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

NAME

4     obrotate — batch-rotate dihedral angles matching SMARTS patterns
5

SYNOPSIS

7     obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle
8

DESCRIPTION

10     The obrotate program rotates the torsional (dihedral) angle of a speci‐
11     fied bond in molecules to that defined by the user. In other words, it
12     does the same as a user setting an angle in a molecular modelling pack‐
13     age, but much faster and in batch mode (i.e. across multiple molecules in
14     a file).
15
16     The four atom IDs required are indexes into the SMARTS pattern, which
17     starts at atom 0 (zero). The angle supplied is in degrees. The two atoms
18     used to set the dihedral angle <atom1> and <atom4> do not need to be con‐
19     nected to the atoms of the bond <atom2> and <atom3> in any way.
20
21     The order of the atoms matters -- the portion of the molecule attached to
22     <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and &
23     <atom4> moves.
24

EXAMPLES

26     Let's say that you want to define the conformation of a large number of
27     molecules with a pyridyl scaffold and substituted with an aliphatic chain
28     at the 3-position, for example for docking or 3D-QSAR purposes.
29
30     To set the value of the first dihedral angle to 90 degrees:
31           obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
32
33     Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C
34     and atoms 5 and 8 define the particular dihedral angle to rotate.
35
36     Since the atoms to define the dihedral do not need to be directly con‐
37     nected, the nitrogen in the pyridine can be used:
38           obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90
39
40     Keep the pyridyl ring fixed and moves the aliphatic chain:
41           obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
42
43     Keep the aliphatic chain fixed and move the pyridyl ring:
44           obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
45

SEE ALSO

47     babel(1), obchiral(1), obfit(1), obgrep(1), obprop(1), obrotate(1).
48
49     The web pages for Open Babel can be found at: <http://openbabel.source‐
50     forge.net/>
51
52     A guide for constructing SMARTS patterns can be found at:
53     <http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html>
54

AUTHORS

56     The obgrep program was contributed by Fabien Fontaine
57
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.sourceforge.net/wiki/THANKS>
62

64     Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
65     Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and other
66     contributors.
67
68      This program is free software; you can redistribute it and/or modify it
69     under the terms of the GNU General Public License as published by the
70     Free Software Foundation version 2 of the License.
71
72      This program is distributed in the hope that it will be useful, but
73     WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
74     ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
75     License for more details.
76
77Open Babel 2.1                   April 7, 2007                  Open Babel 2.1
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