gnu: msmtp: Update to 1.8.10.

[jackhill/guix/guix.git] / gnu / packages / chemistry.scm

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 3bdd406..0540dfc 100644 (file)
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -3,6 +3,8 @@
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
 ;;; Copyright © 2018 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>

+;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
+;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>

 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;


@@ -28,15 +30,20 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages boost)

+  #:use-module (gnu packages check)

   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages gl)

+  #:use-module (gnu packages graphviz)

   #:use-module (gnu packages gv)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages gv)
   #:use-module (gnu packages maths)

+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages perl)

   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)

+  #:use-module (gnu packages sphinx)

   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)


@@ -147,7 +154,7 @@ powerful plugin architecture.")
      `(#:python ,python-2
        ;; No test suite
        #:tests? #f))
      `(#:python ,python-2
        ;; No test suite
        #:tests? #f))

-    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
+    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder.html")

     (synopsis "Analysis of dynamical domains in proteins")
     (description "DomainFinder is an interactive program for the determination
 and characterization of dynamical domains in proteins.  It can infer dynamical
     (synopsis "Analysis of dynamical domains in proteins")
     (description "DomainFinder is an interactive program for the determination
 and characterization of dynamical domains in proteins.  It can infer dynamical


@@ -276,21 +283,21 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
                ;; and Guix contains currently no free molecular viewer that
                ;; could be substituted.
                (("PREFERENCES\\['acroread_path'\\] = ''")
                ;; and Guix contains currently no free molecular viewer that
                ;; could be substituted.
                (("PREFERENCES\\['acroread_path'\\] = ''")

-                (format "PREFERENCES['acroread_path'] = '~a'"
+                (format #f "PREFERENCES['acroread_path'] = '~a'"

                         (which "gv")))
                (("PREFERENCES\\['ncdump_path'\\] = ''")
                         (which "gv")))
                (("PREFERENCES\\['ncdump_path'\\] = ''")

-                (format "PREFERENCES['ncdump_path'] = '~a'"
+                (format #f "PREFERENCES['ncdump_path'] = '~a'"

                         (which "ncdump")))
                (("PREFERENCES\\['ncgen_path'\\] = ''")
                         (which "ncdump")))
                (("PREFERENCES\\['ncgen_path'\\] = ''")

-                (format "PREFERENCES['ncgen_path'] = '~a'"
+                (format #f "PREFERENCES['ncgen_path'] = '~a'"

                         (which "ncgen3")))
                (("PREFERENCES\\['task_manager_path'\\] = ''")
                         (which "ncgen3")))
                (("PREFERENCES\\['task_manager_path'\\] = ''")

-                (format "PREFERENCES['task_manager_path'] = '~a'"
+                (format #f "PREFERENCES['task_manager_path'] = '~a'"

                         (which "task_manager")))
                ;; Show documentation as PDF
                (("PREFERENCES\\['documentation_style'\\] = 'html'")
                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))
                         (which "task_manager")))
                ;; Show documentation as PDF
                (("PREFERENCES\\['documentation_style'\\] = 'html'")
                 "PREFERENCES['documentation_style'] = 'pdf'") ))))))

-    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
+    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN.html")

     (synopsis "Analysis software for Molecular Dynamics trajectories")
     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 simulations.  It is especially designed for the computation and decomposition of
     (synopsis "Analysis software for Molecular Dynamics trajectories")
     (description "nMOLDYN is an interactive analysis program for Molecular Dynamics
 simulations.  It is especially designed for the computation and decomposition of


@@ -299,6 +306,126 @@ is currently not actively maintained and works only with Python 2 and
 NumPy < 1.9.")
     (license license:cecill)))
 
 NumPy < 1.9.")
     (license license:cecill)))
 

