"babel" vs. "obabel" Commands
What are the differences between "babel" and "obabel" commands?
"babel" and "obabel" commands are two commands of the same Open Babel chemical data conversion program with slightly different command line syntaxes.
You can see the syntax differences between "babel" and "obabel" commands by running the "man babel" command:
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 commandline 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:
Here is an example of "obabel" command with a SMILES string:
fyicenter$ 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:
fyicenter$ obabel "-:c1cc(C=O)ccc1C(=O)O" -O out.svg 1 molecule converted
⇒ "babel ... -o svg" - Generating SVG Pictures
⇐ "babel -x..." Command - Extra Output Writing Options
⇑ Understanding "babel" Command Line Syntax
2021-07-19, 1340👍, 0💬
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