Fix pep8 W605 warnings

modules/chempy/sdf.py

@@ -20,8 +20,8 @@
 class SDFRec:
 
     def __init__(self,sdflist):
-        getkee = re.compile("^>\s+<([^>]*)>")
-        gettag = re.compile("^>\s+<[^>]*>\s+\((.*)\)")
+        getkee = re.compile(r"^>\s+<([^>]*)>")
+        gettag = re.compile(r"^>\s+<[^>]*>\s+\((.*)\)")
         ll = len(sdflist)
         if ll<4:
             print(" SDFRec: invalid SDF record format #1")

modules/pmg_tk/skins/normal/__init__.py

@@ -849,7 +849,7 @@ def file_save2(self, sels, multiple_files_flag, state_flag):
                                     # _state004
                                     inter = "_state" + str(stateSave).zfill(len(str(s))+1)
                                     # g either MATCHES *.pdb or not.  If so, save, name_stateXYZ.pdb
-                                    g = re.search("(.*)(\..*)$", save_file)
+                                    g = re.search(r"(.*)(\..*)$", save_file)
                                     if g!=None:
                                         # 1PDB_state004.pdb
                                         save_file = g.groups()[0] + inter + g.groups()[1]
@@ -889,7 +889,7 @@ def file_run(self):
                                         ])
         if len(ofile):
             self.__script__ = ofile
-            if re.search("\.pym*$|\.PYM*$",ofile):
+            if re.search(r"\.pym*$|\.PYM*$",ofile):
                 self.cmd.do("run "+ofile);      
             else:
                 self.cmd.do("@"+ofile);

modules/pymol/internal.py

@@ -249,12 +249,12 @@ def _mpng(prefix, first=-1, last=-1, preserve=0, modal=0,
     try:
         _self.lock(_self)
         fname = prefix
-        if re.search("[0-9]*\.png$",fname): # remove numbering, etc.
-            fname = re.sub("[0-9]*\.png$","",fname)
-        if re.search("[0-9]*\.ppm$",fname):
+        if re.search(r"[0-9]*\.png$",fname): # remove numbering, etc.
+            fname = re.sub(r"[0-9]*\.png$","",fname)
+        if re.search(r"[0-9]*\.ppm$",fname):
             if format<0:
                 format = 1 # PPM
-            fname = re.sub("[0-9]*\.ppm$","",fname)
+            fname = re.sub(r"[0-9]*\.ppm$","",fname)
         if format<0:
             format = 0 # default = PNG
         fname = cmd.exp_path(fname)

modules/pymol/movie.py

@@ -815,7 +815,7 @@ def _encode(filename,first,last,preserve,
 
 
 def find_exe(exe):
-    '''Return full path to executable or None.
+    r'''Return full path to executable or None.
     Excludes C:\Windows\System32\convert.exe
     Tests .exe extension on Unix (e.g. for legacy "mpeg_encode.exe" name).
     '''

modules/pymol/moving.py

@@ -730,7 +730,7 @@ def mset(specification="",frame=1,freeze=0,_self=cmd):
         try:
             _self.lock(_self)
             output=[]
-            input = re.sub("\s"," ",specification)
+            input = re.sub(r"\s"," ",specification)
             input = input.replace("x"," x");
             input = input.replace("-"," -");
             input = input.replace("x ","x");

modules/pymol/parser.py

@@ -45,7 +45,7 @@ class SecurityException(Exception):
                       '|=' :1, '^='  : 1, '>>=' : 1,'<<=' : 1,
                       '**=':1 }
 
-    remove_lists_re = re.compile("\[[^\]]*\]")
+    remove_lists_re = re.compile(r"\[[^\]]*\]")
 
     def complete_sc(st,sc,type_name,postfix, mode=0):
         result = None
@@ -405,7 +405,7 @@ def parse_embed():
                                             nest_securely = 1
                                         else:
                                             nest_securely = secure
-                                        if re.search("\.py$|\.pym$",path) is not None:
+                                        if re.search(r"\.py$|\.pym$",path) is not None:
                                             if self.cmd._feedback(fb_module.parser,fb_mask.warnings):
                                                 print("Warning: use 'run' instead of '@' with Python files?")
                                         layer.script = open(path,'r')

modules/pymol/plugins/installation.py

@@ -20,7 +20,7 @@ class BadInstallationFile(Exception):
     pass
 
 def get_default_user_plugin_path():
-    '''
+    r'''
     User plugin directory defaults to ~/.pymol/startup on Linux and to
     %APPDATA%\pymol\startup on windows.
     '''

modules/pymol/viewing.py

@@ -936,7 +936,7 @@ def chain_session(_self=cmd):
         # assumes locked interpreter
         r = 0
         session_file = str(_self.get("session_file"))
-        re_pat = re.compile("[0-9]+\.")
+        re_pat = re.compile(r"[0-9]+\.")
         if len(session_file): # find next session file, if it exists
             mo = re_pat.search(session_file)
             if mo is not None:
@@ -949,9 +949,9 @@ def chain_session(_self=cmd):
                         new_file = re_pat.sub(new_pat, session_file)
                         # try both PSE and PSW
                         if not os.path.exists(new_file):
-                            new_file = re.sub("\.pse$",".psw",new_file,re.I)
+                            new_file = re.sub(r"\.pse$",".psw",new_file,re.I)
                         if not os.path.exists(new_file):
-                            new_file = re.sub("\.psw$",".pse",new_file,re.I)
+                            new_file = re.sub(r"\.psw$",".pse",new_file,re.I)
                         if os.path.exists(new_file):
                             _self.do("_ cmd.load(r'''"+new_file+"''',format='psw')")
                             return 1

modules/pymol/wizard/pseudoatom.py

@@ -10,7 +10,7 @@ def __init__(self,mode='label',pos='[0.0,0.0,0.0]',_self=cmd):
         Wizard.__init__(self,_self)
         self.mode = mode
         if mode == 'label':
-            self.prefix = 'Label text: \888'
+            self.prefix = r'Label text: \888'
         self.text = ''
         self.pos = pos