From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id QI42KFpOQGM9owAAbAwnHQ (envelope-from ) for ; Fri, 07 Oct 2022 18:05:46 +0200 Received: from aspmx1.migadu.com ([2001:41d0:8:6d80::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id QG9QKFpOQGNwGgEAauVa8A (envelope-from ) for ; Fri, 07 Oct 2022 18:05:46 +0200 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 350D09C92 for ; Fri, 7 Oct 2022 18:05:46 +0200 (CEST) Received: from localhost ([::1]:35886 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1ogpr7-0001i2-4B for larch@yhetil.org; Fri, 07 Oct 2022 12:05:45 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41456) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1ogp26-0000eV-TL for guix-patches@gnu.org; Fri, 07 Oct 2022 11:13:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:38041) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1ogp26-0004Ba-Iu for guix-patches@gnu.org; Fri, 07 Oct 2022 11:13:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1ogp26-0005U7-EC for guix-patches@gnu.org; Fri, 07 Oct 2022 11:13:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#58261] [PATCH 07/11] gnu: Add freesasa. References: Resent-From: David Elsing Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 07 Oct 2022 15:13:02 +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: Liliana Marie Prikler , 58261@debbugs.gnu.org Received: via spool by 58261-submit@debbugs.gnu.org id=B58261.166515555521023 (code B ref 58261); Fri, 07 Oct 2022 15:13:02 +0000 Received: (at 58261) by debbugs.gnu.org; 7 Oct 2022 15:12:35 +0000 Received: from localhost ([127.0.0.1]:37112 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogp1b-0005Sr-L6 for submit@debbugs.gnu.org; Fri, 07 Oct 2022 11:12:34 -0400 Received: from mout01.posteo.de ([185.67.36.65]:38003) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ogp1L-0005SO-6N for 58261@debbugs.gnu.org; Fri, 07 Oct 2022 11:12:30 -0400 Received: from submission (posteo.de [185.67.36.169]) by mout01.posteo.de (Postfix) with ESMTPS id A2766240027 for <58261@debbugs.gnu.org>; 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aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=GSsguEzR; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.03 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=posteo.net header.s=2017 header.b=GSsguEzR; dmarc=fail reason="SPF not aligned (strict)" header.from=posteo.net (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 350D09C92 X-Spam-Score: 6.03 X-Migadu-Scanner: scn1.migadu.com X-TUID: 9PgPqHkyBB/h Liliana Marie Prikler writes: > Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing: >> * gnu/packages/chemistry.scm (freesasa): New variable. >> --- >> =C2=A0gnu/packages/chemistry.scm | 81 >> ++++++++++++++++++++++++++++++++++++++ >> =C2=A01 file changed, 81 insertions(+) >>=20 >> diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm >> index f8fd85814f..223a27a20d 100644 >> --- a/gnu/packages/chemistry.scm >> +++ b/gnu/packages/chemistry.scm >> @@ -34,11 +34,13 @@ (define-module (gnu packages chemistry) >> =C2=A0=C2=A0 #:use-module (gnu packages algebra) >> =C2=A0=C2=A0 #:use-module (gnu packages autotools) >> =C2=A0=C2=A0 #:use-module (gnu packages backup) >> +=C2=A0 #:use-module (gnu packages bison) >> =C2=A0=C2=A0 #:use-module (gnu packages boost) >> =C2=A0=C2=A0 #:use-module (gnu packages check) >> =C2=A0=C2=A0 #:use-module (gnu packages compression) >> =C2=A0=C2=A0 #:use-module (gnu packages cpp) >> =C2=A0=C2=A0 #:use-module (gnu packages documentation) >> +=C2=A0 #:use-module (gnu packages flex) >> =C2=A0=C2=A0 #:use-module (gnu packages fontutils) >> =C2=A0=C2=A0 #:use-module (gnu packages gl) >> =C2=A0=C2=A0 #:use-module (gnu packages graphviz) >> @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry) >> =C2=A0=C2=A0 #:use-module (gnu packages serialization) >> =C2=A0=C2=A0 #:use-module (gnu packages sphinx) >> =C2=A0=C2=A0 #:use-module (gnu packages stb) >> +=C2=A0 #:use-module (gnu packages web) >> =C2=A0=C2=A0 #:use-module (gnu packages xml) >> =C2=A0=C2=A0 #:use-module (guix build-system cmake) >> =C2=A0=C2=A0 #:use-module (guix build-system copy) >> @@ -688,3 +691,81 @@ (define-public gemmi >> =C2=A0@item crystallographic symmetry. >> =C2=A0@end enumerate") >> =C2=A0=C2=A0=C2=A0=C2=A0 (license license:mpl2.0))) >> + >> +(define-public freesasa >> +=C2=A0 (package >> +=C2=A0=C2=A0=C2=A0 (name "freesasa") >> +=C2=A0=C2=A0=C2=A0 (version "2.1.2") >> +=C2=A0=C2=A0=C2=A0 (source (origin >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (method git-fetch) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (uri (git-reference >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (url "https://github.com/mitt= inatten/freesasa") >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (commit version))) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (file-name (git-file-name name version)) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (sha256 >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 (base32 >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 >> "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (modules '((guix build utils))) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (snippet >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 '(begin >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 ;; Remove C files generated by Flex and B= ison >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (for-each delete-file >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 '("src/parser.c" "src/parser.h" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 "src/lexer.c" "src/lexer.h")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #t)))) >> +=C2=A0=C2=A0=C2=A0 (build-system gnu-build-system) >> +=C2=A0=C2=A0=C2=A0 (inputs >> +=C2=A0=C2=A0=C2=A0=C2=A0 (list gemmi json-c libxml2)) >> +=C2=A0=C2=A0=C2=A0 (native-inputs >> +=C2=A0=C2=A0=C2=A0=C2=A0 (list bison flex check autoconf automake pkg-c= onfig doxygen >> perl libtool)) >> +=C2=A0=C2=A0=C2=A0 (outputs '("out" "doc")) >> +=C2=A0=C2=A0=C2=A0 (arguments >> +=C2=A0=C2=A0=C2=A0=C2=A0 (list >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #:configure-flags >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #~(list "--enable-check" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 "--enable-parser-generator" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 "CXXFLAGS=3D-std=3Dc++17" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 "--enable-doxygen") >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #:phases >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 #~(modify-phases %standard-phases >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (add-after 'unpa= ck 'remove-libc++-linking >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (lam= bda _ >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (substitute* "src/Makefile.am" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("-lc\\+\\+") "")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 #t)) > Why? If it's because you're building a shared library, do this in the > next phase. This is libc++ from LLVM and the linking against the standard library is automatic anyway, right? >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (add-after 'unpa= ck 'build-shared-library >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (lam= bda _ >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (substitute* "src/Makefile.am" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("lib_LIBRARIES") "lib_LTLIBRARIES") >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("libfreesasa\\.a") "libfreesasa.la") >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("freesasa_LDADD \\+=3D libfreesasa\\.la" prev) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 (string-append prev "\nlibfreesasa_la_LIBADD" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 " =3D -ljson-c ${libxml2_LIBS}\n= ")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("_a_SOURCES") "_la_SOURCES")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (substitute* "configure.ac" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("AC_PROG_INSTALL" inst) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0 (string-append "AM_PROG_LIBTOOL\n" inst))) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (substitute* "tests/Makefile.am" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (("libfreesasa\\.a") "libfreesasa.la")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 #t)) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (add-before 'bui= ld 'build-lexer-and-parser >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (lam= bda _ >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (with-directory-excursion "src" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (invoke "make" "lexer.h") >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 (invoke "make" "parser.h")) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 #t)) > You can do this in one make. >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (add-after 'inst= all 'install-doc >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (lam= bda _ >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 (copy-recursively >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 "doc/html" >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0 (string-append #$output:doc "/share/doc/" #$name "-" >> #$version)) >> +=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 #t))))) >> +=C2=A0=C2=A0=C2=A0 (home-page "https://freesasa.github.io/") >> +=C2=A0=C2=A0=C2=A0 (synopsis "Library for calculating the solvent acces= sible >> surface area >> +(SASA) of molecules") > "Calculate the..." >> +=C2=A0=C2=A0=C2=A0 (description "FreeSASA is a command line tool and C-= library for >> +calculating solvent accessible surface areas (SASA).=C2=A0 By default L= ee >> & > Use @abbr. I get the error "warning: invalid Texinfo markup", do you have an idea why? >> +Richards' algorithm is used, but Shrake & Rupley's is also >> available.=C2=A0 Both can >> +be parameterized to arbitrary precision, and for high resolution >> versions of >> +the algorithms, the calculations give identical results.") >> +=C2=A0=C2=A0=C2=A0 (license license:expat))) > > Cheers