# coding=utf-8
#
# BSD 3-Clause License
#
# Copyright (c) 2016-21, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# * Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""Distogram container used throughout ConKit"""
import numpy as np
from operator import attrgetter
from conkit.core.distance import Distance
from conkit.io._cache import PARSER_CACHE
from conkit.core.contactmap import ContactMap
[docs]class Distogram(ContactMap):
"""A distogram object to store all associated information. This class inherits methods and attributes
from :obj:`~conkit.core.contactmap.ContactMap`
Examples
--------
>>> import numpy as np
>>> from conkit.core import Distance
>>> from conkit.core import Distogram
>>> distogram = Distogram("example")
>>> distogram.add(Distance(1, 25, (0.25, 0.45, 0.25, 0.05), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
>>> distogram.add(Distance(7, 19, (0.15, 0.15, 0.60, 0.1), ((0, 4), (4, 6), (6, 8), (8, np.inf))))
>>> print(distogram)
Distogram(id="example" ndistances=2)
Attributes
----------
id : str
A unique identifier
original_file_format : str
The original file format used to create the :obj:`~conkit.core.distogram.Distogram` instance
ndistances : int
The number of :obj:`~conkit.core.distance.Distance` instances in the :obj:`~conkit.core.distogram.Distogram`
"""
__slots__ = ["_original_file_format", "_sequence"]
def __init__(self, id):
self._original_file_format = None
super(Distogram, self).__init__(id)
def __repr__(self):
return '{}(id="{}", ndistances={})'.format(self.__class__.__name__, self.id, self.ndistances)
@property
def ndistances(self):
"""The number of :obj:`~conkit.core.distance.Distance` instances
Returns
-------
int
The number of distance pairs in the :obj:`~conkit.core.distogram.Distogram`
"""
return len(self)
@property
def original_file_format(self):
"""The original file format used to create the :obj:`~conkit.core.distogram.Distogram` instance"""
return self._original_file_format
@original_file_format.setter
def original_file_format(self, value):
if not value in PARSER_CACHE.distance_file_parsers.keys():
raise ValueError('Must provide valid distogram format: {}'.format(list(PARSER_CACHE.distance_file_parsers)))
self._original_file_format = value
[docs] def get_unique_distances(self, inplace=False):
"""Filter the :obj:`~conkit.core.distance.Distance` instances so that each residue pairs is present only once
Parameters
----------
inplace : bool, optional
Replace stored distances with the unique distances in the current instance [default: False]
Returns
-------
:obj:`~conkit.core.contactmap.ContactMap`
:obj:`~conkit.core.contactmap.ContactMap` instance, regardless of inplace
"""
distogram = self._inplace(inplace)
unique_pairs = {tuple(sorted(el.id)): el for el in self}
distogram.child_list = list(unique_pairs.values())
distogram.child_dict = unique_pairs
return distogram
[docs] def get_absent_residues(self, seq_len=None):
"""Get residues not represented by any :obj:`~conkit.core.distance.Distance` instance
Parameters
----------
seq_len : int, optional
Sequence length. If not provided, it will be pulled from :attr:`~conkit.core.contactmap.ContactMap.sequence`
[default: None]
Returns
-------
list
A list of absent residues
Raises
------
:exc:`ValueError`
No seq_len was provided and :attr:`~conkit.core.contactmap.ContactMap.sequence` is not defined
"""
if seq_len is None:
if self.sequence is None:
raise ValueError('Need to define a sequence or provide seq_len')
seq_len = self.sequence.seq_len
absent_residues = []
for residue in range(1, seq_len + 1):
if not any([c.id for c in self if residue in c.id]):
absent_residues.append(residue)
return absent_residues
[docs] def as_array(self, seq_len=None, get_weigths=False):
"""Transform the :obj:`~conkit.core.distogram.Distogram` instance into a :obj:numpy.array instance with shape
(seq_len, seq_len) where each element represents the predicted distance between residues
Parameters
----------
seq_len : int, optional
Sequence length. If not provided, it will be pulled from :attr:`~conkit.core.contactmap.ContactMap.sequence`
[default: None]
get_weigths : bool, optional
If True the resulting array contains the confidence for each predicted distance rather than actual distances
[default: False]
Returns
-------
:obj:`numpy.array`
:obj:`numpy.array` instance that represents the distogram. Note: change of residue indexing, now starts in 0
Raises
------
:exc:`ValueError`
No seq_len was provided and :attr:`~conkit.core.contactmap.ContactMap.sequence` is not defined
"""
if seq_len is None:
if self.sequence is None:
raise ValueError('Need to define a sequence or provide seq_len')
seq_len = self.sequence.seq_len
if seq_len < self.highest_residue_number:
raise ValueError('Sequence length does not match contact map')
if get_weigths:
getter = attrgetter('max_score')
else:
getter = attrgetter('predicted_distance')
array = np.full((seq_len + 1, seq_len + 1), np.nan)
for distance in self:
array[distance.res1_seq, distance.res2_seq] = getter(distance)
array[distance.res2_seq, distance.res1_seq] = getter(distance)
array = np.delete(array, 0, axis=0)
array = np.delete(array, 0, axis=1)
return array
[docs] def reshape_bins(self, new_bins):
"""Reshape the predicted distance bins for all :obj:`~conkit.core.distance.Distance` instances. This will
update :attr:`~conkit.core.distance.Distance.distance_scores` and
:attr:`~conkit.core.distance.Distance.distance_bins` to fit the new bins.
