| Message ID | 254dc3bf26b76bf9fbd2da24c0f11eb6f34bb953.1664725832.git.david.elsing@posteo.net |
|---|---|
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| Headers | show |
| Series | Add rdkit. | expand |
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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
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
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 --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)))