diff spring_package/Energy.py @ 37:0be0af9e695d draft

"planemo upload commit c716195a2cc1ed30ff8c4936621091296a93b2fc"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spring_package/Energy.py	Wed Nov 25 14:35:35 2020 +0000
@@ -0,0 +1,35 @@
+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 line in 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