1 files changed, 119 insertions, 0 deletions
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
new file mode 100644
index 0000000000..ed883072b4
--- /dev/null
+++ b/gnu/packages/chemistry.scm
@@ -0,0 +1,119 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages chemistry)
+  #:use-module (guix packages)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix download)
+  #:use-module (gnu packages gv)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages python)
+  #:use-module (guix build-system python))
+
+(define-public domainfinder
+  (package
+    (name "domainfinder")
+    (version "2.0.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/khinsen/"
+                           "domainfinder/downloads/DomainFinder-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-mmtk" ,python2-mmtk)))
+    (arguments
+     `(#:python ,python-2
+       ;; No test suite
+       #:tests? #f))
+    (home-page "http://dirac.cnrs-orleans.fr/DomainFinder")
+    (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
+domains by comparing two protein structures, or from normal mode analysis on a
+single structure.  The software is currently not actively maintained and works
+only with Python 2 and NumPy < 1.9.")
+    (license license:cecill-c)))
+
+(define with-numpy-1.8
+  (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
+
+(define-public nmoldyn
+  (package
+    (name "nmoldyn")
+    (version "3.0.11")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/khinsen/"
+                           "nmoldyn3/downloads/nMOLDYN-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib))
+       ("python-scientific", python2-scientific)
+       ("netcdf", netcdf)
+       ("gv" ,gv)))
+    (propagated-inputs
+     `(("python-mmtk" ,python2-mmtk)))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f  ; No test suite
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'create-linux2-directory
+           (lambda _
+             (mkdir-p "nMOLDYN/linux2")))
+         (add-before 'build 'change-PDF-viewer
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "nMOLDYN/Preferences.py"
+               ;; Set the paths for external executables, substituting
+               ;; gv for acroread.
+               ;; There is also vmd_path, but VMD is not free software
+               ;; and Guix contains currently no free molecular viewer that
+               ;; could be substituted.
+               (("PREFERENCES\\['acroread_path'\\] = ''")
+                (format "PREFERENCES['acroread_path'] = '~a'"
+                        (which "gv")))
+               (("PREFERENCES\\['ncdump_path'\\] = ''")
+                (format "PREFERENCES['ncdump_path'] = '~a'"
+                        (which "ncdump")))
+               (("PREFERENCES\\['ncgen_path'\\] = ''")
+                (format "PREFERENCES['ncgen_path'] = '~a'"
+                        (which "ncgen3")))
+               (("PREFERENCES\\['task_manager_path'\\] = ''")
+                (format "PREFERENCES['task_manager_path'] = '~a'"
+                        (which "task_manager")))
+               ;; Show documentation as PDF
+               (("PREFERENCES\\['documentation_style'\\] = 'html'")
+                "PREFERENCES['documentation_style'] = 'pdf'") ))))))
+    (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/")
+    (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
+neutron scattering spectra, but also computes other quantities.  The software
+is currently not actively maintained and works only with Python 2 and
+NumPy < 1.9.")
+    (license license:cecill)))