@@ -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)
@@ -684,3 +687,86 @@ (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"))))))
+ (outputs '("out" "doc"))
+ (build-system gnu-build-system)
+ (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\\+\\+") ""))))
+ (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 ${libxml2_LIBS}\n"))
+ (("_a_SOURCES") "_la_SOURCES"))
+ (substitute* "configure.ac"
+ (("AC_PROG_INSTALL" inst)
+ (string-append "AM_PROG_LIBTOOL\n" inst)))
+ (substitute* "tests/Makefile.am"
+ (("libfreesasa\\.a") "libfreesasa.la"))))
+ (add-before 'build 'build-lexer-and-parser
+ (lambda _
+ (with-directory-excursion "src"
+ (invoke "make" "lexer.h" "parser.h"))))
+ (add-after 'install 'install-doc
+ (lambda _
+ (copy-recursively
+ "doc/html"
+ (string-append #$output:doc "/share/doc/" #$name "-" #$version)))))))
+ (native-inputs
+ (list autoconf
+ automake
+ bison
+ check
+ doxygen
+ fast-float
+ flex
+ libtool
+ pegtl
+ perl
+ pkg-config))
+ (inputs
+ (list gemmi json-c libxml2))
+ (home-page "https://freesasa.github.io/")
+ (synopsis "Calculate the solvent accessible surface area (SASA) of
+molecules")
+ ;; TODO: @abbr
+ (description "FreeSASA is a command line tool and C-library for
+calculating solvent accessible surface areas. 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)))