optimize a number of functions

- Major optimization of the put_atom_in_box() function.
- Major optimization of the protein_precheck() function.
- Minor optimization in radial_volume_desolvation()
- Optimization in top_up() to scale for large structures.

propka/bonds.py

@@ -370,7 +370,7 @@ class bondmaker:
         for x in range(self.no_box_x):
             for y in range(self.no_box_y):
                 for z in range(self.no_box_z):
-                    self.boxes[self.box_key(x,y,z)] = []
+                    self.boxes[(x,y,z)] = []
 
         # put atoms into boxes
         for atom in atoms:
@@ -380,10 +380,8 @@ class bondmaker:
             self.put_atom_in_box(x,y,z,atom)
 
         # assign bonds
-        keys = self.boxes.keys()
-        for key in keys:
-            self.find_bonds_for_atoms(self.boxes[key])
-
+        for key, value in self.boxes.items():
+            self.find_bonds_for_atoms(value)
 
 
         return
@@ -391,21 +389,21 @@ class bondmaker:
     def put_atom_in_box(self,x,y,z,atom):
         # atom in the x,y,z box and the up to 7 neighboring boxes on
         # one side of the x,y,z box in each dimension
+
         for bx in [x,x+1]:
             for by in [y,y+1]:
                 for bz in [z,z+1]:
-                    key = self.box_key(bx,by,bz)
-                    if key in self.boxes.keys():
+                    key = (bx,by,bz)
+                    try:
                         self.boxes[key].append(atom)
+                    except KeyError:
+                        # No box exists for this coordinate
+                        pass
 
                         #print(atom,'->',key,':',len(self.boxes[key]))
 
         return
 
-    def box_key(self, x, y, z):
-        return '%d-%d-%d'%(x,y,z)
-
-
     def has_bond(self, atom1, atom2):
         if atom1 in atom2.bonded_atoms or atom2 in atom1.bonded_atoms:
             return True