annotate spring_package/Energy.py @ 22:acaff61a09b2 draft

"planemo upload commit 83cb18661a4c7839dbec8d42b6018ddc80defd8f-dirty"

import math

NTYPE = 21
NDIST = 20
NSCALE = 2.0

class Energy:
	def __init__(self):
		self.dfire = list()
		with open("spring_package/dfire/dfire.txt") as file:
			for index, line in enumerate(file):
				self.dfire.append(float(line))

	def get(self, moleculeA, moleculeB):
		result = 0
		chainA = list(moleculeA.calpha.keys())[0]
		chainB = list(moleculeB.calpha.keys())[0]
		for i in moleculeA.calpha[chainA]:
			atomA = moleculeA.calpha[chainA][i]
			indexA = self.toResCode(atomA["residue"])
			for j in moleculeB.calpha[chainB]:
				atomB = moleculeB.calpha[chainB][j]
				indexB = self.toResCode(atomB["residue"])
				dist2 = (atomA["x"] - atomB["x"]) ** 2 + (atomA["y"] - atomB["y"]) ** 2 + (atomA["z"] - atomB["z"]) ** 2
				dist = int ((math.sqrt(dist2) * NSCALE))
				if dist < NDIST:
					index = indexA * NTYPE * NDIST + indexB * NDIST + dist
					result = result + self.dfire[index]
		return result

	def toResCode (self, seq):
		code = dict(ALA=0, CYS=1, ASP=2, GLU=3, PHE=4, GLY=5, HIS=6, ILE=7, LYS=8, LEU=9, MET=10,
					ASN=11, PRO=12, GLN=13, ARG=14, SER=15, THR=16, VAL=17, TRP=18, TYR=19)
		return code[seq] if seq in code else 20