"obabel" vs. "babel" Open Babel Commands

Cheminformatics Tutorials - Herong's Tutorial Examples

∟"obabel" vs. "babel" Open Babel Commands

This section provides a quick summary of differences between on Open Babel 'obabel' new command and 'babel' old command.

What Is "babel" Command? - "babel" was the command to invoke the Open Babel molecule data conversion tool used in old Open Babel releases.

"babel" command had been gradually replaced by the "babel" command in Open Babel 2.x releases. Newer releases are now support only the "obabel" command.

The new "obabel" command uses slightly different command line syntaxes than the old "babel" command. I you have used the "babel" command from older releases before, here is a summary of their differences taken from the "man babel" help text from Open Babel 2.3.1:

herong$ man babel

NAME
  babel, obabel -- a converter for chemistry and molecular modeling data files

SYNOPSIS
  babel, [-H help-options]
  babel, [OPTIONS] [-i input-type] infile [-o output-type] outfile

  obabel [-H help-options]
  obabel [OPTIONS] [-i input-type | -:"SMILES-string"] infile [-o output-type]
    -O outfile

DESCRIPTION
  babel, is a cross-platform program designed to interconvert between many file
  formats used in molecular modeling and computational chemistry and related areas.

  obabel and babel, are slightly different. The first is closer to the normal
  Unix convention for command line programs and more flexible when the user needs
  to specify parameter values on options. With babel this only works when the
  option is the last on the line; with obabel no such restriction applies. It
  further has a shortcut for entering SMILES strings, which can be used in place
  of an input file.

  Open Babel is also a complete programmers toolkit for developing chemistry
  software. For more information, se the Open Babel web pages
  <http://openbabel.org/>.

OPTIONS
  If only input and output files are given, Open Babel will guess the file type
  from the filename extension.

  -:"SMILES-string"
  Enter SMILES string and use it in place of an input file. The SMILES string
  should be enclosed in quotation marks. More than one can be used, and a
  molecule title can be included if enclosed in quotes.

  -a options
    Format-specific input options. See -H format-ID for options allowed by
    a particular format

  ....

As you can see, there are two primary differences on the "obabel" command comparing to the "babel" command:

"obabel ... -O output_file" - Output file name must be specified in the "-O" option.
"obabel -:SMILES ..." - SMILES string can be specified as the input data source in the command line in the "-:" option. Note that no space is allowed between the "-:" flag and the SMILES string.

Here is an example of "obabel" command with a SMILES string:

herong$ obabel -:c1ccccc1 -O out.svg

1 molecule converted

Note that you may need to put the "-:..." option inside double quotes to protect special characters used in the SMILES strings as shown in the following example:

herong$ obabel "-:c1cc(C=O)ccc1C(=O)O" -O out.svg

1 molecule converted

Table of Contents

About This Book

SMILES (Simplified Molecular-Input Line-Entry System)

Open Babel: The Open Source Chemistry Toolbox

►Using Open Babel Command: "obabel"

What Is "obabel" Command

"obabel -i ..." - Input Data Format and Source

"obabel -o ... -O" - Output Data Format and Destination

"obabel -... --..." - Generic Conversion Options

"obabel" Command Option Argument Syntax

"obabel ... --gen2D" - Calculated 2D Coordinates

"obabel ... -f # -l #" - Split Large Molecule File

"obabel -h/-d" - Add/Remove Hydrogens in Molecule Data

"obabel --append ..." - Calculate Molecule Properties

"obabel -L formats" - List of File Formats Supported

"obabel -a..." - Extra Options for Input Reading

"obabel -x..." - Extra Options for Output Writing

►"obabel" vs. "babel" Open Babel Commands

Generating SVG Pictures with Open Babel

Substructure Search with Open Babel

Similarity Search with Open Babel

Fingerprint Index for Fastsearch with Open Babel

Stereochemistry with Open Babel

Command Line Tools Provided by Open Babel

RDKit: Open-Source Cheminformatics Software

rdkit.Chem.rdchem - The Core Module

rdkit.Chem.rdmolfiles - Molecular File Module

rdkit.Chem.rdDepictor - Compute 2D Coordinates

rdkit.Chem.Draw - Handle Molecule Images

Molecule Substructure Search with RDKit

rdkit.Chem.rdmolops - Molecule Operations

Daylight Fingerprint Generator in RDKit

Morgan Fingerprint Generator in RDKit

RDKit Performance on Substructure Search

Introduction to Molecular Fingerprints

OCSR (Optical Chemical Structure Recognition)

AlphaFold - Protein Structure Prediction

Resources and Tools

Cheminformatics Related Terminologies

References

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