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Biskit
Package Biskit :: Module surfaceRacerTools
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Module surfaceRacerTools

source code

Reference data for SurfaceRacer.

Classes [hide private]
  Test
Test class

Functions [hide private]
[float] relExposure(model, absSurf, key='AS', clip=1)
Calculate how exposed an atom is relative to the same atom in a GLY-XXX-GLY tripeptide, an approximation of the unfolded state.
[float] __Nter(a, rel, absSurf, key, i)
Get N-terminal relative exposures.
[float] __Cter(a, rel, absSurf, key, i)
Get C-terminal relative exposures
[float] __bulk(a, rel, absSurf, key, i)
Get relative exposures for everything else.

Variables [hide private]
  ranMS = {'CYS': {'C': 1.969, 'CB': 21.339, 'CA': 8.077, 'O':...
  ranAS = {'CYS': {'C': 0.833, 'CB': 34.358, 'CA': 7.768, 'O':...
  ranMS_C = {'CYS': {'C': 4.901, 'OXT': 16.009, 'CB': 21.505, 'C...
  ranMS_N = {'CYS': {'C': 1.881, 'CB': 20.689, 'CA': 12.751, 'O'...
  ranAS_C = {'CYS': {'C': 3.576, 'OXT': 44.000, 'CB': 35.823, 'C...
  ranAS_N = {'CYS': {'C': 1.431, 'CB': 38.159, 'CA': 19.289, 'O'...
  test = Test()

Function Details [hide private]

relExposure(model, absSurf, key='AS', clip=1)

source code 

Calculate how exposed an atom is relative to the same atom in a GLY-XXX-GLY tripeptide, an approximation of the unfolded state.
Parameters:
  • absSurf ([float]) - Absolute MS OR AS values
  • key (MS|AS) - MS or AS
  • clip (1|0) - clip values above 100% (default: 1)
Returns: [float]
rel - list of relative accessible surfaces

__Nter(a, rel, absSurf, key, i)

source code 

Get N-terminal relative exposures.
Parameters:
  • rel ([float]) - list in which relative exposures are collected
  • absSurf ([float]) - Absolute MS OR AS values
  • key (MS|AS) - MS or AS
Returns: [float]
rel - list of relative accessible surfaces with data from N-terminal residues appended.

__Cter(a, rel, absSurf, key, i)

source code 

Get C-terminal relative exposures
Parameters:
  • rel ([float]) - list in which relative exposures are collected
  • absSurf ([float]) - Absolute MS OR AS values
  • key (MS|AS) - MS or AS
Returns: [float]
rel - list of relative accessible surfaces with data from C-terminal residues appended.

__bulk(a, rel, absSurf, key, i)

source code 

Get relative exposures for everything else.
Parameters:
  • rel ([float]) - list in which relative exposures are collected
  • absSurf ([float]) - Absolute MS OR AS values
  • key (MS|AS) - MS or AS
Returns: [float]
rel - list of relative accessible surfaces with data from ' none-terminal residues appended.

Variables Details [hide private]

ranMS

Value:
{'CYS': {'C': 1.969, 'CB': 21.339, 'CA': 8.077, 'O': 14.038, 'N': 5.71
3, 'SG': 34.959}, 'GLN': {'C': 1.736, 'CB': 18.742, 'CA': 6.384, 'CG':
 20.672, 'O': 14.136, 'CD': 2.825, 'N': 7.409, 'NE2': 23.326, 'OE1': 1
4.894}, 'ILE': {'C': 1.151, 'CB': 7.933, 'CA': 4.369, 'O': 14.185, 'N'
: 5.428, 'CD1': 31.332, 'CG1': 17.690, 'CG2': 28.741}, 'SER': {'C': 2.
336, 'OG': 17.413, 'CB': 26.667, 'CA': 8.803, 'O': 13.894, 'N': 6.849}
, 'VAL': {'C': 1.332, 'CB': 7.877, 'CA': 6.509, 'O': 13.741, 'N': 4.78
6, 'CG1': 31.049, 'CG2': 30.663}, 'LYS': {'C': 1.722, 'CB': 18.077, 'C
...

ranAS

Value:
{'CYS': {'C': 0.833, 'CB': 34.358, 'CA': 7.768, 'O': 29.027, 'N': 5.15
9, 'SG': 76.311}, 'GLN': {'C': 0.694, 'CB': 28.846, 'CA': 3.896, 'CG':
 32.484, 'O': 28.716, 'CD': 2.467, 'N': 7.736, 'NE2': 54.470, 'OE1': 3
2.637}, 'ILE': {'C': 0.336, 'CB': 10.203, 'CA': 2.117, 'O': 26.670, 'N
': 4.723, 'CD1': 63.709, 'CG1': 32.543, 'CG2': 50.456}, 'SER': {'C': 1
.003, 'OG': 47.009, 'CB': 44.666, 'CA': 8.688, 'O': 29.511, 'N': 6.051
}, 'VAL': {'C': 0.491, 'CB': 9.140, 'CA': 5.240, 'O': 23.612, 'N': 2.4
22, 'CG1': 65.475, 'CG2': 59.022}, 'LYS': {'C': 0.713, 'CB': 27.111, '
...