Parameters
----------
new_bins : tuple
A tuple of tuples, where each element corresponds with the upper and lower edges of the intervals for
the new distance bins
Raises
------
:exc:`ValueError`
The new distance bins are not valid
"""
if self.original_file_format == 'pdb':
raise ValueError('Cannot re-shape bins obtained from a PDB structure file')
Distance._assert_valid_bins(new_bins)
for distance in self:
distance._reshape_bins(new_bins)
[docs] @staticmethod
def calculate_rmsd(prediction, model, seq_len=None, calculate_wrmsd=False):
"""Calculate the RMSD between two :obj:`~conkit.core.distogram.Distogram` instances.
Parameters
----------
prediction: :obj:`~conkit.core.distogram.Distogram`
A ConKit :obj:`~conkit.core.distogram.Distogram` used as the prediction for the RMSD
model: :obj:`~conkit.core.distogram.Distogram`
A ConKit :obj:`~conkit.core.distogram.Distogram` used as the model to calculate the RMSD
seq_len: int, optional
Sequence length. If not provided, it will be pulled from :attr:`~conkit.core.contactmap.ContactMap.sequence`
[default: None]
calculate_wrmsd: bool
If set to True wRMSD is calculated using distance confidence scores [default: False]
Returns
-------
list
A list of floats with the RMSD values along the sequence
Raises
------
:exc:`ValueError`
other is not a :obj:`~conkit.core.distogram.Distogram` instance.
"""
if not isinstance(model, Distogram) or not isinstance(prediction, Distogram):
raise ValueError('Need to provide a conkit.core.distogram.Distogram instance')
max_distance = prediction.top.distance_bins[-1][0]
model_array = model.as_array(seq_len=seq_len)
model_array[model_array > max_distance] = max_distance
prediction_array = prediction.as_array(seq_len=seq_len)
prediction_array[prediction_array > max_distance] = max_distance
if prediction_array.shape != model_array.shape:
raise ValueError('Distograms cannot be matched')
difference = prediction_array - model_array
squared_difference = difference ** 2
if calculate_wrmsd:
prediction_weights = prediction.as_array(seq_len=seq_len, get_weigths=True)
squared_difference *= prediction_weights
sum_squared_differences = np.nansum(squared_difference, axis=0)
n_observations_array = np.sum(~np.isnan(squared_difference), axis=0)
rmsd = np.sqrt(sum_squared_differences / n_observations_array)
return rmsd
[docs] def find_residues_within(self, resnum, distance_cutoff):
"""Find all residues within a given distance of a given residue
Parameters
----------
resnum: int
The residue number of the residue of interest
distance_cutoff: int, float
The distance cutoff used to find residues
Returns
-------
set
A set with the residue numbers of residues within the given distance
"""
result = []
for distance in self:
if distance.predicted_distance <= distance_cutoff and resnum in distance.id:
result += list(distance.id)
return set(result)
[docs] @staticmethod
def merge_arrays(distogram_1, distogram_2):
"""Take two :obj:`~conkit.core.distogram.Distogram` instances and merge them together into the same
:obj:`numpy.array` instance. Each half square in this array will correspond with the predicted distances
at each hierarchy
Parameters
----------
distogram_1: :obj:`~conkit.core.distogram.Distogram`
First :obj:`~conkit.core.distogram.Distogram` instance, used to populate top half square of the array
distogram_2: :obj:`~conkit.core.distogram.Distogram`
Second :obj:`~conkit.core.distogram.Distogram` instance, used to populate lower half square of the array
Returns
-------
:obj:`numpy.array`
:obj:`numpy.array` instance that represents the combined distograms.
Raises
------
:exc:`ValueError`
No sequence has been registered for one of the :obj:`~conkit.core.distogram.Distogram` instances
:exc:`ValueError`
The sequence length associated to the :obj:`~conkit.core.distogram.Distogram` instances is incompatible
"""
if distogram_1.sequence is None or distogram_2.sequence is None:
raise ValueError("All hierarchies must have a sequence registered")
if distogram_1.sequence.seq_len != distogram_2.sequence.seq_len:
raise ValueError("Sequence lengths are incompatible")
array = np.full((distogram_1.sequence.seq_len + 1, distogram_1.sequence.seq_len + 1), np.nan)
for distance in distogram_1:
array[distance.res1_seq, distance.res2_seq] = distance.predicted_distance
for distance in distogram_2:
array[distance.res2_seq, distance.res1_seq] = distance.predicted_distance
array = np.delete(array, 0, axis=0)
array = np.delete(array, 0, axis=1)
return array
