Python 3 fixes

async, universal_newlines, string

Author: speleo3

nmr_cnstr.py

@@ -28,7 +28,7 @@ def upl(fname):
     while upl != '':
 
         print(upl, i)
-        cns = string.split(upl)
+        cns = upl.split()
         cmd.dist('upl' + str(i), 'i. ' + cns[0] + ' & n. ' + cns[2], 'i. ' + cns[3] + ' & n. ' + cns[5])
         upl = f.readline()
         i += 1
@@ -50,7 +50,7 @@ def cns(fname):
         if upl == '\n':
             upl = f.readline()
             continue
-        cns = string.split(upl)
+        cns = upl.split()
         print(cns, i)
         if cns[0] == 'assign':
             print('CNS')

plugins/Caver2_1_2.py

@@ -509,7 +509,7 @@ def execute(self, result):
                 return
             elif not os.path.exists(outdir):
                 self.CreateDirectory(outdir)
-            self.stdamString = string.join(self.stdam_list, "+")
+            self.stdamString = "+".join(self.stdam_list)
             # jen to zaskrtnute
             generatedString = ""
             for key in self.s:
@@ -696,7 +696,7 @@ def containsValue(self, array, value):
         return 0
 
     def stdamMessage(self):
-        Pmw.MessageDialog(self.parent, title='Information', message_text='AA: Standard amino acids: \n ' + string.join(self.stdam_list, ", "))
+        Pmw.MessageDialog(self.parent, title='Information', message_text='AA: Standard amino acids: \n ' + ", ".join(self.stdam_list))
 
     def inputAnalyseWrap(self, args):
             # print self.listbox1.curselection()[0] # aby to fungovalo, musi byt bindnute na <<ListboxSelect>>

plugins/annocryst.py

@@ -18,7 +18,6 @@
 
 import Pmw
 import sys
-import string
 import webbrowser
 from pymol import cmd
 from xml.dom.minidom import parseString
@@ -334,7 +333,7 @@ def openRemote(self, pdbURL=''):
             httpRequest = urllib2.Request(url=pdbURL)
             pdbHttpHandle = urllib2.urlopen(httpRequest)
             pdbStr = pdbHttpHandle.read()
-            modelName = string.split(string.split(str(pdbURL), "/")[-1], ".")[0]
+            modelName = str(pdbURL).split("/")[-1].split(".")[0]
             cmd.read_pdbstr(pdbStr, modelName)
             self.status.setvalue(modelName + " loaded")
             self.loadedModels[modelName] = pdbURL
@@ -916,18 +915,18 @@ def select(self, event=None):
             self.annotationservice.selectedText = text
             # notify annotationservice to highlight context in graphical view
             if self.item.label == "context":
-                contextsplit = string.split(text, ";")
+                contextsplit = text.split(";")
                 if len(contextsplit) > 0:
                     view = contextsplit[0]
-                    view = string.replace(view, "view:", "")
-                    view = string.split(view, ",")
+                    view = view.replace("view:", "")
+                    view = view.split(",")
                     viewfloats = []
                     for v in view:
                         viewfloats.append(float(v))
                 if len(contextsplit) > 1:
                     context = contextsplit[1]
                     context = context.replace("ids:", "")
-                    contextids = string.split(context, ",")
+                    contextids = context.split(",")
                 # print "context: " + repr(contextids)
                 # print "view: " + repr(view)
                 self.annotationservice.selectAnnotation(contextids, view)

plugins/apbsplugin.py

@@ -143,7 +143,6 @@
 import os
 import math
 import re
-import string
 import sys
 
 if sys.version_info[0] < 3:
@@ -279,7 +278,7 @@ def verify(name, f):
     searchDirs.append(os.path.join("/sw", "share", "apbs-mpi-lammpi", "tools", "manip"))
     searchDirs.append(os.path.join("/usr", "local", "share", "tools", "manip"))
 
-    searchDirs.extend(string.split(os.environ["PATH"], ":"))
+    searchDirs.extend(os.environ["PATH"].split(":"))
     searchDirs.append(os.path.join("/usr", "local", "bin"))
     searchDirs.append(os.path.join("/opt", "local", "bin"))
     searchDirs.append(os.path.join("/sw", "bin"))

