 58261); Fri, 07 Oct 2022 15:23:06 +0000 Received: (at 58261) by debbugs.gnu.org; 7 Oct 2022 15:22:37 +0000 Received: from localhost ([127.0.0.1]:37178 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogpBN-0005mO-Cj for submit@debbugs.gnu.org; Fri, 07 Oct 2022 11:22:37 -0400 Received: from mout01.posteo.de ([185.67.36.65]:34903) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogpAx-0005jy-1b for 58261@debbugs.gnu.org; Fri, 07 Oct 2022 11:22:12 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id A21CE240029 for <58261@debbugs.gnu.org>; Fri, 7 Oct 2022 17:22:04 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1665156124; bh=v2j+aXjcM887Xx6boUeYaigLN92Up1Ev0/tIWhWAoj0=; h=From:To:Cc:Subject:Date:From; b=XEd5vwtRAEcItEf7NITZ1qsqdvkOosr/g0BXEuRPnnJ+FUHT9lsn7JVx0qEY/0mDg xH8rh7Ge7J9iWtlJ7vpOo6dU47Ia9AuoTr8pSfe0EBttB/lrxj5YMNlWXCIHc0WrSk MVFuB3bNftvLAbDKRcnsnhHwxwXZcUK9/0ykOtTA6MdG7h8eXNjSpdRgt0pKa5vdSZ TOR3H7D3xnhI2GguK2SopI/NQEESGTzwxjCsjs6o+fEWz0REoakBvGQDUD3z0cTTaL u9aueyugM42ijEYMNO7yUJV/Zl53+lE9Et+rp6cSN5GU4K8eASC4yjTF2YUW6TWv9F +p9+1+J3WwABg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4MkX981Pvkz6tpn; Fri, 7 Oct 2022 17:22:04 +0200 (CEST) From: David Elsing Date: Fri, 7 Oct 2022 15:21:48 +0000 Message-Id: <20221007152148.32591-12-david.elsing@posteo.net> In-Reply-To: References: MIME-Version: 1.0 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (avalontoolkit): New variable. --- gnu/packages/chemistry.scm | 93 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 93 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 68d28a52c3..e52dd2f3b6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -928,3 +928,96 @@ (define-public yaehmop (description "@code{YAeHMOP} contains a program and library for performing extended Hückel calculations.") (license license:bsd-2))) + +(define-public avalontoolkit + (package + (name "avalontoolkit") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/avalontoolkit/" + "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_" + version ".source.tar")) + (sha256 + (base32 + "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv")) + (modules '((guix build utils) (ice-9 ftw))) + (snippet + #~(begin + (chdir "..") + (delete-file-recursively "SourceDistribution/java"))))) + (build-system gnu-build-system) + (arguments + (list + ;; There are no tests + #:tests? #f + #:phases + #~(let ((programs '("canonizer" "matchtest" "smi2mol" "struchk"))) + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'remove-free + (lambda _ + ;; Remove incorrect free of getenv result (patch also in rdkit) + (substitute* "common/reaccsio.c" + (("MyFree.*tempdir.*") "")))) + (replace 'build + (lambda _ + (chdir "common") + (let* ((parts + (list + "aacheck" "casutils" "denormal" "depictutil" + "didepict" "fixcharges" "forio" "geometry" "graph" + "hashcode" "layout" "local" "patclean" "pattern" + "perceive" "reaccsio" "rtutils" "set" "shortcut" + "sketch" "ssmatch" "stereo" "symbol_lists" + "symboltable" "utilities")) + (objects (map (lambda (name) (string-append name ".o")) + parts))) + (for-each + (lambda (name) + (display (string-append "Compiling " name ".c\n")) + (invoke "gcc" "-c" "-fPIC" "-O2" + (string-append name ".c") + "-o" (string-append name ".o"))) + parts) + (display "Building shared library\n") + (apply invoke "gcc" "-fPIC" "-shared" "-lm" + "-o" "libavalontoolkit.so" + "canonizer.c" "smi2mol.c" "struchk.c" objects) + (for-each + (lambda (program) + (display (string-append "Building " program "\n")) + (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2" + (string-append "-Wl,-rpath=" #$output "/lib") + "-DMAIN" (string-append program ".c") "-o" program)) + programs)))) + (replace 'install + (lambda _ + ;; Executables + (for-each + (lambda (program) + (install-file program (string-append #$output "/bin"))) + programs) + (for-each + (lambda (name) + (symlink (string-append #$output "/bin/smi2mol") + (string-append #$output "/bin/" name))) + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) + ;; Library + (install-file "libavalontoolkit.so" (string-append #$output "/lib")) + (for-each + (lambda (file) + (install-file file (string-append #$output + "/include/avalontoolkit"))) + (find-files "." "\\.h$")) + (install-file "../license.txt" + (string-append #$output "/share/doc/" + #$name "-" #$version "/")))))))) + (home-page "https://sourceforge.net/projects/avalontoolkit/") + (synopsis "Tools for SMILES and MOL files and for structure fingerprinting") + (description "This package contains a library and programs for +canonicalization of SMILES and MOL files, molecular structure fingerprinting +and rendering molecules.") + (license license:bsd-3)))