Backported PROPKA code base to Python2.

Now this same code can be run with either Python2.7 or Python3.

Source/bonds.py

@@ -1,3 +1,4 @@
+from __future__ import division
 import pickle,sys,os,math,Source.calculations
 
 
@@ -350,9 +351,9 @@ class bondmaker:
         #print('z range: [%6.2f;%6.2f] %6.2f'%(zmin,zmax,zlen))
         
         # how many boxes do we need in each dimension?
-        self.no_box_x = max(1, math.ceil(xlen/box_size))
-        self.no_box_y = max(1, math.ceil(ylen/box_size))
-        self.no_box_z = max(1, math.ceil(zlen/box_size))
+        self.no_box_x = max(1, int(math.ceil(xlen/box_size)))
+        self.no_box_y = max(1, int(math.ceil(ylen/box_size)))
+        self.no_box_z = max(1, int(math.ceil(zlen/box_size)))
 
         #print('No. box x: %6.2f'%self.no_box_x)
         #print('No. box y: %6.2f'%self.no_box_y)

Source/calculations.py

@@ -1,5 +1,5 @@
 
-
+from __future__ import division
 import math, Source.protonate, Source.bonds,copy, sys
 
 

Source/conformation_container.py

@@ -2,6 +2,7 @@
 # Container for molecular conformations
 #
 
+from __future__ import division
 import Source.group, Source.determinants, Source.determinant, Source.ligand, Source.output, Source.coupled_groups, functools
 
 class Conformation_container:

Source/coupled_groups.py

@@ -1,4 +1,5 @@
 
+from __future__ import division
 import math, Source.output, Source.group, Source.lib, itertools
 
 

Source/group.py

@@ -2,6 +2,7 @@
 # Class for storing groups important for propka calculations
 #
 
+from __future__ import division
 import Source.ligand, Source.determinant, Source.ligand_pka_values, math, Source.protonate
 
 my_protonator = Source.protonate.Protonate(verbose=False)

Source/molecular_container.py

@@ -3,7 +3,7 @@
 # Molecular container for storing all contents of pdb files 
 #
 #
-
+from __future__ import division
 import os, Source.pdb, sys, Source.version, Source.output, Source.conformation_container, Source.group, Source.lib
 
 class Molecular_container:

Source/protonate.py

@@ -1,5 +1,6 @@
 #!/usr/bin/python
 
+from __future__ import division
 from Source.vector_algebra import *
 import Source.bonds, Source.pdb, Source.atom
 

Tests/runtest.py

@@ -4,6 +4,7 @@
 
 from subprocess import call
 import os, re
+import sys
 
 pdbs = ['1FTJ-Chain-A',
         '1HPX',
@@ -14,7 +15,7 @@ for pdb in pdbs:
   print('RUNNING '+pdb)
 
   # Run pka calculation
-  call(['../propka.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
+  call([sys.executable, '../propka.py','pdb/'+pdb+'.pdb'], stdout = open(pdb+'.out', 'w+'))
 
   # Test pka predictiona
   result = open('results/'+pdb+'.dat','r')