ranMS_C

Value:
{'CYS': {'C': 4.901, 'OXT': 16.009, 'CB': 21.505, 'CA': 8.895, 'O': 15
.937, 'N': 5.493, 'SG': 32.718}, 'GLN': {'C': 4.268, 'OXT': 16.327, 'C
B': 18.696, 'CA': 6.661, 'CG': 21.508, 'O': 15.993, 'N': 6.289, 'CD': 
2.908, 'NE2': 23.350, 'OE1': 15.560}, 'ILE': {'C': 3.954, 'OXT': 15.89
5, 'CB': 7.210, 'CA': 6.836, 'O': 15.297, 'N': 5.218, 'CD1': 32.674, '
CG1': 17.185, 'CG2': 29.494}, 'SER': {'C': 4.935, 'OG': 17.498, 'CB': 
26.752, 'CA': 9.621, 'O': 15.997, 'N': 6.296, 'OXT': 16.009}, 'VAL': {
'C': 3.886, 'OXT': 16.344, 'CB': 8.237, 'CA': 6.639, 'O': 16.111, 'N':
...

ranMS_N

Value:
{'CYS': {'C': 1.881, 'CB': 20.689, 'CA': 12.751, 'O': 12.456, 'N': 17.
890, 'SG': 33.579}, 'GLN': {'C': 1.838, 'CB': 18.800, 'CA': 12.632, 'C
G': 18.923, 'O': 12.560, 'CD': 3.315, 'N': 17.352, 'NE2': 23.831, 'OE1
': 13.464}, 'ILE': {'C': 1.681, 'CB': 7.893, 'CA': 8.675, 'O': 13.221,
 'N': 18.819, 'CD1': 31.268, 'CG1': 17.636, 'CG2': 27.787}, 'SER': {'C
': 2.303, 'OG': 16.770, 'CB': 26.889, 'CA': 13.107, 'O': 13.152, 'N': 
19.013}, 'VAL': {'C': 1.649, 'CB': 8.327, 'CA': 10.304, 'O': 13.305, '
N': 18.515, 'CG1': 29.069, 'CG2': 30.586}, 'LYS': {'C': 2.076, 'CB': 1
...

ranAS_C

Value:
{'CYS': {'C': 3.576, 'OXT': 44.000, 'CB': 35.823, 'CA': 7.883, 'O': 40
.390, 'N': 3.953, 'SG': 63.386}, 'GLN': {'C': 2.560, 'OXT': 39.663, 'C
B': 23.902, 'CA': 3.636, 'CG': 35.848, 'O': 39.558, 'N': 5.031, 'CD': 
2.604, 'NE2': 52.310, 'OE1': 37.289}, 'ILE': {'C': 2.192, 'OXT': 38.99
0, 'CB': 6.897, 'CA': 4.449, 'O': 35.608, 'N': 3.047, 'CD1': 73.231, '
CG1': 27.316, 'CG2': 53.373}, 'SER': {'C': 3.562, 'OG': 44.874, 'CB': 
45.772, 'CA': 9.377, 'O': 40.102, 'N': 5.281, 'OXT': 44.024}, 'VAL': {
'C': 1.947, 'OXT': 40.714, 'CB': 10.749, 'CA': 4.843, 'O': 38.524, 'N'
...

ranAS_N

Value:
{'CYS': {'C': 1.431, 'CB': 38.159, 'CA': 19.289, 'O': 23.438, 'N': 43.
276, 'SG': 67.559}, 'GLN': {'C': 1.649, 'CB': 31.979, 'CA': 19.263, 'C
G': 23.964, 'O': 21.682, 'CD': 2.755, 'N': 38.957, 'NE2': 56.478, 'OE1
': 31.267}, 'ILE': {'C': 1.024, 'CB': 9.940, 'CA': 8.458, 'O': 24.997,
 'N': 42.475, 'CD1': 68.526, 'CG1': 33.941, 'CG2': 46.229}, 'SER': {'C
': 1.629, 'OG': 48.780, 'CB': 42.463, 'CA': 18.962, 'O': 26.451, 'N': 
43.920}, 'VAL': {'C': 0.936, 'CB': 10.647, 'CA': 12.837, 'O': 25.260, 
'N': 42.960, 'CG1': 52.342, 'CG2': 66.747}, 'LYS': {'C': 1.326, 'CB': 
...

test

Value:
Test()

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