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"babel" Command - From STDIN To STDOUT
Can I use "babel" to convert chemical data from "stdin" to "stdout" without input and output files?
✍: FYIcenter.com
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
2021-07-19, 514👍, 0💬
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