Hierarchy Construction¶

Note

The easiest way to construct a contact file hierarchy is to choose the corresponding parser.

Warning

This example is kept brief, if you are unable to follow the process or want to know more, check out the source code.

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

1. Constructing instances¶

The following blocks of code a purely an outline on how each instance can be created.

1.1 ContactFile¶

>>> from conkit.core import ContactFile
>>> contact_file = ContactFile('<YOUR_ID_HERE>')

1.2 ContactMap¶

>>> from conkit.core import ContactMap
>>> contact_map = ContactMap('<YOUR_ID_HERE')

1.3 Contact¶

>>> from conkit.core import Contact
>>> contact = Contact('res1_seq', 'res2_seq', 'raw_score')

Note

The conkit.core.Contact ID is automatically assigned based on res1_seq and res2_seq attributes.

2. Assembling the hierarchy¶

To assemble a hierarchy, you want to add conkit.core.Contact instances to a conkit.core.ContactMap instance. Then, you can add one or more conkit.core.ContactMap instances to a single conkit.core.ContactFile.

Be aware, the IDs for all instances need to be unique at their level, but can be repeated across multiple instances in higher levels. I.e. a Contact(1, 2, 0.1) can be added only once to ContactMap('map_1') but added to ContactMap('map_2') if desired.

>>> from conkit.core import Contact, ContactMap, ContactFile
>>> contact_file = ContactFile('example')
>>> for i in range(1, 4):
...     contact_map = ContactMap('map_{0}'.format(i))
...
...     for j in range(1, 11):
...         contact = Contact(i, j, 0.1)
...         contact_map.add(contact)
...
...     contact_file.add(contact_map)

In the example above we create a single contact file hierarchy that will contain three contact maps with each 10 contacts. Can you see it?