A publication's conditions are stored as metadata on the field FISHPUBCONTEXT on the version level object. 

You can use the standard API calls that manipulate a publication.

The field is long text and the context is an xml doc with the following structure:

<features>

   <feature name-"{condition-name} value="{condition-value}" />

   ....

   <feature name-"{condition-name} value="{condition-value}" />

</features>

If you want to see what the value looks like on an existing publication, open it in publication manager.  On the content tab right click on the header bar for the metadata and choose Add/Remove Columns.  On the dialog that opens, click show advanced columns and Context to the displayed columns.

If you look at the raw text that you send/receive through the API, all the XML reserved characters are converted to their respective entities.

<ishfield name="FISHPUBCONTEXT" level="version" xml:space="preserve">&lt;features&gt;&lt;feature name="{condition-name}" value="{condition-value}" /&gt;&lt;feature name="{condition-name}" value="{condition-value}" /&gt;&lt;feature name="PSE" value="SS" /&gt;&lt;/features&gt;</ishfield>

Thanks Greg!

Thanks Greg!