Collections:
"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, 823🔥, 0💬
Popular Posts:
Molecule Summary: ID: FYI-1004908 Names: InChIKey: WOXKDUGGOYFFRN-UHFFFAOYS A-NSMILES: CN6CC(=O)N3C(...
Molecule Summary: ID: FYI-1003057 Names: InChIKey: JUQSUBXNHVMDLB-WCQYABFAS A-NSMILES: N#Cc3cc(c2cc(...
Molecule Summary: ID: FYI-1003808 Names: InChIKey: WGYIRKDEZBKNCI-UHFFFAOYS A-NSMILES: C1OCOCOCOCOCO...
Molecule Summary: ID: FYI-1003120 Names: InChIKey: NPYPAHLBTDXSSS-UHFFFAOYS A-NSMILES: [K+] Received...
Molecule Summary: ID: FYI-1002198 Names: InChIKey: NNZMAUMXMGGQOF-JSKKQJDMS A-NSMILES: COc6cccc(C3C(...