obrotate (1) - Linux Manuals

obrotate: batch-rotate dihedral angles matching SMARTS patterns

NAME

obrotate - batch-rotate dihedral angles matching SMARTS patterns

SYNOPSIS

'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle

DESCRIPTION

The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modelling package, but much faster and in batch mode (i.e. across multiple molecules in a file).

The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way.

The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves.

EXAMPLES

Let's say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for docking or 3D-QSAR purposes.

To set the value of the first dihedral angle to 90 degrees:

"obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"

Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate.

Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used:

"obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90"

Keep the pyridyl ring fixed and moves the aliphatic chain:

"obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90"

Keep the aliphatic chain fixed and move the pyridyl ring:

"obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90"

AUTHORS

The obgrep program was contributed by An Fabien Fontaine

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

COPYRIGHT

Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison and other contributors.

 This program 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 version 2 of the License.

 This program 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.