"obabel" Command Option Argument Syntax

Cheminformatics Tutorials - Herong's Tutorial Examples

∟"obabel" Command Option Argument Syntax

This section provides tutorial examples to demonstrate different ways to specify Open Babel 'obabel' command option arguments.

Open Babel "obabel" command supports different ways to specify option arguments on the command line. Here are some guidelines on how to use them.

If a "obabel" command option takes an argument, you can specify the argument in two ways:

Argument follows the option flag with spaces to separate them, like "-i sdf". This makes the command line more readable.
Argument follows the option flag immediately with no space, like "-isdf". This makes the command line less readable.

If an option argument contains special characters, you should place it in double quotes or single quotes to protect it. Here are some examples:

herong$ obabel tyrosine.sdf -o smiles -s c(C)c
  -bash: syntax error near unexpected token `('

herong$ # using double quotes to protect ()
herong$ obabel tyrosine.sdf -o smiles -s "c(C)c"
  c1cc(ccc1CC(C(=O)O)N)O
  1 molecule converted

herong$ # using single quotes to protect ()
herong$ obabel tyrosine.sdf -o smiles -s 'c(C)c'
  c1cc(ccc1CC(C(=O)O)N)O
  1 molecule converted

herong$ # putting option flag and argument together
herong$ obabel tyrosine.sdf -o smiles "-sc(C)c"
  c1cc(ccc1CC(C(=O)O)N)O
  1 molecule converted

herong$ # putting option flag and argument together
herong$ obabel tyrosine.sdf -o smiles "-s c(C)c"
  c1cc(ccc1CC(C(=O)O)N)O
  1 molecule converted

herong$ # using double quotes to protect ' and space
herong$ obabel tyrosine.sdf -o smiles --title "John's molecule"
  c1cc(ccc1CC(C(=O)O)N)O  John's molecule
  1 molecule converted