annotate spring_package/Energy.py @ 17:c790d25086dc draft

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author guerler
date Wed, 28 Oct 2020 05:11:56 +0000
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1 import math
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2
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3 NTYPE = 21
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4 NDIST = 20
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5 NSCALE = 2.0
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6
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7 class Energy:
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8 def __init__(self):
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9 self.dfire = list()
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10 with open("spring_package/dfire/dfire.txt") as file:
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11 for index, line in enumerate(file):
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12 self.dfire.append(float(line))
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13
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14 def get(self, moleculeA, moleculeB):
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15 result = 0
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16 chainA = list(moleculeA.calpha.keys())[0]
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17 chainB = list(moleculeB.calpha.keys())[0]
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18 for i in moleculeA.calpha[chainA]:
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19 atomA = moleculeA.calpha[chainA][i]
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20 indexA = self.toResCode(atomA["residue"])
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21 for j in moleculeB.calpha[chainB]:
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22 atomB = moleculeB.calpha[chainB][j]
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23 indexB = self.toResCode(atomB["residue"])
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24 dist2 = (atomA["x"] - atomB["x"]) ** 2 + (atomA["y"] - atomB["y"]) ** 2 + (atomA["z"] - atomB["z"]) ** 2
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25 dist = int ((math.sqrt(dist2) * NSCALE))
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26 if dist < NDIST:
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27 index = indexA * NTYPE * NDIST + indexB * NDIST + dist
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28 result = result + self.dfire[index]
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29 return result
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30
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31 def toResCode (self, seq):
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32 code = dict(ALA=0, CYS=1, ASP=2, GLU=3, PHE=4, GLY=5, HIS=6, ILE=7, LYS=8, LEU=9, MET=10,
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33 ASN=11, PRO=12, GLN=13, ARG=14, SER=15, THR=16, VAL=17, TRP=18, TYR=19)
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34 return code[seq] if seq in code else 20