# BSD 3-Clause License
#
# Copyright (c) 2016-19, 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.
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# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
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# * 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.
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# 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
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"""Amino acid specific distance calculator"""
__author__ = "Felix Simkovic"
__date__ = "13 Aug 2018"
__version__ = "1.0"
[docs]class DynamicDistances(object):
"""Dynamic distance calculator
Description
-----------
The data stored in this class corresponds to Supplementary Table 3
in [1]_.
Examples
--------
>>> DynamicDistances.cutoff('A', 'Y')
9.121
>>> DynamicDistances.percentile('A', 'Y')
0.443
References
----------
.. [1] Kamisetty et al. (2013). Assessing the utility of coevolution based residue-residue
contact predictions in a sequence and structure rich era. PNAS 110(39), 15674-9.
"""
__slots__ = ()
_CB_CB_CUTOFF = {
"A": {
"A": 5.381,
"C": 6.057,
"E": 7.124,
"D": 6.388,
"G": 5.201,
"F": 8.162,
"I": 6.587,
"H": 7.591,
"K": 8.327,
"M": 7.605,
"L": 6.707,
"N": 6.766,
"Q": 7.583,
"P": 6.412,
"S": 5.829,
"R": 9.365,
"T": 5.982,
"W": 9.252,
"V": 5.854,
"Y": 9.121,
},
"C": {
"A": 6.057,
"C": 6.426,
"E": 7.449,
"D": 6.985,
"G": 5.777,
"F": 9.026,
"I": 7.476,
"H": 8.422,
"K": 8.494,
"M": 8.265,
"L": 7.685,
"N": 7.205,
"Q": 7.962,
"P": 7.157,
"S": 6.59,
"R": 9.46,
"T": 6.801,
"W": 9.752,
"V": 6.941,
"Y": 9.362,
},
"D": {
"A": 6.388,
"C": 6.985,
"E": 8.945,
"D": 8.001,
"G": 6.135,
"F": 9.111,
"I": 7.472,
"H": 8.634,
"K": 9.306,
"M": 8.401,
"L": 7.696,
"N": 7.672,
"Q": 8.601,
"P": 7.321,
"S": 6.76,
"R": 10.123,
"T": 6.971,
"W": 9.867,
"V": 6.972,
"Y": 9.979,
},
"E": {
"A": 7.124,
"C": 7.449,
"E": 9.863,
"D": 8.945,
"G": 7.036,
"F": 9.403,
"I": 7.949,
"H": 9.454,
"K": 9.842,
"M": 8.87,
"L": 7.696,
"N": 7.672,
"Q": 8.601,
"P": 7.321,
"S": 6.76,
"R": 10.123,
"T": 6.971,
"W": 9.867,
"V": 6.972,
"Y": 9.979,
},
"F": {
"A": 8.162,
"C": 9.026,
"E": 9.403,
"D": 9.111,
"G": 7.966,
"F": 10.903,
"I": 9.602,
"H": 9.602,
"K": 9.344,
"M": 10.253,
"L": 9.9,
"N": 9.168,
"Q": 9.506,
"P": 8.895,
"S": 8.694,
"R": 10.577,
"T": 9.03,
"W": 11.758,
"V": 9.057,
"Y": 10.999,
},
"G": {
"A": 5.201,
"C": 5.777,
"E": 7.036,
"D": 6.135,
"G": 4.467,
"F": 7.966,
"I": 6.413,
"H": 7.472,
"K": 8.216,
"M": 7.383,
"L": 6.554,
"N": 6.321,
"Q": 7.297,
"P": 6.14,
"S": 5.51,
"R": 9.166,
"T": 5.619,
"W": 8.966,
"V": 5.671,
"Y": 9.098,
},
"H": {
"A": 7.591,
"C": 8.422,
"E": 9.454,
"D": 8.634,
"G": 7.472,
"F": 9.602,
"I": 8.523,
"H": 10.606,
"K": 9.582,
"M": 9.396,
"L": 8.676,
"N": 8.672,
"Q": 9.391,
"P": 8.537,
"S": 8.051,
"R": 10.879,
"T": 8.221,
"W": 10.661,
"V": 8.179,
"Y": 10.843,
},
"I": {
"A": 6.587,
"C": 7.476,
"E": 7.949,
"D": 7.472,
"G": 6.413,
"F": 9.602,
"I": 8.096,
"H": 8.523,
"K": 8.329,
"M": 8.874,
"L": 8.342,
"N": 7.631,
"Q": 8.302,
"P": 7.554,
"S": 7.142,
"R": 9.746,
"T": 7.442,
"W": 10.47,
"V": 7.441,
"Y": 9.719,
},
"K": {
"A": 8.327,
"C": 8.494,
"E": 9.842,
"D": 9.306,
"G": 8.216,
"F": 9.344,
"I": 8.329,
"H": 9.582,
"K": 10.662,
"M": 9.096,
"L": 8.479,
"N": 9.319,
"Q": 9.667,
"P": 9.198,
"S": 8.792,
"R": 11.322,
"T": 8.715,
"W": 10.136,
"V": 8.077,
"Y": 10.627,
},
"L": {
"A": 6.707,
"C": 7.685,
"E": 8.077,
"D": 7.696,
"G": 6.554,
"F": 9.9,
"I": 8.342,
"H": 8.676,
"K": 8.479,
"M": 9.122,
"L": 8.522,
"N": 7.889,
"Q": 8.48,
