diff mbox series

[bug#58261,07/11] gnu: Add freesasa.

Message ID 254dc3bf26b76bf9fbd2da24c0f11eb6f34bb953.1664725832.git.david.elsing@posteo.net
State New
Headers
Series Add rdkit. |

Commit Message

David Elsing Oct. 3, 2022, 12:19 a.m. UTC 
* gnu/packages/chemistry.scm (freesasa): New variable.
---
 gnu/packages/chemistry.scm | 81 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 81 insertions(+)

Comments

Liliana Marie Prikler Oct. 4, 2022, 8:02 a.m. UTC | #1 
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.
> +          (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.
> +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
David Elsing Oct. 7, 2022, 3:12 p.m. UTC | #2 
Liliana Marie Prikler <liliana.prikler@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
Liliana Marie Prikler Oct. 7, 2022, 3:19 p.m. UTC | #3 
Am Freitag, dem 07.10.2022 um 15:12 +0000 schrieb David Elsing:
> Liliana Marie Prikler <liliana.prikler@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?
> > 
Typo'd?  @abbr{SASA, solvent accessible surface areas}
diff mbox series

Patch

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))
+          (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 ${libxml2_LIBS}\n"))
+                (("_a_SOURCES") "_la_SOURCES"))
+              (substitute* "configure.ac"
+                (("AC_PROG_INSTALL" inst)
+                 (string-append "AM_PROG_LIBTOOL\n" inst)))
+              (substitute* "tests/Makefile.am"
+                (("libfreesasa\\.a") "libfreesasa.la"))
+              #t))
+          (add-before 'build 'build-lexer-and-parser
+            (lambda _
+              (with-directory-excursion "src"
+                (invoke "make" "lexer.h")
+                (invoke "make" "parser.h"))
+              #t))
+          (add-after 'install 'install-doc
+            (lambda _
+              (copy-recursively
+               "doc/html"
+               (string-append #$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")
+    (description "FreeSASA is a command line tool and C-library for
+calculating solvent accessible surface areas (SASA).  By default Lee &
+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)))