plugins/bnitools.py

@@ -1141,7 +1141,7 @@ def bni_fetch(parent, typ="pdb"):
                 typ = ["2fofc", "fofc"]
             for source in typ:
                 print("# Fetch %s of %s" % (source, code))
-                cmd.fetch(code, async=0, type=source)
+                cmd.fetch(code, type=source)
             if __pymol_version__ < 1.4:
                 print("# Pymol < 1.4 detected.(v. %s)" % __pymol_version__)
                 print("# Maps are mixed up. FoFc is 2FoFc and FoFc is 2FoFc.")
@@ -1199,7 +1199,7 @@ def bni_fetch(parent, typ="pdb"):
         for code in PDBcode:
             for source in typ:
                 print("# Fetch %s of %s" % (source, code))
-                cmd.fetch(code, async=0, type=source)
+                cmd.fetch(code, type=source)
                 if source == "pdb1":
                     cmd.split_states(code)
                     cmd.delete(code)
@@ -1290,10 +1290,9 @@ def combine_sele(selections=None, check="enabled", name="sele"):
     print("# BNI - Tools v. %s" % __version__)
     print("# Combined selections: %s" % sele_names)
     print("# to (%s)" % name)
-def _set_bni_ray(setting="set", app=None, async=1):
+def _set_bni_ray(setting="set", app=None, async_=1):
     '''Run sidebar input
     '''
-    async = int(_remove_brakets(async))
     width = 100
     dpi = 200
     width_unit = "mm"
@@ -1367,9 +1366,9 @@ def _set_bni_ray(setting="set", app=None, async=1):
         dpi = 1200
         print("# width: %s %s" % (width, width_unit))
         print("# resolution: %s dpi" % dpi)
-    if async == 1:
+    if async_ == 1:
         print("# Ray is working in the background")
-    bni_ray(width, width_unit=width_unit, dpi=dpi, async=async)
+    bni_ray(width, width_unit=width_unit, dpi=dpi, {'async': async_})
 def bni_ray(width, name_png=None, dpi="300", width_unit="cm", **arg):
     '''Ray specified with dpi and width.
     USAGE: bni_ray(width,dpi="300",width_unit="cm",name_png=None,**arg)

plugins/emovie.py

@@ -33,7 +33,6 @@
     from tkinter import messagebox as tkMessageBox
     from tkinter import filedialog as tkFileDialog
 
-import string
 import os
 import pickle
 import time
@@ -1473,7 +1472,7 @@ def __init__(self, root, title="Save"):
         # split the string using "." as the delimiter string and check if last entry is "pse" or "emov" if so, remove them
         # if not, add emov to string
 
-        splitFileName = string.split(fileName, ".")
+        splitFileName = fileName.split(".")
         if splitFileName[len(splitFileName) - 1] == "pse":
             fileName = fileName[:-4]
         elif splitFileName[len(splitFileName) - 1] == "emov":
@@ -1555,7 +1554,7 @@ def apply(self):
         # split the string using "." as the delimiter string and check if last entry is "pse" or "emov" if so, remove them
         # if not, add emov to string
 
-        splitFileName = string.split(fileName, ".")
+        splitFileName = fileName.split(".")
         if splitFileName[len(splitFileName) - 1] == "pse":
             fileName = fileName[:-4]
         elif splitFileName[len(splitFileName) - 1] == "emov":
@@ -1649,7 +1648,7 @@ def __init__(self, root, title="Load"):
         # if it does not have an extension of either .pse or .emov, we will use it as is
         # if it has an extenstion of either .pse or .emov, we will strip away that extension
 
-        splitFileName = string.split(fileName, ".")
+        splitFileName = fileName.split(".")
 
         if splitFileName[len(splitFileName) - 1] == "emov":
             fileName = fileName[:-5]
@@ -1745,7 +1744,7 @@ def apply(self):
         # if it does not have an extension of either .pse or .emov, we will use it as is
         # if it has an extenstion of either .pse or .emov, we will strip away that extension
 
-        splitFileName = string.split(fileName, ".")
+        splitFileName = fileName.split(".")
 
         if splitFileName[len(splitFileName) - 1] == "emov":
             fileName = fileName[:-5]
@@ -2447,8 +2446,8 @@ def cmpStoryBoard(a, b):
     elif b[0] == "-":
         return 1
 
-    x = string.split(a[0], "-")
-    y = string.split(b[0], "-")
+    x = a[0].split("-")
+    y = b[0].split("-")
 
     xStartFrame = int(x[0])
     yStartFrame = int(y[0])
@@ -2520,7 +2519,7 @@ def getActionValues(action):
 
