From patchwork Sun Mar 30 22:06:57 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: David Elsing X-Patchwork-Id: 41042 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 5C42227BBEA; Sun, 30 Mar 2025 23:09:29 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham 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 8CAE227BBE2 for ; Sun, 30 Mar 2025 23:09:28 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tz0q8-0000mm-1X; Sun, 30 Mar 2025 18:09:12 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tz0q1-0000k2-BW for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1tz0pz-0006cl-Lb for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:05 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=8Z+iNX0Bh3mpB/zcY2r2R4S1jEmilCkbmUEzk5tqTQU=; b=RaGFWaqYN7597aCz7D9gLsHnBxKwbW+YRmr2kLo60HJ/Pp4QvXd6Fi+90/GQwuZks0jWbiNhxF47JdzSSSkb56rKbdKdMmP2bpsDgOn7N3Q0ZfXaTgX8sob5Cxv9W2mzVIeyX8K+IW3tPdj1FdMOkPTzGpQJ74oX5iawitkoE05q+MxY7VKQAKq25PD1MfzKPJnchdROmtrtTmmefOHN3lwdTbziPvbWzOKk6JuKx4iQ/sAlG817KjZpkrBoj4dVnmA3KsqCV2gPyQX3KC4m99DdbPJA/74OWGT6I3XOWu6iwjr9Ow3SZBBhlO7o9/FhvEsvzbCEdCXaozqispOSgA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tz0pz-0001AQ-GL for guix-patches@gnu.org; Sun, 30 Mar 2025 18:09:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77394] [PATCH 4/5] gnu: Add pubchem-align3d. Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 30 Mar 2025 22:09:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77394 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77394@debbugs.gnu.org Cc: David Elsing Received: via spool by 77394-submit@debbugs.gnu.org id=B77394.17433725114349 (code B ref 77394); Sun, 30 Mar 2025 22:09:03 +0000 Received: (at 77394) by debbugs.gnu.org; 30 Mar 2025 22:08:31 +0000 Received: from localhost ([127.0.0.1]:38360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tz0pS-00017y-JQ for submit@debbugs.gnu.org; Sun, 30 Mar 2025 18:08:30 -0400 Received: from mout02.posteo.de ([185.67.36.66]:49423) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tz0pI-00016L-Gi for 77394@debbugs.gnu.org; Sun, 30 Mar 2025 18:08:22 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout02.posteo.de (Postfix) with ESMTPS id A8003240101 for <77394@debbugs.gnu.org>; Mon, 31 Mar 2025 00:08:14 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1743372494; bh=AIE23fd5hlRIOPxB3yqKxZgYbiLCFi7Z23XyEhZUinY=; h=From:To:Cc:Subject:Date:Message-ID:MIME-Version: Content-Transfer-Encoding:From; b=LPZ/kkFc0wYiSOg18IxmK/Mt3JwMTlGyCLf9clPuPn4rmsKYYOtI4ffxR1yn4x7Xc jqHov4XUS97TgTxe0W3vi4Kk4ARwcb07KZDqGVCQ/dp8iP3h018K07pOfCFjUvy5aA 2GLWPuOGfEl0zxWFHZHbTF9k7mlH3lSpmDB/9Md/LaV2l0vhL2Z5tzU82f6i5m0NOK GlxCW6Pxktb6OI0663VkvqoHmIHyB/ryzuc/oElEYHud2kE2GnPN5G6SLRhOJ0JP+R IX8CwOtsFJfpvdBfAB8Gr5TPYxoB/Syt5PuoRrCUi9HqOsiwClHQOT/d9/U6DfWPmU +aIHIn+rIhv3A== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4ZQpL56F7qz6v0J; Mon, 31 Mar 2025 00:08:13 +0200 (CEST) From: David Elsing Date: Sun, 30 Mar 2025 22:06:57 +0000 Message-ID: <20250330220745.25337-4-david.elsing@posteo.net> In-Reply-To: <20250330220421.24480-1-david.elsing@posteo.net> References: <20250330220421.24480-1-david.elsing@posteo.net> 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/chemistry.scm (pubchem-align3d): New variable. --- gnu/packages/chemistry.scm | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 36227916b6..c1e0586534 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -1066,6 +1066,52 @@ (define-public ringdecomposerlib other ring topology descriptions.") (license license:bsd-3))) +(define-public pubchem-align3d + (let ((commit "daefab3dd0c90ca56da9d3d5e375fe4d651e6be3") + (revision "0")) + (package + (name "pubchem-align3d") + (version (git-version "0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ncbi/pubchem-align3d") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1nj1zz5nvn5h3dyj66zi11mmvmzpq3b8y51fld9bkxnsmk17h05m")))) + (build-system gnu-build-system) + (arguments + (list + #:tests? #f ; circular dependency with rdkit + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda _ + (invoke "g++" + "-o" "libpubchem-align3d.so" + "-O2" "-g" "-fPIC" "-shared" + "shape_functions1.cpp" "shape_functions2.cpp" + "shape_neighbor.cpp"))) + (replace 'install + (lambda _ + (for-each + (lambda (file) + (install-file + file + (string-append #$output "/include/pubchem-align3d"))) + (find-files "." "\\.hpp")) + (install-file "libpubchem-align3d.so" + (string-append #$output "/lib"))))))) + (home-page "https://github.com/ncbi/pubchem-align3d") + (synopsis "C++ library for aligning small molecules") + (description "This is a generic C++ library that can be used to rapidly +align two small molecules in 3D space, with shape - and optionally color - +Tanimoto scoring.") + (license license:public-domain)))) + (define-public rdkit (package (name "rdkit")