annotate spring_package/Energy.py @ 40:06337927c198 draft

"planemo upload commit 68723d88e81923739538c34722bc9be164dd4646"
author guerler
date Sat, 23 Jan 2021 14:42:46 +0000
parents 172398348efd
children
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1 import math
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2 from os.path import dirname, realpath
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4 NTYPE = 21
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5 NDIST = 20
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6 NSCALE = 2.0
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8
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9 class Energy:
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10 def __init__(self):
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11 self.dfire = list()
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12 dirPath = dirname(realpath(__file__))
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13 with open("%s/Energy.data" % dirPath) as file:
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14 for line in file:
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15 self.dfire.append(float(line))
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17 def get(self, residuesA, residuesB):
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18 result = 0
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19 for atomA in residuesA:
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20 indexA = self.toResCode(atomA["alignedResidue"])
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21 for atomB in residuesB:
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22 indexB = self.toResCode(atomB["alignedResidue"])
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23 dist2 = ((atomA["x"] - atomB["x"]) ** 2 +
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24 (atomA["y"] - atomB["y"]) ** 2 +
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25 (atomA["z"] - atomB["z"]) ** 2)
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26 dist = int((math.sqrt(dist2) * NSCALE))
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27 if dist < NDIST:
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28 index = indexA * NTYPE * NDIST + indexB * NDIST + dist
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29 result = result + self.dfire[index]
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30 return result
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32 def getClashes(self, moleculeA, moleculeB, minDist=5.0):
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33 minDist = minDist ** 2
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34 clashes = 0
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35 chainA = list(moleculeA.calpha.keys())[0]
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36 chainB = list(moleculeB.calpha.keys())[0]
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37 calphaA = moleculeA.calpha[chainA]
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38 calphaB = moleculeB.calpha[chainB]
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39 lenA = len(calphaA.keys())
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40 lenB = len(calphaB.keys())
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41 if lenA > lenB:
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42 temp = calphaB
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43 calphaB = calphaA
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44 calphaA = temp
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45 lenA = len(calphaA.keys())
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46 lenB = len(calphaB.keys())
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47 for i in calphaA:
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48 atomA = calphaA[i]
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49 for j in calphaB:
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50 atomB = calphaB[j]
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51 dist2 = ((atomA["x"] - atomB["x"]) ** 2 +
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52 (atomA["y"] - atomB["y"]) ** 2 +
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53 (atomA["z"] - atomB["z"]) ** 2)
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54 if dist2 < minDist:
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55 clashes = clashes + 1
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56 break
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57 return clashes / float(lenA)
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59 def toResCode(self, seq):
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60 code = dict(A=0, C=1, D=2, E=3, F=4, G=5, H=6, I=7, K=8, L=9, M=10,
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61 N=11, P=12, Q=13, R=14, S=15, T=16, V=17, W=18, Y=19)
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62 return code[seq] if seq in code else 20