/usr/lib/python2.7/dist-packages/cogent/data/energy_params.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 | #!/usr/bin/env python
"""EnergyParams class and instances of entropy and enthalpy params.
The enthalpy and entropy params for the 10 Watson-Crick nearest-neighbor
interactions, initiation corrections, and symmetry corrections
are taken from SantaLucia, PNAS vol 95 1460-1465
GC_INIT is the initiation parameter for duplexes that contain AT LEAST ONE
GC base pair, while AT_INIT is the initiation parameter for duplexes that
contain ONLY AT base pairs. (quoted from SantaLucia, Allawi, and Seneviratne,
Biochemistry, 1996, 3555-3562.)
The SYM term is added into the entropy or enthalpy calculation IFF the
sequence is self-complementary (seq = revComp of seq)
"""
__author__ = "Amanda Birmingham"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Amanda Birmingham", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Amanda Birmingham"
__email__ = "amanda.birmingham@thermofisher.com"
__status__ = "Production"
class EnergyParams(object):
"""A data structure to hold parameters used in energy calculations"""
def __init__(self, nearest_neighbor_vals, gc_init, at_init, sym_correct):
"""Store the input params for later reference
nearest_neighbor_vals: a dictionary or dictionary-castable object
keyed by each nearest-neighbor pair and holding a value for each.
gc_init: a floating-point castable value holding the initiation
parameter for duplexes that contain AT LEAST ONE GC base pair
at_init: a floating-point castable value holding the initiation
parameter for duplexes that contain ONLY AT base pairs
sym_correct: a floating-point castable value that is added into the
calculation if a sequence is self-complementary
"""
self.nearestNeighbors = dict(nearest_neighbor_vals)
self.gcInit = float(gc_init)
self.atInit = float(at_init)
self.symCorrection = float(sym_correct)
#end __init__
#end EnergyParams
#--------------------------
#Enthalpies are in kcal/mol, assumed to be salt concentration independent
_NN_ENTHALPIES = { "AA":-7.9, "TT":-7.9, "AT":-7.2, "TA":-7.2, \
"CA":-8.5, "TG":-8.5, "GT":-8.4, "AC":-8.4, \
"CT":-7.8, "AG":-7.8, "GA":-8.2, "TC":-8.2, \
"CG":-10.6, "GC":-9.8, "GG":-8.0, "CC":-8.0}
_ENTHALPY_GC_INIT = 0.1
_ENTHALPY_AT_INIT = 2.3
_ENTHALPY_SYM = 0
#--------------------------
#--------------------------
#Entropies are in cal/Kelvin*mol, at 1 M NaCl
_NN_ENTROPIES = { "AA":-22.2, "TT":-22.2, "AT":-20.4, "TA":-21.3, \
"CA":-22.7, "TG":-22.7, "GT":-22.4, "AC":-22.4, \
"CT":-21.0, "AG":-21.0, "GA":-22.2, "TC":-22.2, \
"CG":-27.2, "GC":-24.4, "GG":-19.9, "CC":-19.9}
_ENTROPY_GC_INIT = -2.8
_ENTROPY_AT_INIT = 4.1
_ENTROPY_SYM = -1.4
#--------------------------
#--------------------------
#Module level public EnergyParams instances (one for entropy, one for energy)
ENTHALPY_PARAMS = EnergyParams(_NN_ENTHALPIES,_ENTHALPY_GC_INIT, \
_ENTHALPY_AT_INIT, _ENTHALPY_SYM)
ENTROPY_PARAMS = EnergyParams(_NN_ENTROPIES, _ENTROPY_GC_INIT, \
_ENTROPY_AT_INIT, _ENTROPY_SYM)
#--------------------------
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