diff spring_package/Energy.py @ 17:c790d25086dc draft

"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_package/Energy.py	Wed Oct 28 05:11:56 2020 +0000
@@ -0,0 +1,34 @@
+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
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