from __future__ import print_function
__author__ = 'Felix Simkovic'
__date__ = '02 Dec 2016'
__version__ = '0.1'
import logging
logger = logging.getLogger(__name__)
[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,
'V': 0.246,
'Y': 0.767,
},
'G': {
'A': 0.269,
'C': 0.129,
'E': 0.249,
'D': 0.193,
'G': 0.017,
'F': 0.219,
'I': 0.179,
'H': 0.206,
'K': 0.358,
'M': 0.255,
'L': 0.125,
'N': 0.169,
'Q': 0.216,
'P': 0.245,
'S': 0.153,
'R': 0.334,
'T': 0.12,
'W': 0.239,
'V': 0.107,
'Y': 0.267,
},
'H': {
'A': 0.38,
'C': 0.203,
'E': 0.443,
'D': 0.325,
'G': 0.206,
'F': 0.542,
'I': 0.379,
'H': 0.333,
'K': 0.714,
'M': 0.342,
'L': 0.401,
'N': 0.289,
'Q': 0.401,
'P': 0.457,
'S': 0.435,
'R': 0.595,
'T': 0.417,
'W': 0.458,
'V': 0.383,
'Y': 0.554,
},
'I': {
'A': 0.214,
'C': 0.295,
'E': 0.453,
'D': 0.341,
'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,
'S': 0.342,
'R': 0.557,
'T': 0.259,
'W': 0.397,
'V': 0.242,
'Y': 0.589,
},
'K': {
'A': 0.55,
'C': 0.521,
'E': 0.434,
'D': 0.343,
'G': 0.358,
'F': 0.441,
'I': 0.582,
'H': 0.714,
'K': 0.738,
'M': 0.611,
'L': 0.591,
'N': 0.398,
'Q': 0.521,
'P': 0.55,
'S': 0.445,
'R': 0.648,
'T': 0.464,
'W': 0.47,
'V': 0.634,
'Y': 0.704,
},
'L': {
'A': 0.25,
'C': 0.206,
'E': 0.475,
'D': 0.348,
'G': 0.125,
'F': 0.26,
'I': 0.261,
'H': 0.401,
'K': 0.591,
'M': 0.318,
'L': 0.198,
'N': 0.279,
'Q': 0.411,
'P': 0.317,
'S': 0.287,
'R': 0.578,
'T': 0.19,
'W': 0.331,
'V': 0.179,
'Y': 0.611,
},
'M': {
'A': 0.394,
'C': 0.439,
'E': 0.511,
'D': 0.361,
'G': 0.255,
'F': 0.377,
'I': 0.327,
'H': 0.342,
'K': 0.611,
'M': 0.457,
'L': 0.318,
'N': 0.31,
'Q': 0.498,
'P': 0.388,
'S': 0.369,
'R': 0.641,
'T': 0.292,
'W': 0.397,
'V': 0.295,
'Y': 0.661,
},
'N': {
'A': 0.349,
'C': 0.24,
'E': 0.423,
'D': 0.337,
'G': 0.169,
'F': 0.393,
'I': 0.341,
'H': 0.289,
'K': 0.398,
'M': 0.31,
'L': 0.279,
'N': 0.249,
'Q': 0.373,
'P': 0.334,
'S': 0.305,
'R': 0.372,
'T': 0.262,
'W': 0.458,
'V': 0.232,
'Y': 0.586,
},
'P': {
'A': 0.399,
'C': 0.259,
'E': 0.475,
'D': 0.416,
'G': 0.245,
'F': 0.425,
'I': 0.336,
'H': 0.457,
'K': 0.55,
'M': 0.388,
'L': 0.317,
'N': 0.334,
'Q': 0.41,
'P': 0.339,
'S': 0.321,
'R': 0.506,
'T': 0.32,
'W': 0.462,
'V': 0.298,
'Y': 0.506,
},
'Q': {
'A': 0.356,
'C': 0.347,
'E': 0.45,
'D': 0.357,
'G': 0.216,
'F': 0.451,
'I': 0.406,
'H': 0.401,
'K': 0.521,
'M': 0.498,
'L': 0.411,
'N': 0.373,
'Q': 0.436,
'P': 0.41,
'S': 0.408,
'R': 0.535,
'T': 0.378,
'W': 0.49,
'V': 0.359,
'Y': 0.547,
},
'R': {
'A': 0.485,
'C': 0.491,
'E': 0.363,
'D': 0.327,
'G': 0.334,
'F': 0.738,
'I': 0.557,
'H': 0.595,
'K': 0.648,
'M': 0.641,
'L': 0.578,
'N': 0.372,
'Q': 0.535,
'P': 0.506,
'S': 0.483,
'R': 0.704,
'T': 0.477,
'W': 0.889,
'V': 0.514,
'Y': 0.822,
},
'S': {
'A': 0.291,
'C': 0.24,
'E': 0.446,
'D': 0.323,
'G': 0.153,
'F': 0.394,
'I': 0.342,
'H': 0.435,
'K': 0.445,
'M': 0.369,
'L': 0.287,
'N': 0.305,
'Q': 0.408,
'P': 0.321,
'S': 0.292,
'R': 0.483,
'T': 0.214,
'W': 0.497,
'V': 0.205,
'Y': 0.467,
},
'T': {
'A': 0.378,
'C': 0.181,
'E': 0.409,
'D': 0.307,
'G': 0.12,
'F': 0.264,
'I': 0.259,
'H': 0.417,
'K': 0.464,
'M': 0.292,
'L': 0.19,
'N': 0.262,
'Q': 0.378,
'P': 0.32,
'S': 0.214,
'R': 0.477,
'T': 0.188,
'W': 0.315,
'V': 0.138,
'Y': 0.43,
},
'V': {
'A': 0.312,
'C': 0.173,
'E': 0.51,
'D': 0.287,
'G': 0.107,
'F': 0.246,
'I': 0.242,
'H': 0.383,
'K': 0.634,
'M': 0.295,
'L': 0.179,
'N': 0.232,
'Q': 0.359,
'P': 0.298,
'S': 0.205,
'R': 0.514,
'T': 0.138,
'W': 0.271,
'V': 0.145,
'Y': 0.535,
},
'W': {
'A': 0.29,
'C': 0.417,
'E': 0.493,
'D': 0.475,
'G': 0.239,
'F': 0.447,
'I': 0.397,
'H': 0.458,
'K': 0.47,
'M': 0.397,
'L': 0.331,
'N': 0.458,
'Q': 0.49,
'P': 0.462,
'S': 0.497,
'R': 0.889,
'T': 0.315,
'W': 0.473,
