misc

Author: almarashi95

PolymerChain.py

@@ -610,7 +610,7 @@ def solvate(
         #######################################################################################################
         f = open("tmp.inp", "w")
         f.write(
-            f"dimension chsize {int(chsize)}\nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
+            f"dimension chsize {int(chsize)} \nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
         )
         f.write(f"open unit 1 card name {self.id.lower()}.psf\n")
         f.write(f"read psf card unit 1 \n")
@@ -671,7 +671,7 @@ def solvate(
         print("invoking charmm-process")
         f = open("tmp.inp", "w")
         f.write(
-            f"dimension chsize {int(chsize)}\nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
+            f"dimension chsize {int(chsize)} \nioformat extended\nstream {self.toppar}\nset parall {n_proc}\n"
         )
         f.write(
             f"open unit 1 card name {self.id.lower()}_in_{solvent_res.lower()}.psf\n"

misc.py

@@ -92,6 +92,35 @@ def solvation_coordinates(x, y, z, solvent_res, atoms):
     return "slvnt.crd"
 
 
+def fsolvation_coordinates(x, y, z, solvent_res, atoms):
+    # for now only works for water
+    coords = product(x, y, z)
+    f = open("slvnt.crd", "w")
+    f.write("* NONE *\n")
+    f.write(f"*  DATE {date.today()} CREATED BY TEAPUN\n*\n")
+    f.write(f"     {len(list(coords))*len(atoms)}  EXT\n")
+    coords = product(x, y, z)
+    ctr1 = 1
+    for ctr, c in enumerate(coords):
+        x = c[0]
+        y = c[1]
+        z = c[2]
+        f.write(
+            f"{ctr1:10d}{ctr+1:10d}  {solvent_res:<8.8s}  {atoms[0]:<8.8s}{x+1:20.10f}{y:20.10f}{z+1:20.10f}  {solvent_res:<8.8s}  {ctr+1:<8d}0.0000000000\n"
+        )
+        ctr1 += 1
+        f.write(
+            f"{ctr1:10d}{ctr+1:10d}  {solvent_res:<8.8s}  {atoms[1]:<8.8s}{x:20.10f}{y+1:20.10f}{z+1:20.10f}  {solvent_res:<8.8s}  {ctr+1:<8d}0.0000000000\n"
+        )
+        ctr1 += 1
+        f.write(
+            f"{ctr1:10d}{ctr+1:10d}  {solvent_res:<8.8s}  {atoms[2]:<8.8s}{x:20.10f}{y:20.10f}{z:20.10f}  {solvent_res:<8.8s}  {ctr+1:<8d}0.0000000000\n"
+        )
+        ctr1 += 1
+    f.close()
+    return "slvnt.crd"
+
+
 def pack_system(
     polymerchainpdb,
     n,