"P": 7.751,
"S": 7.394,
"R": 9.852,
"T": 7.642,
"W": 10.707,
"V": 7.633,
"Y": 9.889,
},
"M": {
"A": 7.605,
"C": 8.265,
"E": 8.87,
"D": 8.401,
"G": 7.383,
"F": 10.253,
"I": 8.874,
"H": 9.396,
"K": 9.096,
"M": 9.53,
"L": 9.122,
"N": 8.55,
"Q": 9.102,
"P": 8.247,
"S": 8.01,
"R": 10.25,
"T": 8.397,
"W": 11.11,
"V": 8.335,
"Y": 10.4,
},
"N": {
"A": 6.766,
"C": 7.205,
"E": 8.485,
"D": 7.672,
"G": 6.321,
"F": 9.168,
"I": 7.631,
"H": 8.672,
"K": 9.319,
"M": 8.55,
"L": 7.889,
"N": 7.682,
"Q": 8.502,
"P": 7.497,
"S": 7.081,
"R": 10.135,
"T": 7.159,
"W": 9.976,
"V": 7.219,
"Y": 10.039,
},
"P": {
"A": 6.412,
"C": 7.157,
"E": 7.938,
"D": 7.321,
"G": 6.14,
"F": 8.895,
"I": 7.554,
"H": 8.537,
"K": 9.198,
"M": 8.247,
"L": 7.751,
"N": 7.497,
"Q": 8.308,
"P": 7.288,
"S": 6.937,
"R": 10.266,
"T": 7.062,
"W": 9.719,
"V": 7.063,
"Y": 9.965,
},
"Q": {
"A": 7.583,
"C": 7.962,
"E": 9.328,
"D": 8.601,
"G": 7.297,
"F": 9.506,
"I": 8.302,
"H": 9.391,
"K": 9.667,
"M": 9.102,
"L": 8.48,
"N": 8.502,
"Q": 9.074,
"P": 8.308,
"S": 7.807,
"R": 10.61,
"T": 8.055,
"W": 10.429,
"V": 8.008,
"Y": 10.534,
},
"R": {
"A": 9.365,
"C": 9.46,
"E": 10.713,
"D": 10.123,
"G": 9.166,
"F": 10.577,
"I": 9.746,
"H": 10.879,
"K": 11.322,
"M": 10.25,
"L": 9.852,
"N": 10.135,
"Q": 10.61,
"P": 10.266,
"S": 9.753,
"R": 12.05,
"T": 9.764,
"W": 11.355,
"V": 9.513,
"Y": 11.615,
},
"S": {
"A": 5.829,
"C": 6.59,
"E": 7.483,
"D": 6.76,
"G": 5.51,
"F": 8.694,
"I": 7.142,
"H": 8.051,
"K": 8.792,
"M": 8.01,
"L": 7.394,
"N": 7.081,
"Q": 7.807,
"P": 6.937,
"S": 6.19,
"R": 9.753,
"T": 6.45,
"W": 9.77,
"V": 6.567,
"Y": 9.594,
},
"T": {
"A": 5.982,
"C": 6.801,
"E": 7.628,
"D": 6.971,
"G": 5.619,
"F": 9.03,
"I": 7.442,
"H": 8.221,
"K": 8.715,
"M": 8.397,
"L": 7.642,
"N": 7.159,
"Q": 8.055,
"P": 7.062,
"S": 6.45,
"R": 9.764,
"T": 6.676,
"W": 9.98,
"V": 6.791,
"Y": 9.813,
},
"V": {
"A": 5.854,
"C": 6.941,
"E": 7.404,
"D": 6.972,
"G": 5.671,
"F": 9.057,
"I": 7.441,
"H": 8.179,
"K": 8.077,
"M": 8.335,
"L": 7.633,
"N": 7.219,
"Q": 8.008,
"P": 7.063,
"S": 6.567,
"R": 9.513,
"T": 6.791,
"W": 10.021,
"V": 6.759,
"Y": 9.442,
},
"W": {
"A": 9.252,
"C": 9.752,
"E": 10.303,
"D": 9.867,
"G": 8.966,
"F": 11.758,
"I": 10.47,
"H": 10.661,
"K": 10.136,
"M": 11.11,
"L": 10.707,
"N": 9.976,
"Q": 10.429,
"P": 9.719,
"S": 9.77,
"R": 11.355,
"T": 9.98,
"W": 12.806,
"V": 10.021,
"Y": 11.807,
},
"Y": {
"A": 9.121,
"C": 9.362,
"E": 10.544,
"D": 9.979,
"G": 9.098,
"F": 10.999,
"I": 9.719,
"H": 10.843,
"K": 10.627,
"M": 10.4,
"L": 9.889,
"N": 10.039,
"Q": 10.534,
"P": 9.965,
"S": 9.594,
"R": 11.615,
"T": 9.813,
"W": 11.807,
"V": 9.442,
"Y": 11.536,
},
}
_CB_CB_PERCENT = {
"A": {
"A": 0.262,
"C": 0.394,
"E": 0.34,
"D": 0.289,
"G": 0.269,
"F": 0.26,
"I": 0.214,
"H": 0.38,
"K": 0.55,
"M": 0.394,
"L": 0.25,
"N": 0.349,
"Q": 0.356,
"P": 0.399,
"S": 0.291,
"R": 0.485,
"T": 0.378,
"W": 0.29,
"V": 0.312,
"Y": 0.443,
},
"C": {
"A": 0.394,
"C": 0.178,
"E": 0.538,
"D": 0.299,
"G": 0.129,
"F": 0.286,
"I": 0.295,
"H": 0.203,
"K": 0.521,
"M": 0.439,
"L": 0.206,
"N": 0.24,
"Q": 0.347,
"P": 0.259,
"S": 0.24,
"R": 0.491,
"T": 0.181,
"W": 0.417,
"V": 0.173,
"Y": 0.585,
},
"D": {
"A": 0.289,
"C": 0.299,
"E": 0.354,
"D": 0.392,
"G": 0.193,
"F": 0.351,
"I": 0.341,
"H": 0.325,
"K": 0.343,
"M": 0.361,
"L": 0.348,
"N": 0.337,
"Q": 0.357,
"P": 0.416,
"S": 0.323,
"R": 0.327,
"T": 0.307,
"W": 0.475,
"V": 0.287,
"Y": 0.676,
},
"E": {
"A": 0.34,
"C": 0.538,
"E": 0.389,
"D": 0.354,
"G": 0.249,
"F": 0.512,
"I": 0.453,
"H": 0.443,
"K": 0.434,
"M": 0.511,
"L": 0.475,
"N": 0.423,
"Q": 0.45,
