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.

Tests/pkacalc_test.py

@@ -7,7 +7,7 @@ import unittest
 
 # Setting this up as a direct translation of the original runtest.py script
 # that will be run as part of 'python setup.py test'. This takes on the
-# order of 30s to run.
+# order of 10s to run.
 
 class SystemTest(unittest.TestCase):
     """

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, value in self.boxes.items():
-        for key in keys:
+            self.find_bonds_for_atoms(value)
-            self.find_bonds_for_atoms(self.boxes[key])
-
 
 
         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)
+                    key = (bx,by,bz)
-                    if key in self.boxes.keys():
+                    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

propka/calculations.py

@@ -364,12 +364,11 @@ def radial_volume_desolvation(parameters, group):
         # desolvation
         if sq_dist < parameters.desolv_cutoff_squared:
             # use a default relative volume of 1.0 if the volume of the element is not found in parameters
-            dv = 1.0
-            if atom.element in parameters.VanDerWaalsVolume.keys():
-                dv = parameters.VanDerWaalsVolume[atom.element]
             # insert check for methyl groups
             if atom.element == 'C' and atom.name not in ['CA','C']:
                 dv = parameters.VanDerWaalsVolume['C4']
+            else:
+                dv = parameters.VanDerWaalsVolume.get(atom.element, 1.0)
 
             dv_inc = dv/max(min_distance_4th, sq_dist*sq_dist)
 #            dv_inc = dv/(sq_dist*sq_dist) - dv/(parameters.desolv_cutoff_squared*parameters.desolv_cutoff_squared)

propka/conformation_container.py

@@ -390,19 +390,12 @@ class Conformation_container:
 
     def top_up(self, other):
         """ Tops up self with all atoms found in other but not in self """
+        my_residue_labels = { a.residue_label for a in self.atoms }
         for atom in other.atoms:
-            if not self.have_atom(atom):
+            if not atom.residue_label in my_residue_labels:
                 self.copy_atom(atom)
         return
 
-    def have_atom(self, atom):
-        res = False
-        for a in self.atoms:
-            if a.residue_label == atom.residue_label:
-                res = True
-                break
-        return res
-
     def find_group(self, group):
         for g in self.groups:
             if g.atom.residue_label == group.atom.residue_label:

propka/pdb.py

@@ -50,11 +50,17 @@ def protein_precheck(conformations, names):
     for name in names:
         atoms = conformations[name].atoms
 
-        res_ids = []
+        # Group the atoms by their residue:
-        [res_ids.append(resid_from_atom(a)) for a in atoms if not res_ids.count(resid_from_atom(a))]
+        atoms_by_residue = {}
+        for a in atoms:
+            if a.element != 'H':
+                res_id = resid_from_atom(a)
+                try:
+                    atoms_by_residue[res_id].append(a)
+                except KeyError:
+                    atoms_by_residue[res_id] = [a]
 
-        for res_id in res_ids:
+        for res_id, res_atoms in atoms_by_residue.items():
-            res_atoms = [a for a in atoms if resid_from_atom(a) == res_id and a.element != 'H']
             resname = res_atoms[0].resName
             residue_label = '%3s%5s'%(resname, res_id)