Introduction to NMR-STAR

To understand how the library works, you first need to understand the NMR-STAR terminology and file format. If you are already familiar with NMR-STAR, feel free to jump ahead to the section on this library.

A NMR-STAR entry/file is composed of one or more saveframes (conceptually you should think of a saveframe as loosely resembling objects in an object-relational data model), each of which contain tags and loops. There can only be one of each tag in a saveframe. If a tag has multiple values, the only way to represent it is to place it inside a loop. A loop is simply a set of tags with multiple values.

Therefore, hierarchically, you can picture a NMR-STAR file as a tree where the entry is the trunk, the large branches are the saveframes, and each saveframe may contain one or more loops - the branches.

Here is a very simple example of a NMR-STAR file:

data_dates
    save_special_dates_saveframe_1
        _Special_Dates.Type     Holidays
        loop_
            _Events.Date
            _Events.Description
            12/31/2017 "New Year's Eve"
            01/01/2018 "New Year's Day"
        stop_
    save_

In the previous example, the entry name is dates because that is what follows the data_ tag. Next, there is one saveframe, with a name of special_dates_saveframe_1 and a tag prefix (which corresponds to the saveframe category) of Special_Dates. There is one tag in the saveframe, with a tag name of Type and a value of Holidays. There is also one loop of category events that has information about two different events (though an unlimited number of events could be present).

The first datum in each row corresponds to the first tag, Date, and the second corresponds to the second tag, Description.

Values in NMR-STAR format need to be quoted if they contain a space, tab, vertical tab, or newline in the value. This library takes care of that for you, but it is worth knowing. That is why in the example the dates are not quoted, but the event descriptions are.

Go on to the PyNMR-STAR quick start.