Subject: [PATCH v2 07/13] gnu: Add freesasa.

From: David Elsing <[email-masked]>
Date: Fri, 7 Oct 2022 15:21:44 +0000

* gnu/packages/chemistry.scm (freesasa): New variable.
---
 gnu/packages/chemistry.scm | 86 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 86 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index d8f1608a3a..681e026186 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)
@@ -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)))
-- 
2.37.0