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"""ContactFile container used throughout ConKit"""
from __future__ import division
from __future__ import print_function
__author__ = "Felix Simkovic"
__date__ = "03 Aug 2016"
__version__ = "1.0"
from conkit.core.entity import Entity
[docs]class ContactFile(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 : str
The author of the :obj:`~conkit.core.contactfile.ContactFile`
method : list, str
The :obj:`~conkit.core.contactfile.ContactFile`-specific method
remark : list, str
The :obj:`~conkit.core.contactfile.ContactFile`-specific remarks
target : str
The target name
top_map : :obj:`~conkit.core.contactmap.ContactMap`
The first :obj:`~conkit.core.contactmap.ContactMap` entry in :obj:`~conkit.core.contactfile.ContactFile`
"""
__slots__ = ["author", "target", "_method", "_remark"]
def __init__(self, id):
"""Initialise a new contact map
Parameters
----------
id : str
A unique identifier for this :obj:`~conkit.core.contactfile.ContactFile`
"""
self.author = None
self.target = None
self._method = []
self._remark = []
super(ContactFile, self).__init__(id)
def __repr__(self):
return '{}(id="{}" nmaps={})'.format(self.__class__.__name__, self.id, len(self))
@property
def method(self):
"""The :obj:`~conkit.core.contactfile.ContactFile`-specific method"""
return self._method
@method.setter
def method(self, method):
"""Set the :obj:`~conkit.core.contactfile.ContactFile` method
Parameters
----------
method : str, list
The method will be added to the list of methods
"""
self._method += Entity.listify(method)
@property
def remark(self):
"""The :obj:`~conkit.core.contactfile.ContactFile`-specific remarks"""
return self._remark
@remark.setter
def remark(self, remark):
"""Set the :obj:`~conkit.core.contactfile.ContactFile` remark
Parameters
----------
remark : str, list
The remark will be added to the list of remarks
"""
self._remark += Entity.listify(remark)
@property
def top_map(self):
"""The first :obj:`~conkit.core.contactmap.ContactMap` entry"""
return self.top
[docs] def sort(self, kword, reverse=False, inplace=False):
"""Sort the :obj:`~conkit.core.contactfile.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:`~conkit.core.contactmap.ContactMap`
The reference to the :obj:`~conkit.core.contactmap.ContactMap`, regardless of `inplace`
Raises
------
:exc:`ValueError`
`kword` not in :obj:`~conkit.core.contactfile.ContactFile`
"""
contact_file = self._inplace(inplace)
contact_file._sort(kword, reverse)
return contact_file