Python3 support

Signed-off-by: Justin Lecher <jlec@gentoo.org>
Pymol-Scripts · Dec 7, 2015 · dbd3b1a · dbd3b1a
1 parent dc23f72
commit dbd3b1a
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Showing 3 changed files with 28 additions and 25 deletions.
diff --git a/modevectors.py b/modevectors.py
@@ -1,6 +1,7 @@
 '''
 See more here: http://www.pymolwiki.org/index.php/Modevectors
 '''
+from __future__ import print_function
 from pymol.cgo import *    # get constants
 from math import *
 from pymol import cmd
@@ -37,7 +38,7 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
     factor                   1.0               Float   Multiplies each mode vector length by a specified factor.
                                                        Values between 0 and 1 will decrease the relative mode vector length.
                                                        Values greater than 1 will increase the relative mode vector length.
-    notail                   0                 Integer Hides tails and only uses cones (porcupine plot) 
+    notail                   0                 Integer Hides tails and only uses cones (porcupine plot)
     """
 
     framefirst = cmd.get_model(first_obj_frame, first_state)
@@ -55,8 +56,8 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
 
     headrgb = headrgb.strip('" []()')
     tailrgb = tailrgb.strip('" []()')
-    hr, hg, hb = map(float, headrgb.split(','))
-    tr, tg, tb = map(float, tailrgb.split(','))
+    hr, hg, hb = list(map(float, headrgb.split(',')))
+    tr, tg, tb = list(map(float, tailrgb.split(',')))
 
     version = cmd.get_version()[1]
     arrow = []
@@ -138,10 +139,10 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
                     " ATMNUM " + str(atom.index)
 #				print current_atom
                 if 'current_atom' not in atom_lookup:
-                    print "\nError: " + current_atom + " from \""\
+                    print("\nError: " + current_atom + " from \""\
                           + last_obj_frame +\
-                          " \"is not found in \"" + first_obj_frame + "\"."
-                    print "\nPlease check your input and/or selections and try again."
+                          " \"is not found in \"" + first_obj_frame + "\".")
+                    print("\nPlease check your input and/or selections and try again.")
                     exit_flag = True
                     break
 
@@ -168,10 +169,10 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
     ###################################################
 
     if len(x2) != len(x1):
-        print "\nError: \"" + first_obj_frame +\
+        print("\nError: \"" + first_obj_frame +\
               "\" and \"" + last_obj_frame +\
-              "\" contain different number of residue/atoms."
-        print "\nPlease check your input and/or selections and try again."
+              "\" contain different number of residue/atoms.")
+        print("\nPlease check your input and/or selections and try again.")
         return
     else:
         # Continue with representing modevectors!
@@ -232,7 +233,7 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
         intfactor = int(factor)
         if version < 1.1:  # Version >= 1.1 has cone primitive
             for i in range(100, 0, -1):  # i=100 is tip of cone
-                print i
+                print(i)
                 t1 = seg * i
                 t2 = seg * (i + 1)
                 radius = arrow_head_radius * (1.0 - i / (100.0))  # Radius of each disc that forms cone
@@ -257,13 +258,13 @@ def modevectors(first_obj_frame, last_obj_frame, first_state=1, last_state=1, ou
 
     if stat == "show":
         natoms = skipcounter + keepcounter
-        print "\nTotal number of atoms = " + str(natoms)
-        print "Atoms skipped = " + str(skipcounter)
+        print("\nTotal number of atoms = " + str(natoms))
+        print("Atoms skipped = " + str(skipcounter))
         if keepcounter - cutoff_counter > 0:
-            print "Atoms counted = " + str(keepcounter - cutoff_counter) + " (see PyMOL object \"" + objectname + "\")"
+            print("Atoms counted = " + str(keepcounter - cutoff_counter) + " (see PyMOL object \"" + objectname + "\")")
         else:
-            print "Atoms counted = " + str(keepcounter - cutoff_counter) + " (Empty CGO object not loaded)"
-        print "Atoms cutoff  = " + str(cutoff_counter)  # Note that cutoff occurs AFTER skipping!
+            print("Atoms counted = " + str(keepcounter - cutoff_counter) + " (Empty CGO object not loaded)")
+        print("Atoms cutoff  = " + str(cutoff_counter))  # Note that cutoff occurs AFTER skipping!
     if keepcounter - cutoff_counter > 0:
         cmd.delete(objectname)
         cmd.load_cgo(arrow, objectname)  # Ray tracing an empty object will cause a segmentation fault.  No arrows = Do not display in PyMOL!!!

diff --git a/movie_color_fade.py b/movie_color_fade.py
@@ -16,6 +16,7 @@
 '''
 #-------------------------------------------------------------------------------
 # IMPORT
+from __future__ import print_function
 from pymol import cmd
 from pymol import stored
 #-------------------------------------------------------------------------------
@@ -72,7 +73,7 @@ def movie_color_fade(
     movie_color_fade auto,white,auto,skyblue,ss s
     movie_color_fade auto,white,auto,red,ss h
     movie_color_fade auto,white,auto,grey,ss l+""
-    #####    
+    #####
 
 SEE ALSO
 
@@ -93,7 +94,7 @@ def movie_color_fade(
         endframe = 1
 
     if startframe == endframe:
-        print "start == end"
+        print("start == end")
         return False
 
     if startframe > endframe:
@@ -106,14 +107,14 @@ def movie_color_fade(
         endcolor = cmd.get_color_tuple(endcolor)
         diffcolor = [b - a for a, b in zip(startcolor, endcolor)]
     except:
-        print "Input error - please provide regular colors"
+        print("Input error - please provide regular colors")
         return False
 
     for frame in range(startframe, endframe + 1):
         # calculate intermediates
         frac = float(frame - startframe) / (endframe - startframe)
         endcolor = [a * frac for a in diffcolor]
-        endcolor = map(sum, zip(startcolor, endcolor))
+        endcolor = list(map(sum, list(zip(startcolor, endcolor))))
         colorname = selection + "_" + str(frame)
         # define new color
         cmd.set_color(colorname, endcolor)

diff --git a/nmr_cnstr.py b/nmr_cnstr.py
@@ -17,6 +17,7 @@
 ##############################################################################################################
 '''
 
+from __future__ import print_function
 
 def upl(fname):
 
@@ -26,7 +27,7 @@ def upl(fname):
 #
     while upl != '':
 
-        print upl, i
+        print(upl, i)
         cns = string.split(upl)
         cmd.dist('upl' + str(i), 'i. ' + cns[0] + ' & n. ' + cns[2], 'i. ' + cns[3] + ' & n. ' + cns[5])
         upl = f.readline()
@@ -44,21 +45,21 @@ def cns(fname):
     f = open(fname, 'r')
     i = 1
     upl = f.readline()
-    print upl, i
+    print(upl, i)
     while upl != '':
         if upl == '\n':
             upl = f.readline()
             continue
         cns = string.split(upl)
-        print cns, i
+        print(cns, i)
         if cns[0] == 'assign':
-            print 'CNS'
+            print('CNS')
             if cns[5] == 'HB*':
-                print 'CNS***'
+                print('CNS***')
             cmd.dist('upl' + str(i), 'i. ' + cns[2] + ' & n. ' + cns[5], 'i. ' + cns[7] + ' & n. ' + cns[10])
         i += 1
         upl = f.readline()
-        print '*' + upl + '*', i
+        print('*' + upl + '*', i)
 
     f.close()
     cmd.set('dash_gap', 0.05)