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class RotTable:
"""Represents the rotation table"""
__ORIGINAL_ROT_TABLE = {\
"AA": [35.62, 7.2, -154, 0.06, 0.6, 0],\
"AC": [34.4, 1.1, 143, 1.3, 5, 0],\
"AG": [27.7, 8.4, 2, 1.5, 3, 0],\
"AT": [31.5, 2.6, 0, 1.1, 2, 0],\
"CA": [34.5, 3.5, -64, 0.9, 34, 0],\
"CC": [33.67, 2.1, -57, 0.07, 2.1, 0],\
"CG": [29.8, 6.7, 0, 1.1, 1.5, 0],\
"CT": [27.7, 8.4, -2, 1.5, 3, 0],\
"GA": [36.9, 5.3, 120, 0.9, 6, 0],\
"GC": [40, 5, 180, 1.2, 1.275, 0],\
"GG": [33.67, 2.1, 57, 0.07, 2.1, 0],\
"GT": [34.4, 1.1, -143, 1.3, 5, 0],\
"TA": [36, 0.9, 0, 1.1, 2, 0],\
"TC": [36.9, 5.3, -120, 0.9, 6, 0],\
"TG": [34.5, 3.5, 64, 0.9, 34, 0],\
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"TT": [35.62, 7.2, 154, 0.06, 0.6, 0]\
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__CORRESPONDANCE = {\
"AC": "GT",\
"AG": "CT",\
"AT": "AT",\
"CA": "TG",\
"CG": "CG",\
"CT": "AG",\
"GA": "TC",\
"GC": "GC",\
"GT": "AC",\
"TA": "TA",\
"TC": "GA",\
"TG": "CA",\
__SOUS_CORRESPONDANCE = {\
"AA": "TT",\
"AC": "GT",\
"AG": "CT",\
"AT": "AT",\
"CA": "TG",\
"CC": "GG",\
"CG": "CG",\
"GA": "TC",\
"GC": "GC",\
"TA": "TA"\
}
# get the angles in each axis (x, y, z), considering the deviation
self.rot_table[dinucleotide] = RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][:3]
# get a random deviation, considering the "limits" given in the last 3 columns
# of __ORIGINAL_ROT_TABLE
delta = numpy.random.uniform(low = -RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3], high= RotTable.__ORIGINAL_ROT_TABLE[dinucleotide][i+3])
self.rot_table[dinucleotide][i] += delta
self.rot_table[RotTable.__SOUS_CORRESPONDANCE[dinucleotide]][i] += delta
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def corr(self):
return self.__CORRESPONDANCE
###################
# WRITING METHODS #
###################
#table = RotTable()
#table.rot_table["AA"] --> [35.62, 7.2, -154]
###################
# READING METHODS #
###################
def getTwist(self, dinucleotide):