conkit.core.contactfile module¶

ContactFile container used throughout ConKit

class ContactFile(id)[source]¶

Bases: conkit.core._entity._Entity

A contact file object representing a single prediction file

The contact file class represents a data structure to hold all predictions with a single contact map file. It contains functions to store, manipulate and organise contact maps.

Examples

>>> from conkit.core import ContactMap, ContactFile
>>> contact_file = ContactFile("example")
>>> contact_file.add(ContactMap("foo"))
>>> contact_file.add(ContactMap("bar"))
>>> print(contact_file)
ContactFile(id="example" nseq=2)

Attributes

author	The author of the ContactFile
method	The ContactFile-specific method
remark	The ContactFile-specific remarks
target	The target name
top_map	The first ContactMap entry in ContactFile

Methods

add(entity)	Add a child to the Entity
copy()	Create a shallow copy of Entity
deepcopy()	Create a deep copy of Entity
remove(id)	Remove a child
sort(kword[, reverse, inplace])	Sort the ContactFile

author¶

The author of the ContactFile

method¶

The ContactFile-specific method

remark¶

The ContactFile-specific remarks

sort(kword, reverse=False, inplace=False)[source]¶

Sort the ContactFile

Parameters:	kword : str The dictionary key to sort contacts by reverse : bool, optional Sort the contact pairs in descending order [default: False] inplace : bool, optional Replace the saved order of contacts [default: False]
Returns:	obj The reference to the ContactMap, regardless of inplace
Raises:	ValueError kword not in ContactFile

target¶

The target name

top_map¶

The first ContactMap entry in ContactFile