Can I use "babel" to convert chemical data from "stdin" to "stdout" without input and output files?

Yes, you can use "babel" to convert chemical data from "stdin" to "stdout" without input and output files. Just use "-i ..." and "-o" flags to specify input data format and output data format.

For example, the following "babel" command converts a SMILES string to a molecule SDF file from "stdin", the keyboard, to "stdout", the screen:

fyicenter$ babel -i smiles -o sdf --gen3D
c1ccccc1
<Ctrl-D>

OpenBabel05212009473D

12 12  0  0  0  0  0  0  0  0999 V2000
  -0.7600    1.1690   -0.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.6329    1.2445   -0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
   1.3950    0.0760    0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
   0.7644   -1.1682    0.0017 C   0  0  0  0  0  0  0  0  0  0  0  0
  -0.6284   -1.2439    0.0006 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.3905   -0.0753   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
  -1.3538    2.0793   -0.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
   1.1245    2.2136   -0.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
   2.4802    0.1351    0.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   1.3581   -2.0784    0.0031 H   0  0  0  0  0  0  0  0  0  0  0  0
  -1.1199   -2.2130    0.0011 H   0  0  0  0  0  0  0  0  0  0  0  0
  -2.4757   -0.1346   -0.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
 1  6  1  0  0  0  0
 1  2  2  0  0  0  0
 1  7  1  0  0  0  0
 2  3  1  0  0  0  0
 2  8  1  0  0  0  0
 3  4  2  0  0  0  0
 3  9  1  0  0  0  0
 4  5  1  0  0  0  0
 4 10  1  0  0  0  0
 5  6  2  0  0  0  0
 5 11  1  0  0  0  0
 6 12  1  0  0  0  0
M  END
$$$$

1 molecule converted
79 audit log messages 

 

⇒ "babel -... --..." Command - Generic Conversion Options

⇐ "babel" Command - Use "-o ..." as Output Delimiter

⇑ Understanding "babel" Command Line Syntax

⇑⇑ Open Babel Tutorials