Fixed backslashes that were improperly interpreted as escapes (#4804)

wrappers/python/openmm/__init__.py

@@ -13,7 +13,7 @@ from . import version
 
 if sys.platform == 'win32':
     _path = os.environ['PATH']
-    os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % {
+    os.environ['PATH'] = r'%(lib)s;%(lib)s\plugins;%(path)s' % {
         'lib': version.openmm_library_path, 'path': _path}
     try:
         with os.add_dll_directory(version.openmm_library_path):

wrappers/python/openmm/app/gromacsgrofile.py

@@ -59,7 +59,7 @@ def _isfloat(word):
     @return answer Boolean which specifies whether the string is any number
 
     """
-    return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word)
+    return match(r'^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word)
 
 def _is_gro_coord(line):
     """ Determines whether a line contains GROMACS data or not

wrappers/python/openmm/app/internal/amber_file_parser.py

@@ -62,7 +62,7 @@ from . import customgbforces as customgb
 #=============================================================================================
 
 # A regex for extracting print format info from the FORMAT lines.
-FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?")
+FORMAT_RE_PATTERN=re.compile(r"([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?")
 
 # Pointer labels which map to pointer numbers at top of prmtop files
 POINTER_LABELS  = """

wrappers/python/openmm/app/internal/pdbstructure.py

@@ -1075,7 +1075,7 @@ if __name__=='__main__':
             subdir = "ae"
             full_subdir = os.path.join(pdb_dir, subdir)
             for pdb_file in os.listdir(full_subdir):
-                if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
+                if not re.match(r"pdb.%2s.\.ent\.gz" % subdir , pdb_file):
                     continue
                 full_pdb_file = os.path.join(full_subdir, pdb_file)
                 parse_one_pdb(full_pdb_file)
@@ -1086,7 +1086,7 @@ if __name__=='__main__':
                 if not os.path.isdir(full_subdir):
                     continue
                 for pdb_file in os.listdir(full_subdir):
-                    if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
+                    if not re.match(r"pdb.%2s.\.ent\.gz" % subdir , pdb_file):
                         continue
                     full_pdb_file = os.path.join(full_subdir, pdb_file)
                     parse_one_pdb(full_pdb_file)

wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py

@@ -355,16 +355,16 @@ class PdbxReader(object):
         mmcifRe = re.compile(
             r"(?:"
 
-             "(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
+            r"(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
 
-             "(?:['](.*?)(?:[']\s|[']$))"       "|"  # single quoted strings
-             "(?:[\"](.*?)(?:[\"]\s|[\"]$))"    "|"  # double quoted strings             
+            r"(?:['](.*?)(?:[']\s|[']$))"       "|"  # single quoted strings
+            r"(?:[\"](.*?)(?:[\"]\s|[\"]$))"    "|"  # double quoted strings             
 
-             "(?:\s*#.*$)"                      "|"  # comments (dumped)
+            r"(?:\s*#.*$)"                      "|"  # comments (dumped)
 
-             "(\S+)"                                 # unquoted words
+            r"(\S+)"                                 # unquoted words
 
-             ")")
+            r")")
 
         fileIter = iter(ifh)
 
@@ -423,15 +423,15 @@ class PdbxReader(object):
         mmcifRe = re.compile(
             r"(?:"
 
-             "(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
+            r"(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
 
-             "(?:['\"](.*?)(?:['\"]\s|['\"]$))"   "|"    # quoted strings
+            r"(?:['\"](.*?)(?:['\"]\s|['\"]$))"   "|"    # quoted strings
 
-             "(?:\s*#.*$)"                      "|"  # comments (dumped)
+            r"(?:\s*#.*$)"                      "|"  # comments (dumped)
 
-             "(\S+)"                                 # unquoted words
+            r"(\S+)"                                 # unquoted words
 
-             ")")
+            r")")
 
 
         """

wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py

@@ -344,16 +344,16 @@ class PdbxReader(object):
         mmcifRe = re.compile(
             r"(?:"
 
-             "(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
+            r"(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
 
-             "(?:['](.*?)(?:[']\s|[']$))"       "|"  # single quoted strings
-             "(?:[\"](.*?)(?:[\"]\s|[\"]$))"    "|"  # double quoted strings             
+            r"(?:['](.*?)(?:[']\s|[']$))"       "|"  # single quoted strings
+            r"(?:[\"](.*?)(?:[\"]\s|[\"]$))"    "|"  # double quoted strings             
 
-             "(?:\s*#.*$)"                      "|"  # comments (dumped)
+            r"(?:\s*#.*$)"                      "|"  # comments (dumped)
 
-             "(\S+)"                                 # unquoted words
+            r"(\S+)"                                 # unquoted words
 
-             ")")
+            r")")
 
         fileIter = iter(ifh)
 
@@ -416,15 +416,15 @@ class PdbxReader(object):
         mmcifRe = re.compile(
             r"(?:"
 
-             "(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
+            r"(?:_(.+?)[.](\S+))"               "|"  # _category.attribute
 
-             "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|"  # quoted strings
+            r"(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|"  # quoted strings
 
-             "(?:\s*#.*$)"                      "|"  # comments (dumped)
+            r"(?:\s*#.*$)"                      "|"  # comments (dumped)
 
-             "(\S+)"                                 # unquoted words
+            r"(\S+)"                                 # unquoted words
 
-             ")")
+            r")")
 
         fileIter = iter(ifh)
 

wrappers/python/openmm/app/metadynamics.py

@@ -244,7 +244,7 @@ class Metadynamics(object):
         # Check for any files updated by other processes.
 
         fileLoaded = False
-        pattern = re.compile('bias_(.*)_(.*)\.npy')
+        pattern = re.compile(r'bias_(.*)_(.*)\.npy')
         for filename in os.listdir(self.biasDir):
             match = pattern.match(filename)
             if match is not None:

wrappers/python/src/swig_doxygen/swig_lib/python/extend.i

@@ -388,7 +388,7 @@ Parameters:
     def deserialize(inputString):
       """Reconstruct an object that has been serialized as XML."""
       import re
-      match = re.search("<([^?]\S*)", inputString)
+      match = re.search(r"<([^?]\S*)", inputString)
       if match is None:
         raise ValueError("Invalid input string")
       type = match.groups()[0]