What's available? Online help

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Getting help information from the command line


 babel -H

will produce a large page on the basic usage of OpenBabel, with many command-line options. To see a list of the file formats that are supported, see below. (The commands are identical for the alternative obabel interface.)

Many features of OpenBabel are provided by plugins, which are independent pieces of code which in some cases may be added after the program has been compiled or installed. To see a list of the plugin categories that are present:

 babel -L

These will probably include:

formats file formats, such as smiles, pdb, sdf and many more.
descriptors numerical or text properties of molecules, e.g. logP, inchi
ops command-line options, e.g. --gen3D, --sort
fingerprints binary representation of molecules for sub-structure searches etc.
charges models for assigning partial charges to atoms, e.g. gasteiger

To see a list of the plugins within a particular category add the name of the category, for instance:

 babel -L formats

To see only formats for reading files:

 babel -L formats read    OR
 babel -L formats input

And similarly for write or output formats.

To get more details about a particular format (or any other plugin), use its ID (name), for instance:

 babel -L sdf

This will provide the command-line options specific to that format and sometimes other information.

To get a detailed description of all the types within a category, use:

 babel -L ops verbose

Getting help information in the GUI

The available formats are shown in dropdown boxes and the available options in the middle panel.

Detailed information on the selected format can be shown with the Format Info buttons.

A list of the plugin categories is under a Plugins menu entry. Clicking the the name for a particular type provides its details and also puts its ID on the clipboard so it can be pasted into an editbox in the options panel.