diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/chemistry.scm | 94 |
1 files changed, 94 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 1242417c57..c13890001f 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -905,3 +905,97 @@ emphasis on quality rather than speed.") Orbital Package} contains a program and library for performing extended Hückel calculations and analyzing the results.") (license license:bsd-2))) + +(define-public avalon-toolkit + (package + (name "avalon-toolkit") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://sourceforge/avalontoolkit/" + "AvalonToolkit_" (substring version 0 3) "/AvalonToolkit_" + version ".source.tar")) + (sha256 + (base32 + "0rnnyy6axs2da7aa4q6l30ldavbk49v6l22llj1adn74h1i67bpv")) + (modules '((guix build utils) (ice-9 ftw))) + (snippet + #~(begin + (delete-file-recursively "../SourceDistribution/java"))))) + (build-system gnu-build-system) + (arguments + (list + ;; There are no intended tests + #:tests? #f + #:phases + #~(let ((programs '("canonizer" "matchtest" "sketch" "smi2mol" "struchk"))) + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ (chdir "common"))) + (delete 'configure) + (add-before 'build 'dont-free-static-memory + (lambda _ + (substitute* "reaccsio.c" + (("MyFree\\(.*tempdir\\)" m) + (string-append "/* freeing memory from getenv is bad */" + "// " m))))) + ;; The makefile has incorrect compiler flags and is missing some + ;; object files, so we build it ourselves. + (replace 'build + (lambda _ + (for-each + (lambda (part) + (format #t "Compiling ~a.c ~~> ~a.o~%" part part) + (invoke #$(cc-for-target) "-c" "-fPIC" "-O2" + (string-append part ".c") + "-o" (string-append part ".o"))) + (list "aacheck" "casutils" "denormal" "depictutil" + "didepict" "fixcharges" "forio" "geometry" + "graph" "hashcode" "layout" "local" "pattern" + "perceive" "reaccsio" "rtutils" "set" "shortcut" + "sketch" "ssmatch" "stereo" "symbol_lists" + "symboltable" "utilities")) + (display "Building libavalontoolkit.so\n") + (apply invoke "gcc" "-fPIC" "-shared" "-lm" + "-o" "libavalontoolkit.so" "canonizer.c" "smi2mol.c" + "struchk.c" "patclean.c" (find-files "." "\\.o$")) + ;; patclean is not built here as there is an undeclared + ;; variable in main(). + (for-each + (lambda (program) + (display (string-append "Building " program "\n")) + (invoke "gcc" "-L." "-lavalontoolkit" "-lm" "-O2" + (string-append "-Wl,-rpath=" #$output "/lib") + "-DMAIN" (string-append program ".c") "-o" program)) + programs))) + (replace 'install + (lambda _ + ;; Executables + (for-each + (lambda (program) + (install-file program (string-append #$output "/bin"))) + programs) + (for-each + (lambda (name) + (symlink (string-append #$output "/bin/smi2mol") + (string-append #$output "/bin/" name))) + '("mol2smi" "rdf2smi" "mol2tbl" "mol2sma" "smi2rdf")) + ;; Library + (install-file "libavalontoolkit.so" + (string-append #$output "/lib")) + (for-each + (lambda (file) + (install-file file (string-append #$output + "/include/avalontoolkit"))) + (find-files "." "\\.h$")) + (install-file "../license.txt" + (string-append #$output "/share/doc/" + #$name "-" #$version "/")))))))) + (home-page "https://sourceforge.net/projects/avalontoolkit/") + (synopsis "Tools for SMILES and MOL files and for structure fingerprinting") + (description "This package contains a library and programs for +canonicalization of SMILES and MOL files, molecular structure fingerprinting +and rendering molecules.") + (license license:bsd-3))) |