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

# obgrep(1)

an advanced molecular search program using SMARTS

## NAME

**obgrep** – an advanced molecular search program using SMARTS

## SYNOPSIS

**obgrep** \[*OPTIONS*\] *SMARTS-pattern* *filename*

## DESCRIPTION

The **obgrep** tool can be used to search for molecules inside multi-molecule database files (e.g., SMILES, SDF, etc.) or across multiple files.

## OPTIONS

If only a filename is given, **obgrep** will attempt to guess the file type from the filename extension.

- **-c**

  Print the number of matches

- **-f**

  Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the *SMARTS-pattern*

- **-i** *format*

  Specifies input and output format, see [obabel(1)](/obabel/1.md) for available formats

- **-n**

  Only print the name of the molecules

- **-t** *#*

  Print a molecule only if the pattern occurs # times inside the molecule

- **-v**

  Invert the matching, print non-matching molecules

## EXAMPLES

Note that in all examples, the SMARTS pattern is enclosed in single quotes '...' to ensure it is not changed by the shell.

Print all the molecules with a methylamine group:

```
obgrep 'CN' database.smi
```

Print all the molecules without a methylamine group:

```
obgrep -v 'CN' database.smi
```

Print the number of molecules without a methylamine group:

```
obgrep -v -c 'CN' database.smi
```

Print methylamine (if it exists in the file):

```
obgrep -f 'CN' database.smi
```

Print methylamine and/or methanol (if they exist):

```
obgrep -f 'C[N,O]' database.smi
```

Print all molecules with aromatic carbon in all SMILES files in the directory (i.e., \*.smi)

```
obgrep 'c' *.smi
```

## SEE ALSO

[obabel(1)](/obabel/1.md), [obfit(1)](/obfit/1.md), [obrotate(1)](/obrotate/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) 2001-2007 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.