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ChemicalToolBoX update.
author Bjoern Gruening <bjoern.gruening@gmail.com>
date Fri, 19 Jul 2013 16:28:47 +0200
parents 47d2bf691908
children 987b62da416d
comparison
equal deleted inserted replaced
14:47d2bf691908 15:b4eaf75cac77
32 #end if 32 #end if
33 33
34 "${method_opts.query_opts.targets}" 34 "${method_opts.query_opts.targets}"
35 #else: 35 #else:
36 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that. 36 ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
37 ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype. 37 ## Furthermore OpenBabel is really picky with file extensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
38 ## A workaround is to create a symlink with a proper file-extension. 38 ## A workaround is to create a symlink with a proper file-extension.
39 #import tempfile 39 #import tempfile
40 #set $temp_file = tempfile.NamedTemporaryFile() 40 #set $temp_file = tempfile.NamedTemporaryFile()
41 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext) 41 #set $temp_link = "%s.%s" % ($temp_file.name, $method_opts.query.ext)
42 $temp_file.close() 42 $temp_file.close()
93 </test> 93 </test>
94 </tests> 94 </tests>
95 <help> 95 <help>
96 96
97 97
98 **What it does** 98 .. class:: infomark
99 99
100 Similarity search of compounds using fingerprint data sets. Depending on the input either chemfp_ of `Open Babel`_ is used. 100 **What this tool does**
101 101
102 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
102 103
103 **References** 104 .. _chemfp: http://chemfp.com/
105 .. _FastSearch: http://openbabel.org/wiki/FastSearch
104 106
105 Please reference the `Open Babel`_ or the chemfp_ project. 107 -----
106 108
107 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33. `DOI:10.1186/1758-2946-3-33`_ 109 .. class:: infomark
108 The Open Babel Package http://openbabel.sourceforge.net/
109 110
111 **Cite**
110 112
111 .. _DOI:10.1186/1758-2946-3-33: http://www.jcheminf.com/content/3/1/33 113 | The chemfp_ project
112 .. _chemfp: http://chemfp.com/ 114 |
113 .. _`Open Babel`: http://openbabel.org/ 115 | N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch and G R Hutchison - `Open Babel: An open chemical toolbox`_
116
117 .. _`Open Babel: An open chemical toolbox`: http://www.jcheminf.com/content/3/1/33
118
114 119
115 </help> 120 </help>
116 </tool> 121 </tool>