"obabel -... --..." - Generic Conversion Options

Cheminformatics Tutorials - Herong's Tutorial Examples

∟"obabel -... --..." - Generic Conversion Options

This section provides quick introductions on generic conversion options for the Open Babel 'obabel' command that apply to all formats.

Open Babel "obabel" command supports a number of generic conversion options that applies all input and output formats. Here are some examples:

--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 format-ID
      Output formatting information and options for format specified

-Hall
      Output formatting information and options for all 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

-L category
      Lists plugin classes of this category
      Use just -L for a list of plugin categories

-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

-zin  Decompress the input with gzip