Update data model

[brindakv]

The data model needs to be updated to comply with the current IHM-dictionary.

Examples of the different kinds of updates involved:

• Add a row to existing Vocab table: Add values CYS, BMSO and DHSO to _ihm_cross_link_list.linker_type
• Add a new table: ihm_pseudo_site with columns _ihm_pseudo_site.id (key, int), _ihm_pseudo_site.Cartn_x (float), _ihm_pseudo_site.Cartn_y (float), _ihm_pseudo_site.Cartn_z (float), _ihm_pseudo_site.radius (float), _ihm_pseudo_site.description (text)
• Add a new column to an existing table with fkey: Add _ihm_pseudo_site_feature.pseudo_site_id with fkey pointing to _ihm_pseudo_site.id
• Remove columns from an existing table: Remove _ihm_pseudo_site_feature.Cartn_x, _ihm_pseudo_site_feature.Cartn_y, _ihm_pseudo_site_feature.Cartn_z, _ihm_pseudo_site_feature.radius and _ihm_pseudo_site_feature.description
• Add a new column and a related new Vocab table: _ihm_cross_link_restraint.pseudo_site_flag with values Yes and No

[svoinea]

Committed a script at https://github.com/informatics-isi-edu/protein-database/blob/master/config-scripts/schema-updates/model_updates.py to update the model for the above examples.