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"babel" Command Option Argument Syntax
How to write "babel" command option argument properly? What's the difference between "-isdf" and "-i sdf"?
✍: FYIcenter.com
There is no difference between "-isdf" and "-i sdf".
Both are valid "babel" option "-i" with an argument of "sdf".
If a "babel" command option takes an argument, you can specify the argument in two ways:
If an option argument contains special characters, you should place it in double quotes or single quotes to protect it. Here are some examples:
fyicenter$ babel tyrosine.sdf -o smiles -s c(C)c -bash: syntax error near unexpected token `(' fyicenter$ # using double quotes to protect () fyicenter$ babel tyrosine.sdf -o smiles -s "c(C)c" c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted 43 audit log messages fyicenter$ # using single quotes to protect () fyicenter$ babel tyrosine.sdf -o smiles -s 'c(C)c' c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted 43 audit log messages fyicenter$ # putting option flag and argument together fyicenter$ babel tyrosine.sdf -o smiles "-sc(C)c" c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted 43 audit log messages fyicenter$ # putting option flag and argument together fyicenter$ babel tyrosine.sdf -o smiles "-s c(C)c" c1cc(ccc1CC(C(=O)O)N)O 1 molecule converted 43 audit log messages fyicenter$ # using double quotes to protect ' and space fyicenter$ babel tyrosine.sdf -o smiles --title "John's molecule" c1cc(ccc1CC(C(=O)O)N)O John's molecule 1 molecule converted 43 audit log messages
⇒ "babel ... -f # -l #" - Split Large Molecule File
⇐ "babel -... --..." Command - Generic Conversion Options
2020-12-26, 463👍, 0💬
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