GNU bug report logs - #58261
[PATCH 00/11] Add rdkit.

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From: David Elsing <david.elsing <at> posteo.net>
To: Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at>, 58261 <at> debbugs.gnu.org
Subject: [bug#58261] [PATCH 07/11] gnu: Add freesasa.
Date: Fri, 07 Oct 2022 15:12:08 +0000

Liliana Marie Prikler <liliana.prikler <at> ist.tugraz.at> writes:

> Am Montag, dem 03.10.2022 um 00:19 +0000 schrieb David Elsing:
>> * gnu/packages/chemistry.scm (freesasa): New variable.
>> ---
>>  gnu/packages/chemistry.scm | 81
>> ++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 81 insertions(+)
>> 
>> 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)
>>    #:use-module (gnu packages algebra)
>>    #:use-module (gnu packages autotools)
>>    #:use-module (gnu packages backup)
>> +  #:use-module (gnu packages bison)
>>    #:use-module (gnu packages boost)
>>    #:use-module (gnu packages check)
>>    #:use-module (gnu packages compression)
>>    #:use-module (gnu packages cpp)
>>    #:use-module (gnu packages documentation)
>> +  #:use-module (gnu packages flex)
>>    #:use-module (gnu packages fontutils)
>>    #:use-module (gnu packages gl)
>>    #:use-module (gnu packages graphviz)
>> @@ -54,6 +56,7 @@ (define-module (gnu packages chemistry)
>>    #:use-module (gnu packages serialization)
>>    #:use-module (gnu packages sphinx)
>>    #:use-module (gnu packages stb)
>> +  #:use-module (gnu packages web)
>>    #:use-module (gnu packages xml)
>>    #:use-module (guix build-system cmake)
>>    #:use-module (guix build-system copy)
>> @@ -688,3 +691,81 @@ (define-public gemmi
>>  @item crystallographic symmetry.
>>  @end enumerate")
>>      (license license:mpl2.0)))
>> +
>> +(define-public freesasa
>> +  (package
>> +    (name "freesasa")
>> +    (version "2.1.2")
>> +    (source (origin
>> +              (method git-fetch)
>> +              (uri (git-reference
>> +                    (url "https://github.com/mittinatten/freesasa")
>> +                    (commit version)))
>> +              (file-name (git-file-name name version))
>> +              (sha256
>> +               (base32
>> +               
>> "07wdnahf3g355ryaiqvfxd5f4rl54wv8jwxcbn0nia89fqysbv0f"))
>> +              (modules '((guix build utils)))
>> +              (snippet
>> +               '(begin
>> +                  ;; Remove C files generated by Flex and Bison
>> +                  (for-each delete-file
>> +                            '("src/parser.c" "src/parser.h"
>> +                              "src/lexer.c" "src/lexer.h"))
>> +                  #t))))
>> +    (build-system gnu-build-system)
>> +    (inputs
>> +     (list gemmi json-c libxml2))
>> +    (native-inputs
>> +     (list bison flex check autoconf automake pkg-config doxygen
>> perl libtool))
>> +    (outputs '("out" "doc"))
>> +    (arguments
>> +     (list
>> +      #:configure-flags
>> +      #~(list "--enable-check"
>> +              "--enable-parser-generator"
>> +              "CXXFLAGS=-std=c++17"
>> +              "--enable-doxygen")
>> +      #:phases
>> +      #~(modify-phases %standard-phases
>> +          (add-after 'unpack 'remove-libc++-linking
>> +            (lambda _
>> +              (substitute* "src/Makefile.am"
>> +                (("-lc\\+\\+") ""))
>> +              #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?
>> +          (add-after 'unpack 'build-shared-library
>> +            (lambda _
>> +              (substitute* "src/Makefile.am"
>> +                (("lib_LIBRARIES") "lib_LTLIBRARIES")
>> +                (("libfreesasa\\.a") "libfreesasa.la")
>> +                (("freesasa_LDADD \\+= libfreesasa\\.la" prev)
>> +                 (string-append prev "\nlibfreesasa_la_LIBADD"
>> +                                " = -ljson-c ${libxml2_LIBS}\n"))
>> +                (("_a_SOURCES") "_la_SOURCES"))
>> +              (substitute* "configure.ac"
>> +                (("AC_PROG_INSTALL" inst)
>> +                 (string-append "AM_PROG_LIBTOOL\n" inst)))
>> +              (substitute* "tests/Makefile.am"
>> +                (("libfreesasa\\.a") "libfreesasa.la"))
>> +              #t))
>> +          (add-before 'build 'build-lexer-and-parser
>> +            (lambda _
>> +              (with-directory-excursion "src"
>> +                (invoke "make" "lexer.h")
>> +                (invoke "make" "parser.h"))
>> +              #t))
> You can do this in one make.
>> +          (add-after 'install 'install-doc
>> +            (lambda _
>> +              (copy-recursively
>> +               "doc/html"
>> +               (string-append #$output:doc "/share/doc/" #$name "-"
>> #$version))
>> +              #t)))))
>> +    (home-page "https://freesasa.github.io/")
>> +    (synopsis "Library for calculating the solvent accessible
>> surface area
>> +(SASA) of molecules")
> "Calculate the..."
>> +    (description "FreeSASA is a command line tool and C-library for
>> +calculating solvent accessible surface areas (SASA).  By default Lee
>> &
> 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.  Both can
>> +be parameterized to arbitrary precision, and for high resolution
>> versions of
>> +the algorithms, the calculations give identical results.")
>> +    (license license:expat)))
>
> Cheers

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