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From de5020b3c831cf6813456528eef0b6a297ebeed6 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Tue, 18 Feb 2025 16:30:20 -0800
Subject: [PATCH] Fixed backslashes that were improperly interpreted as escapes
---
wrappers/python/openmm/__init__.py | 2 +-
wrappers/python/openmm/app/gromacsgrofile.py | 2 +-
.../openmm/app/internal/amber_file_parser.py | 2 +-
.../openmm/app/internal/pdbstructure.py | 4 ++--
.../app/internal/pdbx/reader/PdbxParser.py | 22 +++++++++----------
.../app/internal/pdbx/reader/PdbxReader.py | 22 +++++++++----------
wrappers/python/openmm/app/metadynamics.py | 2 +-
.../src/swig_doxygen/swig_lib/python/extend.i | 2 +-
8 files changed, 29 insertions(+), 29 deletions(-)
Index: openmm/wrappers/python/openmm/__init__.py
===================================================================
--- openmm.orig/wrappers/python/openmm/__init__.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/__init__.py 2025-02-19 17:29:34.752366954 +0100
@@ -13,7 +13,7 @@
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):
Index: openmm/wrappers/python/openmm/app/gromacsgrofile.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/gromacsgrofile.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/gromacsgrofile.py 2025-02-19 17:29:34.752366954 +0100
@@ -59,7 +59,7 @@
@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
Index: openmm/wrappers/python/openmm/app/internal/amber_file_parser.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/internal/amber_file_parser.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/internal/amber_file_parser.py 2025-02-19 17:29:34.752366954 +0100
@@ -62,7 +62,7 @@
#=============================================================================================
# 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 = """
Index: openmm/wrappers/python/openmm/app/internal/pdbstructure.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/internal/pdbstructure.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/internal/pdbstructure.py 2025-02-19 17:29:34.752366954 +0100
@@ -1068,7 +1068,7 @@
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)
@@ -1079,7 +1079,7 @@
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)
Index: openmm/wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/internal/pdbx/reader/PdbxParser.py 2025-02-19 17:29:34.752366954 +0100
@@ -355,16 +355,16 @@
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 @@
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")")
"""
Index: openmm/wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/internal/pdbx/reader/PdbxReader.py 2025-02-19 17:29:34.752366954 +0100
@@ -344,16 +344,16 @@
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 @@
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)
Index: openmm/wrappers/python/openmm/app/metadynamics.py
===================================================================
--- openmm.orig/wrappers/python/openmm/app/metadynamics.py 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/openmm/app/metadynamics.py 2025-02-19 17:29:34.752366954 +0100
@@ -244,7 +244,7 @@
# 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:
Index: openmm/wrappers/python/src/swig_doxygen/swig_lib/python/extend.i
===================================================================
--- openmm.orig/wrappers/python/src/swig_doxygen/swig_lib/python/extend.i 2025-02-19 17:29:34.756366992 +0100
+++ openmm/wrappers/python/src/swig_doxygen/swig_lib/python/extend.i 2025-02-19 17:29:34.752366954 +0100
@@ -371,7 +371,7 @@
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]
|
