Using Open Babel Command: "obabel"

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Using Open Babel Command: "obabel"

This chapter provides introductions and tutorial examples on Open Babel 'obabel' command. Topics include command line syntax; '-i/-o' for input and output formats; '-O' for output file; '-a/-x' for extra options specific for an input/output format.

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

Takeaways:

Open Babel "obabel" command reads and converts molecule data in 184 different types of formats.
"obabel" command requires input options to be specified first as "obabel [-i<input-type>] <infilename> [-o<output-type>] -O<outfilename>...".
"-i ..." and "-o ..." are the most important options to specify data formats for input and output.
"-aA..." and "-xA..." can be used to pass extra options for reading and writing molecule data in a specific format.
"-f #" and "-l #" can be used to extract a chunk of molecules from a large molecule collection.
"-h" or "-d" option can be used to add or remove implicit hydrogen atoms in molecule data.
"--append ..." option can be used to calculate molecule properties and append them in the "title" field of output data.
"babel" command is phased out in Open Babel 3+ releases now.