     # first we get the startFrame and the endFrame
     frames = action[0]
-    t = string.split(frames, "-")
+    t = frames.split("-")
     startFrame = t[0]  # the first token is the start frame
     if len(t) == 2:
         endFrame = t[1]
@@ -2537,24 +2536,24 @@ def getActionValues(action):
         return result
     elif actionType == "Morph":
         info = action[2]
-        q = string.split(info, ";")
-        p = string.split(q[0], " ")
-        r = string.split(q[1], " ")
+        q = info.split(";")
+        p = q[0].split(" ")
+        r = q[1].split(" ")
         morphName = p[len(p) - 1]
         direction = r[len(r) - 1]
 
         result = (startFrame, endFrame, actionType, morphName, direction)
         return result
     elif actionType == "Scene Set":
         info = action[2]
-        q = string.split(info, " ")
+        q = info.split(" ")
         sceneName = q[len(q) - 1]
 
         result = (startFrame, endFrame, actionType, sceneName)
         return result
     elif actionType == "Zoom":
         info = action[2]
-        q = string.split(info, " ")
+        q = info.split(" ")
         if len(q) == 2:
             amtZoom = q[1]
         else:
@@ -2569,21 +2568,21 @@ def getActionValues(action):
         return result
     elif actionType == "Rotation":
         info = action[2]
-        q = string.split(info, ";")
-        p = string.split(q[0], " ")
-        r = string.split(q[1], " ")
+        q = info.split(";")
+        p = q[0].split(" ")
+        r = q[1].split(" ")
         axis = p[1]
         degrees = r[2]
 
         result = (startFrame, endFrame, actionType, axis, degrees)
         return result
     elif actionType == "Fading":
         info = action[2]
-        q = string.split(info, ";")
-        p = string.split(q[0], " ")
-        r = string.split(q[1], " ")
-        s = string.split(q[2], " ")
-        u = string.split(q[3], " ")
+        q = info.split(";")
+        p = q[0].split(" ")
+        r = q[1].split(" ")
+        s = q[2].split(" ")
+        u = q[3].split(" ")
         molecule = p[len(p) - 1]
         representation = r[len(r) - 1]
         fadeFrom = s[len(s) - 1]
@@ -2596,10 +2595,10 @@ def getActionValues(action):
         return result
     elif actionType == "Worm":
         info = action[2]
-        q = string.split(info, ";")
-        p = string.split(q[0], " ")
-        r = string.split(q[1], " ")
-        s = string.split(r[len(r) - 1], "-")
+        q = info.split(";")
+        p = q[0].split(" ")
+        r = q[1].split(" ")
+        s = r[-1].split("-")
         molecule = p[len(p) - 1]
         startAA = s[0]
         endAA = s[1]
@@ -2973,23 +2972,23 @@ def get_frame_states(fstring):
     1:1-10     # this is crap, don't know what happens
     """
 
-    t = string.split(fstring, ":")
+    t = fstring.split(":")
     frames = t[0]  # the first token is frame range
     if len(t) == 2:
         states = t[1]  # the second token is state range
     else:
         states = '1'  # only state number 1 is used
 
     # parse frame substring
-    t = string.split(frames, "-")
+    t = frames.split("-")
     firstFrame = int(t[0])  # first token is starting frame
     if len(t) == 2:
         lastFrame = int(t[1])  # second token is end frame
     else:
         lastFrame = firstFrame  # only one frame is used
 
     # parse state substring
-    t = string.split(states, "-")
+    t = states.split("-")
     firstState = int(t[0])  # first token is starting state
     if len(t) == 2:
         lastState = int(t[1])  # second token is end state

plugins/mtsslWizard.py

@@ -1748,7 +1748,7 @@ class UripLabel:
 	numberToFind = {'painstaking': 1000, 'thorough search': 200, 'quick search': 50}
 	numberOfTries = {'painstaking': 100000, 'thorough search': 20000, 'quick search': 3000}
 	info = "\nFor the Urip label, the vdW restraints are by default set to 'loose' to account for possible polar interactions between the amide bonds and the DNA backbone."
-	errorMessage = "Check atom nomenclature. The ribose atoms are sometimes called C2* instead of C2'\nThis can be changed e.g. by 'alter all, name=string.replace(name,\"*\",\"'\")' in PyMOL."
+	errorMessage = "Check atom nomenclature. The ribose atoms are sometimes called C2* instead of C2'\nThis can be changed e.g. by 'alter all, name=name.replace(\"*\",\"'\")' in PyMOL."
 	trialAtomSphereRadius = 7.5
 	exclusionSphereRadius = 5.5
 	pdbStr = """HEADER    URIPSL\n

poseview.py

@@ -80,6 +80,7 @@ def poseview(ligand='organic inorganic', protein='polymer', width=0, height=0,
             print(' poseview: running...')
 
         process = subprocess.Popen(args,
+                                   universal_newlines=True,
                                    stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
         stdout, _ = process.communicate()