"P": 0.475,
"S": 0.446,
"R": 0.363,
"T": 0.409,
"W": 0.493,
"V": 0.51,
"Y": 0.469,
},
"F": {
"A": 0.26,
"C": 0.286,
"E": 0.512,
"D": 0.351,
"G": 0.219,
"F": 0.46,
"I": 0.347,
"H": 0.542,
"K": 0.441,
"M": 0.377,
"L": 0.26,
"N": 0.393,
"Q": 0.451,
"P": 0.425,
"S": 0.394,
"R": 0.738,
"T": 0.264,
"W": 0.447,
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"Y": 0.767,
},
"G": {
"A": 0.269,
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"G": 0.017,
"F": 0.219,
"I": 0.179,
"H": 0.206,
"K": 0.358,
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"L": 0.125,
"N": 0.169,
"Q": 0.216,
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"S": 0.153,
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"T": 0.12,
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},
"H": {
"A": 0.38,
"C": 0.203,
"E": 0.443,
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"G": 0.206,
"F": 0.542,
"I": 0.379,
"H": 0.333,
"K": 0.714,
"M": 0.342,
"L": 0.401,
"N": 0.289,
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"P": 0.457,
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"W": 0.458,
"V": 0.383,
"Y": 0.554,
},
"I": {
"A": 0.214,
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"E": 0.453,
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"G": 0.179,
"F": 0.347,
"I": 0.321,
"H": 0.379,
"K": 0.582,
"M": 0.327,
"L": 0.261,
"N": 0.341,
"Q": 0.406,
"P": 0.336,
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"R": 0.557,
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},
"K": {
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"W": 0.47,
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"Y": 0.704,
},
"L": {
"A": 0.25,
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},
"M": {
"A": 0.394,
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"E": 0.511,
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"F": 0.377,
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},
"N": {
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"P": {
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},
"Q": {
"A": 0.356,
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"G": 0.216,
"F": 0.451,
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},
"R": {
"A": 0.485,
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},
"S": {
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"C": 0.24,
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"K": 0.445,
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"L": 0.287,
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"R": 0.483,
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"W": 0.497,
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"Y": 0.467,
},
"T": {
"A": 0.378,
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},
"V": {
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},
"W": {
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"Y": 0.684,
},
"Y": {
"A": 0.443,
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"E": 0.469,
"D": 0.676,
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"S": 0.467,
"R": 0.822,
"T": 0.43,
"W": 0.684,
"V": 0.535,
"Y": 0.855,
},
}
[docs] @classmethod
def cutoff(cls, x, y):
"""Return the amino acid pair-specific cB-cB cutoff
Parameters
----------
x : str
Single-letter amino acid
y : str
Single-letter amino acid
"""
return cls._CB_CB_CUTOFF[x][y]
[docs] @classmethod
def percentile(cls, x, y):
"""Return 95-97 percentile data
Parameters
----------
x : str
Single-letter amino acid
y : str
Single-letter amino acid
"""
return cls._CB_CB_PERCENT[x][y]
