Python3 support

removes print statements without paranthesis and lambda unpacking (PEP3113)

FiveConf.py

@@ -72,8 +72,8 @@ def main(f, settings):
         WasAbove90 = False
         rotangle = 2*(0.5*pi-angle)
     OldAtomCoords = outAtom.GetVector()
-    print "Atom " + str(outAtom.GetAtomicNum()) + " will be rotated by " +\
-        str(rotangle*57.3) + ' degrees'
+    print("Atom " + str(outAtom.GetAtomicNum()) + " will be rotated by " +\
+        str(rotangle*57.3) + ' degrees')
     RotateAtom(outAtom, AxisAtoms[0], AxisAtoms[1], rotangle)
     angle2 = FindRotAngle(AxisAtoms[0], AxisAtoms[1], outAtom, norm)
 
@@ -82,7 +82,7 @@ def main(f, settings):
     if ((angle2 > 0.5*pi) and WasAbove90) or ((angle2 < 0.5*pi) and not WasAbove90):
         #Flip the sign of the rotation angle, restore the coords
         #and rotate the atom in the opposite direction
-        print "Atom was rotated the wrong way, switching the direction"
+        print("Atom was rotated the wrong way, switching the direction")
         rotangle = -rotangle
         outAtom.SetVector(OldAtomCoords)
         RotateAtom(outAtom, AxisAtoms[0], AxisAtoms[1], rotangle)
@@ -93,7 +93,7 @@ def main(f, settings):
             RotateAtom(atom, AxisAtoms[0], AxisAtoms[1], rotangle)
             RotatedAtoms.append(atom)
         else:
-            print "Atom already rotated, skipping"
+            print("Atom already rotated, skipping")
 
     obconversion.SetOutFormat("sdf")
     obconversion.WriteFile(obmol, f[:-4] + 'rot.sdf')
@@ -228,7 +228,7 @@ def LstSqPlane(atom1, atom2, atom3, atom4):
     # Inital guess of the plane
     [a0, b0, c0], d0 = FindPlane(atom1, atom2, atom3)
 
-    f = lambda (a, b, c, d): PlaneError([atom1, atom2, atom3, atom4], a, b, c, d)
+    f = lambda a: PlaneError([atom1, atom2, atom3, atom4], a[0], a[1], a[2], a[3])
     res = sciopt.minimize(f, (a0, b0, c0, d0), method='nelder-mead')
     plane = list(res.x)
 

Karplus.py

@@ -51,8 +51,8 @@ def Karplus(f, inputformat):
                 DihedralHs.append([atom.GetIdx()] + DihedNeighbours)                
 
     if len(DihedralHs)==0:
-        print "No dihedral protons found, Karplus J value prediction " + \
-            "impossible, quitting."
+        print("No dihedral protons found, Karplus J value prediction " + \
+            "impossible, quitting.")
         quit()
 
     Jmatrix, Jlabels = CalcJMatrix(obmol, DihedralHs)

TreeRenum.py

@@ -12,7 +12,7 @@ def FindAllPaths(molgraph, start, end, path=[]):
     if start == end:
         return [path]
     if start not in [x[0] for x in molgraph]:
-        print "No such node in graph"
+        print("No such node in graph")
         return []
     paths = []
     for node in molgraph[start-1][1:]:
@@ -26,7 +26,7 @@ def FindAllPaths(molgraph, start, end, path=[]):
 def FindTerminatingPaths(molgraph, start, trunk, path=[]):
     path = path + [start]
     if start not in [x[0] for x in molgraph]:
-        print "No such node in graph"
+        print("No such node in graph")
         return []
     paths = []
     for node in molgraph[start-1][1:]:
@@ -109,7 +109,7 @@ def TreeRenumSDF(f, ExpNMR):
         if anum == 6:
             NMRmap.append(['C' + str(atom), 'C' + str(i)])
         i += 1
-    print NMRmap
+    print(NMRmap)
     RenumNMR(ExpNMR, NMRmap)
 
 
@@ -118,7 +118,7 @@ def RenumNMR(ExpNMR, NMRmap):
     NMRfile = f.read(1000000)
     f.close()
 
-    print '\nOld NMR file:\n' + NMRfile
+    print('\nOld NMR file:\n' + NMRfile)
 
     #Replace old atom labels with new atom labels
     #tag replacements with '_' to avoid double replacement
@@ -131,7 +131,7 @@ def RenumNMR(ExpNMR, NMRmap):
     #Strip temporary udnerscore tags
     NMRfile = NMRfile.replace('_', '')
 
-    print '\nNew NMR file:\n' + NMRfile
+    print('\nNew NMR file:\n' + NMRfile)
     f = open(ExpNMR + 'r', 'w')
     f.write(NMRfile)
     f.close()