'V': 0.271,
'Y': 0.684,
},
'Y': {
'A': 0.443,
'C': 0.585,
'E': 0.469,
'D': 0.676,
'G': 0.267,
'F': 0.767,
'I': 0.589,
'H': 0.554,
'K': 0.704,
'M': 0.661,
'L': 0.611,
'N': 0.586,
'Q': 0.547,
'P': 0.506,
'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]
[docs]class RosettaFunctionConstructs(object):
"""Storage for string formats of different Rosetta energy function constructs
Description
-----------
For more information on the different energy functions, please refer to the
corresponding references or the official `RosettaCommons documentation`_
.. _RosettaCommons documentation: https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file
"""
__slots__ = ()
_ATOMPAIR = "AtomPair {atom1: >2} {res1_seq: >4} {atom2: >2} {res2_seq: >4} "
_SCALARWEIGHTED = "SCALARWEIGHTEDFUNC {scalar_score: .3f} "
@property
def BOUNDED_default(self):
"""Simple bounded energy function"""
construct = RosettaFunctionConstructs._ATOMPAIR + "BOUNDED {lower_bound: >.3f} {upper_bound: >.3f} 1 0.5 #"
return construct
@property
def BOUNDED_gremlin(self):
"""Energy function according to [2]_
References
----------
.. [2] Ovchinnekov et al. (2015). Large-scale determination of previously unsolved
protein structures using evolutionary information. Elife 3(4), e09248.
"""
construct = (
RosettaFunctionConstructs._ATOMPAIR
+ RosettaFunctionConstructs._SCALARWEIGHTED
+ "BOUNDED 0 {lower_bound: >.3f} 1 0.5"
)
return construct
@property
def FADE(self):
"""Energy function according to [3]_ and [4]_
References
----------
.. [3] Simkovic et al. (2016). Residue contacts predicted by evolutionary covariance
extend the application of ab initio molecular replacement to larger and more
challenging protein folds. IUCrJ 3(Pt 4), 259-270.
.. [4] Michel et al. (2014). PconsFold: improved contact predictions improve protein
models. Bioinformatics 30(17), i482-i488
"""
construct = RosettaFunctionConstructs._ATOMPAIR + "FADE -10 19 10 {energy_bonus: >5.2f} 0"
return construct
@property
def FADE_default(self):
"""Energy function according to [4]_
References
----------
.. [4] Michel et al. (2014). PconsFold: improved contact predictions improve protein
models. Bioinformatics 30(17), i482-i488
"""
construct = RosettaFunctionConstructs._ATOMPAIR + "FADE -10 19 10 -15.00 0"
return construct
@property
def FLAT_HARMONIC(self):
"""ROSETTA FLAT_HARMONIC energy function"""
construct = RosettaFunctionConstructs._ATOMPAIR + "FLAT_HARMONIC {x0: >.2f} {stddev: >.2f} {tol: >.2f}"
return construct
@property
def GAUSSIAN(self):
"""Simple Gaussian energy function"""
construct = RosettaFunctionConstructs._ATOMPAIR + "GAUSSIANFUNC {mean: >.2f} {stddev: >.2f} TAG"
return construct
@property
def SIGMOID_default(self):
"""Simple sigmoidal energy function"""
construct = RosettaFunctionConstructs._ATOMPAIR + "SIGMOID 8.00 1.00 #ContactMap: {raw_score: >4.3f}"
return construct
@property
def SIGMOID_gremlin(self):
"""Energy function according to [2]_
References
----------
.. [2] Ovchinnekov et al. (2015). Large-scale determination of previously unsolved
protein structures using evolutionary information. Elife 4, e09248.
"""
construct = (
RosettaFunctionConstructs._ATOMPAIR
+ RosettaFunctionConstructs._SCALARWEIGHTED
+ "SUMFUNC 2 SIGMOID {sigmoid_cutoff: >6.3f} {sigmoid_slope: >6.3f} CONSTANTFUNC -0.5"
)
return construct
[docs]class Saint2FunctionConstructs(object):
"""Storage for string formats of different SAINT2 energy function constructs
"""
__slots__ = ()
@property
def DEFAULT(self):
"""Default format"""
# Actually a contact format but keep it as restraints style
construct = "{res1_seq: >4} {res2_seq: >4} {raw_score: >4.3f}"
return construct
