def get_contact_density(contact_list, seq_length):
"""Credits to Felix Simkovic; code taken from GitHub rigdenlab/conkit"""
x = np.array([i for c in contact_list for i in np.arange(c[1], c[0] + 1)],
dtype=np.int64)[:, np.newaxis]
bw = bandwidth_factory('amise')(x).bw
kde = KernelDensity(bandwidth=bw).fit(x)
x_fit = np.arange(1, seq_length + 1)[:, np.newaxis]
density = np.exp(kde.score_samples(x_fit)).tolist()
density_max = max(density)
density = [int(round(float(i) / density_max, 1) * 10) for i in density]
return density
def get_contact_density(self, bw_method="amise"):
"""Calculate the contact density in the contact map using Gaussian kernels
Various algorithms can be used to estimate the bandwidth. To calculate the
bandwidth for an 1D data array ``X`` with ``n`` data points and ``d`` dimensions,
the listed algorithms have been implemented. Please note, in rules 2 and 3, the
value of :math:`\\sigma` is the smaller of the standard deviation of ``X`` or
the normalized interquartile range.
Parameters
----------
bw_method : str, optional
The bandwidth estimator to use [default: amise]
Returns
-------
list
The list of per-residue density estimates
Raises
------
:exc:`ImportError`
Cannot find scikit-learn package
:exc:`ValueError`
Undefined bandwidth method
:exc:`ValueError`
:obj:`~conkit.core.contactmap.ContactMap` is empty
"""
try:
import sklearn.neighbors
except ImportError as e:
raise ImportError(e)
if self.empty:
raise ValueError("ContactMap is empty")
x = np.array(
[i for c in self for i in np.arange(c.res1_seq, c.res2_seq + 1)],
dtype=np.int64)[:, np.newaxis]
x_fit = np.arange(x.min(), x.max() + 1)[:, np.newaxis]
from conkit.misc.bandwidth import bandwidth_factory
bandwidth = bandwidth_factory(bw_method)(x).bw
kde = sklearn.neighbors.KernelDensity(bandwidth=bandwidth).fit(x)
return np.exp(kde.score_samples(x_fit)).tolist()
def calculate_contact_density(self, bw_method="amise"):
"""Calculate the contact density in the contact map using Gaussian kernels
Various algorithms can be used to estimate the bandwidth. To calculate the
bandwidth for an 1D data array ``X`` with ``n`` data points and ``d`` dimensions,
the listed algorithms have been implemented. Please note, in rules 2 and 3, the
value of :math:`\\sigma` is the smaller of the standard deviation of ``X`` or
the normalized interquartile range.
Parameters
----------
bw_method : str, optional
The bandwidth estimator to use [default: amise]
Returns
-------
list
The list of per-residue density estimates
Raises
------
RuntimeError
Cannot find SciKit package
ValueError
Undefined bandwidth method
"""
try:
import sklearn.neighbors
except ImportError:
raise RuntimeError("Cannot find SciKit package")
if self.empty:
raise ValueError("ContactMap is empty")
# TODO: Chunan suggested to fix this bug - results are usually marginally better
# REM: Bug in Sadowski's algorithm, res2 is excluded from list to train KDE
# REM: Remember to change test cases when corrected implementation benchmarked
# x = np.array([i for c in self for i in np.arange(c.res1_seq, c.res2_seq + 1)])[:, np.newaxis]
x = np.array([i for c in self for i in np.arange(c.res1_seq, c.res2_seq)])[:, np.newaxis]
x_fit = np.arange(x.min(), x.max() + 1)[:, np.newaxis]
from conkit.misc.bandwidth import bandwidth_factory
bandwidth = bandwidth_factory(bw_method)(x).bw
kde = sklearn.neighbors.KernelDensity(bandwidth=bandwidth).fit(x)
return np.exp(kde.score_samples(x_fit)).tolist()
def test_bandwidth_factory_9(self):
with self.assertRaises(ValueError):
bandwidth.bandwidth_factory("garbage")
def test_bandwidth_factory_8(self):
with self.assertRaises(ValueError):
bandwidth.bandwidth_factory("silvermn")
def test_bandwidth_factory_6(self):
with self.assertRaises(ValueError):
bandwidth.bandwidth_factory("SILVERMAN")
def test_bandwidth_factory_5(self):
obj = bandwidth.bandwidth_factory("silverman")
self.assertEqual(str(obj),
"<class 'conkit.misc.bandwidth.SilvermanBW'>")
def test_bandwidth_factory_4(self):
obj = bandwidth.bandwidth_factory("scott")
self.assertEqual(str(obj), "<class 'conkit.misc.bandwidth.ScottBW'>")
def test_bandwidth_factory_3(self):
obj = bandwidth.bandwidth_factory("linear")
self.assertEqual(str(obj), "<class 'conkit.misc.bandwidth.LinearBW'>")
def test_bandwidth_factory_2(self):
obj = bandwidth.bandwidth_factory("bowman")
self.assertEqual(str(obj), "<class 'conkit.misc.bandwidth.BowmanBW'>")
def test_bandwidth_factory_1(self):
obj = bandwidth.bandwidth_factory("amise")
self.assertEqual(str(obj), "<class 'conkit.misc.bandwidth.AmiseBW'>")
