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"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats?
✍: FYIcenter.com
"babel" commands supports a number of generic conversion options that
applies all input and output formats as listed below:
--addtotitle
Append text to the current molecule title
--addformula
Append the molecular formula after the current molecule title
-b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O
-c Center atomic coordinates at (0,0,0)
-C Combine molecules in first file with others having the same name
-e Continue after errors
-d Delete Hydrogens
---errorlevel 2
Filter the level of errors and warnings displayed:
1 = critical errors only
2 = include warnings too (default)
3 = include informational messages too
4 = include "audit log" messages of changes to data
5 = include debugging messages too
-f # For multiple entry input, start import with molecule # as the first entry
-F Output the available fingerprint types
-h Add hydrogens
-H Output usage information
-H format-ID
Output formatting information and options for format specified
-Hall
Output formatting information and options for all formats
-i<format-ID>
Specifies input format, see below for the available formats
-j
--join
Join all input molecules into a single output molecule entry
-k Translate computational chemistry modeling keywords
(e.g., GAMESS and Gaussian)
-m Produce multiple output files, to allow:
- Splitting one input file - put each molecule into consecutively numbered output files
- Batch conversion - convert each of multiple input files into a specified output format
-l # For multiple entry input, stop import with molecule # as the last entry
-o format-ID
Specifies output format, see below for the available formats
-O outfile
Specify the output file. This option applies to obabel only.
-p Add Hydrogens appropriate for pH (use transforms in phmodel.txt)
--property
Add or replace a property (e.g., in an MDL SD file)
-s SMARTS
Convert only molecules matching the SMARTS pattern specified
--separate
Separate disconnected fragments into individual molecular records
-t All input files describe a single molecule
--title title
Add or replace molecular title
-v SMARTS
Convert only molecules NOT matching SMARTS pattern specified
-z Compress the output with gzip
⇒ "babel" Command Option Argument Syntax
⇐ "babel" Command - From STDIN To STDOUT
2021-07-19, 1370🔥, 0💬
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