---
name: "obrotate"
section: "1"
platform: "linux"
package: "openbabel"
version: "3.2.1-1"
release: "Arch Linux 2026-11-01"
platforms: ["linux"]
url: "https://new.carta.tech/obrotate"
---

# obrotate(1)

batch-rotate dihedral angles matching SMARTS patterns

## NAME

**obrotate** – batch-rotate dihedral angles matching SMARTS patterns

## SYNOPSIS

**obrotate** *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 pattern, 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
```

## SEE ALSO

[obabel(1)](/obabel/1.md), [obchiral(1)](/obchiral/1.md), [obfit(1)](/obfit/1.md), [obgrep(1)](/obgrep/1.md), [obprop(1)](/obprop/1.md).

The web pages for Open Babel can be found at: \<**https://openbabel.org/**\>

A guide for constructing SMARTS patterns can be found at: \<**https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html**\>

## AUTHORS

The obgrep program was contributed by Fabien Fontaine

Open Babel is developed by a cast of many, including current maintainers Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who have contributed fixes and additions. For more contributors to Open Babel, see \<**https://openbabel.org/docs/Introduction/thanks.html**\>

## 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.