1obspectrophore(1)           User's Reference Manual          obspectrophore(1)
2

NAME

4     obspectrophore — SPECTROPHORE calculator
5

SYNOPSIS

7     obspectrophore [options] -i input_file
8
9     obspectrophore [-u | -h]
10

DESCRIPTION

12     obspectrophore can be used to generate Spectrophores, which are one-
13     dimensional descriptors generated from the property fields surrounding
14     the molecules.  This technology allows the accurate description of mole‐
15     cules in terms of their surface properties or fields. Comparison of mole‐
16     cules property fields provides a robust structure-independent method of
17     aligning actives from different chemical classes. When applied to mole‐
18     cules such as ligands and drugs, Spectrophores can be used as powerful
19     molecular descriptors in the fields of chemoinformatics, virtual screen‐
20     ing, and QSAR modeling.
21

OPTIONS

23     -i file
24           Specifies the molecular input file from which Spectrophores are to
25           be calculated. The filetype is automatically detected from the file
26           extension.
27
28     -n value
29           Specifies the kind of normalization that should be performed. Valid
30           values are (without quotes): No (default), ZeroMean, UnitStd and
31           ZeroMeanAndUnitStd.
32
33     -a value
34           Specifies the required accuracy expressed as the angular stepsize.
35           Only the following discrete values are allowed: 1 | 2 | 5 | 10 | 15
36           | 20 (default) | 30 | 36 | 45 | 60
37
38     -s value
39           Specifies the kind of cages that should be used in terms of the
40           underlying pointgroup: P1 or P-1. Valid values are (without
41           quotes): No (default), Unique, Mirror and All.
42
43     -r value
44           Specifies the required resolution expressed as a real positive num‐
45           ber. The default value is 3.0 Angstrom. Negative values or a value
46           equal to 0 generate an error message.
47
48     -u    Display implementation details.
49
50     -h    Display help message.
51

SEE ALSO

53     babel(1).
54
55     The web pages for Open Babel can be found at: <http://openbabel.org/>
56

AUTHORS

58     Open Babel is developed by a cast of many, including currrent maintainers
59     Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
60     have contributed fixes and additions.  For more contributors to Open
61     Babel, see <http://openbabel.org/wiki/THANKS>
62

64     Copyright (C) 2005-2010 by Silicos NV
65
66     This program is free software; you can redistribute it and/or modify it
67     under the terms of the GNU General Public License as published by the
68     Free Software Foundation version 2 of the License.
69
70     The algorithm in this software has been covered by patent WO2009146735.
71     However, Silicos NV and the inventors of the above mentioned patent
72     assure that no patent infringment claims will be issued against individu‐
73     als or institutions that use this software under the GNU General Public
74     License.
75
76     This program is distributed in the hope that it will be useful, but WITH‐
77     OUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
78     FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
79     more details.
80
81Open Babel 2.3                   June 2, 2012                   Open Babel 2.3
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