ConKit ContactFile Hierarchy Construction

If you wish to construct it as part of a new development to store your contact information, you might find the following helpful.


1. How to create a Contact?

>>> from conkit.core import Contact
>>> contact = Contact(1, 10, 1.0)

The example above creates a contact between residues 1 and 10 and assigns a raw_score of 1.0 to it. By default, this contact has many more default attributes assigned, such as the distance value often seen in columns 3 and 4 in the Casp RR format.

2. How to create a ContactMap?

>>> from conkit.core import ContactMap
>>> cmap = ContactMap('example')

This example shows you how to create a ContactMap which can store a Contact.

3. How to create a ContactFile?

>>> from conkit.core import ContactFile
>>> cmap = ContactFile('example')

This example shows you how to create a ContactFile which can store a ContactMap.


Above is an outline for the different contact-related entities. Each higher entity allows you to store one or more lower-level ones, i.e. you can store one or more ContactMap entities in a single ContactFile. Similarly, you could many Contact entities in a ContactMap; however, be aware that all must have unique IDs.

To illustrate how you can combine the entities, look at the following:

>>> from conkit.core import Contact, ContactMap, ContactFile
>>> cfile = ContactFile('example_file')
>>> cmap = ContactMap('example_map')
>>> contact = Contact(1, 10, 1.0)
>>> # Add the contact to the contact map
>>> cmap.add(contact)
>>> # Add the contact map to the contact file
>>> cfile.add(cmap)

Note, the order in which you add entities does not matter. We could also add the cmap to the cfile before adding the contact to the cmap.

Once you have constructed your hierarchy, all related functions are available to you.