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comparison spring_package/Energy.py @ 17:c790d25086dc draft

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"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"
author guerler
date Wed, 28 Oct 2020 05:11:56 +0000
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16:16eb2acaaa20 17:c790d25086dc
1 import math
2
3 NTYPE = 21
4 NDIST = 20
5 NSCALE = 2.0
6
7 class Energy:
8 def __init__(self):
9 self.dfire = list()
10 with open("spring_package/dfire/dfire.txt") as file:
11 for index, line in enumerate(file):
12 self.dfire.append(float(line))
13
14 def get(self, moleculeA, moleculeB):
15 result = 0
16 chainA = list(moleculeA.calpha.keys())[0]
17 chainB = list(moleculeB.calpha.keys())[0]
18 for i in moleculeA.calpha[chainA]:
19 atomA = moleculeA.calpha[chainA][i]
20 indexA = self.toResCode(atomA["residue"])
21 for j in moleculeB.calpha[chainB]:
22 atomB = moleculeB.calpha[chainB][j]
23 indexB = self.toResCode(atomB["residue"])
24 dist2 = (atomA["x"] - atomB["x"]) ** 2 + (atomA["y"] - atomB["y"]) ** 2 + (atomA["z"] - atomB["z"]) ** 2
25 dist = int ((math.sqrt(dist2) * NSCALE))
26 if dist < NDIST:
27 index = indexA * NTYPE * NDIST + indexB * NDIST + dist
28 result = result + self.dfire[index]
29 return result
30
31 def toResCode (self, seq):
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,
33 ASN=11, PRO=12, GLN=13, ARG=14, SER=15, THR=16, VAL=17, TRP=18, TYR=19)
34 return code[seq] if seq in code else 20