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1 | ;;; GNU Guix --- Functional package management for GNU |
2 | ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net> | |
3 | ;;; | |
4 | ;;; This file is part of GNU Guix. | |
5 | ;;; | |
6 | ;;; GNU Guix is free software; you can redistribute it and/or modify it | |
7 | ;;; under the terms of the GNU General Public License as published by | |
8 | ;;; the Free Software Foundation; either version 3 of the License, or (at | |
9 | ;;; your option) any later version. | |
10 | ;;; | |
11 | ;;; GNU Guix is distributed in the hope that it will be useful, but | |
12 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of | |
13 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
14 | ;;; GNU General Public License for more details. | |
15 | ;;; | |
16 | ;;; You should have received a copy of the GNU General Public License | |
17 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. | |
18 | ||
19 | (define-module (gnu packages chemistry) | |
20 | #:use-module (guix packages) | |
21 | #:use-module ((guix licenses) #:prefix license:) | |
22 | #:use-module (guix download) | |
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23 | #:use-module (gnu packages gv) |
24 | #:use-module (gnu packages maths) | |
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25 | #:use-module (gnu packages python) |
26 | #:use-module (guix build-system python)) | |
27 | ||
28 | (define-public domainfinder | |
29 | (package | |
30 | (name "domainfinder") | |
31 | (version "2.0.5") | |
32 | (source | |
33 | (origin | |
34 | (method url-fetch) | |
35 | (uri (string-append "https://bitbucket.org/khinsen/" | |
36 | "domainfinder/downloads/DomainFinder-" | |
37 | version ".tar.gz")) | |
38 | (sha256 | |
39 | (base32 | |
40 | "1z26lsyf7xwnzwjvimmbla7ckipx6p734w7y0jk2a2fzci8fkdcr")))) | |
41 | (build-system python-build-system) | |
42 | (inputs | |
43 | `(("python-mmtk" ,python2-mmtk))) | |
44 | (arguments | |
45 | `(#:python ,python-2 | |
46 | ;; No test suite | |
47 | #:tests? #f)) | |
48 | (home-page "http://dirac.cnrs-orleans.fr/DomainFinder") | |
49 | (synopsis "Analysis of dynamical domains in proteins") | |
50 | (description "DomainFinder is an interactive program for the determination | |
51 | and characterization of dynamical domains in proteins. It can infer dynamical | |
52 | domains by comparing two protein structures, or from normal mode analysis on a | |
53 | single structure. The software is currently not actively maintained and works | |
54 | only with Python 2 and NumPy < 1.9.") | |
55 | (license license:cecill-c))) | |
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56 | |
57 | (define with-numpy-1.8 | |
58 | (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8)))) | |
59 | ||
60 | (define-public nmoldyn | |
61 | (package | |
62 | (name "nmoldyn") | |
63 | (version "3.0.11") | |
64 | (source | |
65 | (origin | |
66 | (method url-fetch) | |
67 | (uri (string-append "https://bitbucket.org/khinsen/" | |
68 | "nmoldyn3/downloads/nMOLDYN-" | |
69 | version ".tar.gz")) | |
70 | (sha256 | |
71 | (base32 | |
72 | "1mvmz3lkr217kdrd8cvdr1d82y58wp1403c9rnd943mijgq8xb5a")))) | |
73 | (build-system python-build-system) | |
74 | (inputs | |
75 | `(("python-matplotlib" ,(with-numpy-1.8 python2-matplotlib)) | |
76 | ("python-scientific", python2-scientific) | |
77 | ("netcdf", netcdf) | |
78 | ("gv" ,gv))) | |
79 | (propagated-inputs | |
80 | `(("python-mmtk" ,python2-mmtk))) | |
81 | (arguments | |
82 | `(#:python ,python-2 | |
83 | #:tests? #f ; No test suite | |
84 | #:phases | |
85 | (modify-phases %standard-phases | |
86 | (add-before 'build 'create-linux2-directory | |
87 | (lambda _ | |
88 | (mkdir-p "nMOLDYN/linux2"))) | |
89 | (add-before 'build 'change-PDF-viewer | |
90 | (lambda* (#:key inputs #:allow-other-keys) | |
91 | (substitute* "nMOLDYN/Preferences.py" | |
92 | ;; Set the paths for external executables, substituting | |
93 | ;; gv for acroread. | |
94 | ;; There is also vmd_path, but VMD is not free software | |
95 | ;; and Guix contains currently no free molecular viewer that | |
96 | ;; could be substituted. | |
97 | (("PREFERENCES\\['acroread_path'\\] = ''") | |
98 | (format "PREFERENCES['acroread_path'] = '~a'" | |
99 | (which "gv"))) | |
100 | (("PREFERENCES\\['ncdump_path'\\] = ''") | |
101 | (format "PREFERENCES['ncdump_path'] = '~a'" | |
102 | (which "ncdump"))) | |
103 | (("PREFERENCES\\['ncgen_path'\\] = ''") | |
104 | (format "PREFERENCES['ncgen_path'] = '~a'" | |
105 | (which "ncgen3"))) | |
106 | (("PREFERENCES\\['task_manager_path'\\] = ''") | |
107 | (format "PREFERENCES['task_manager_path'] = '~a'" | |
108 | (which "task_manager"))) | |
109 | ;; Show documentation as PDF | |
110 | (("PREFERENCES\\['documentation_style'\\] = 'html'") | |
111 | "PREFERENCES['documentation_style'] = 'pdf'") )))))) | |
112 | (home-page "http://dirac.cnrs-orleans.fr/nMOLDYN/") | |
113 | (synopsis "Analysis software for Molecular Dynamics trajectories") | |
114 | (description "nMOLDYN is an interactive analysis program for Molecular Dynamics | |
115 | simulations. It is especially designed for the computation and decomposition of | |
116 | neutron scattering spectra, but also computes other quantities. The software | |
117 | is currently not actively maintained and works only with Python 2 and | |
118 | NumPy < 1.9.") | |
119 | (license license:cecill))) |