+(define-public tng
+  (package
+    (name "tng")
+    (version "1.8.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/gromacs/tng.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("zlib" ,zlib)))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'remove-bundled-zlib
+           (lambda _
+             (delete-file-recursively "external")
+             #t))
+         (replace 'check
+           (lambda _
+             (invoke "../build/bin/tests/tng_testing")
+             #t)))))
+    (home-page "https://github.com/gromacs/tng")
+    (synopsis "Trajectory Next Generation binary format manipulation library")
+    (description "TRAJNG (Trajectory next generation) is a program library for
+handling molecular dynamics (MD) trajectories.  It can store coordinates, and
+optionally velocities and the H-matrix.  Coordinates and velocities are
+stored with user-specified precision.")
+    (license license:bsd-3)))
+
+(define-public gromacs
+  (package
+    (name "gromacs")
+    (version "2020.2")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
+                                  version ".tar.gz"))
+              (sha256
+               (base32
+                "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
+              ;; Our version of tinyxml2 is far newer than the bundled one and
+              ;; require fixing `testutils' code. See patch header for more info
+              (patches (search-patches "gromacs-tinyxml2.patch"))))
+    (build-system cmake-build-system)
+    (arguments
+     `(#:configure-flags
+       (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
+             ;; Unbundling
+             "-DGMX_USE_LMFIT=EXTERNAL"
+             "-DGMX_BUILD_OWN_FFTW=off"
+             "-DGMX_EXTERNAL_BLAS=on"
+             "-DGMX_EXTERNAL_LAPACK=on"
+             "-DGMX_EXTERNAL_TNG=on"
+             "-DGMX_EXTERNAL_ZLIB=on"
+             "-DGMX_EXTERNAL_TINYXML2=on"
+             (string-append "-DTinyXML2_DIR="
+                            (assoc-ref %build-inputs "tinyxml2"))
+             ;; Workaround for cmake/FindSphinx.cmake version parsing that does
+             ;; not understand the guix-wrapped `sphinx-build --version' answer
+             (string-append "-DSPHINX_EXECUTABLE_VERSION="
+                            ,(package-version python-sphinx)))
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fixes
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Still bundled: part of gromacs, source behind registration
+             ;; but free software anyways
+             ;;(delete-file-recursively "src/external/vmd_molfile")
+             ;; Still bundled: threads-based OpenMPI-compatible fallback
+             ;; designed to be bundled like that
+             ;;(delete-file-recursively "src/external/thread_mpi")
+             ;; Unbundling
+             (delete-file-recursively "src/external/lmfit")
+             (delete-file-recursively "src/external/clFFT")
+             (delete-file-recursively "src/external/fftpack")
+             (delete-file-recursively "src/external/build-fftw")
+             (delete-file-recursively "src/external/tng_io")
+             (delete-file-recursively "src/external/tinyxml2")
+             (delete-file-recursively "src/external/googletest")
+             (copy-recursively (assoc-ref inputs "googletest-source")
+                               "src/external/googletest")
+             ;; This test warns about the build host hardware, disable
+             (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
+               (("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
+                "void __guix_disabled()"))
+             #t)))))
+    (native-inputs
+     `(("doxygen" ,doxygen)
+       ("googletest-source" ,(package-source googletest))
+       ("graphviz" ,graphviz)
+       ("pkg-config" ,pkg-config)
+       ("python" ,python)
+       ("python-pygments" ,python-pygments)
+       ("python-sphinx" ,python-sphinx)))
+    (inputs
+     `(("fftwf" ,fftwf)
+       ("hwloc" ,hwloc-2 "lib")
+       ("lmfit" ,lmfit)
+       ("openblas" ,openblas)
+       ("perl" ,perl)
+       ("tinyxml2" ,tinyxml2)
+       ("tng" ,tng)))
+    (home-page "http://www.gromacs.org/")
+    (synopsis "Molecular dynamics software package")
+    (description "GROMACS is a versatile package to perform molecular dynamics,
+i.e. simulate the Newtonian equations of motion for systems with hundreds to
+millions of particles.  It is primarily designed for biochemical molecules like
+proteins, lipids and nucleic acids that have a lot of complicated bonded
+interactions, but since GROMACS is extremely fast at calculating the nonbonded
+interactions (that usually dominate simulations) many groups are also using it
+for research on non-biological systems, e.g. polymers.  GROMACS supports all the
+usual algorithms you expect from a modern molecular dynamics implementation.")
+    (license license:lgpl2.1+)))
+

 (define-public openbabel
   (package
     (name "openbabel")
 (define-public openbabel
   (package
     (name "openbabel")