Fix invalid escape sequences (W605) Part 2

Semi-automated with:

ruff check --fix --select W605 scripts

Author: speleo3

scripts/forster_distance_calculator.py

@@ -1,4 +1,4 @@
-'''
+r'''
 Described at PyMOL wiki:
 http://www.pymolwiki.org/index.php/forster_distance_calculator
 
@@ -77,7 +77,7 @@ def forster(D_Exi="ATTO488Exi.txt", D_Emi="ATTO488Emi.txt", A_Exi="ATTO590Exi.tx
     print("The .plt should be opened with gnuplot to make the graphs.")
     print("The created graphs are .eps files.")
     print("They can be converted to pdf with the program: epstopdf or eps2pdf")
-    print('Part of LaTeX: C:\Program Files (x86)\MiKTeX 2.9\miktex' + "\\" + "bin")
+    print(r'Part of LaTeX: C:\Program Files (x86)\MiKTeX 2.9\miktex' + "\\" + "bin")
     print("Or download here: http://tinyurl.com/eps2pdf")
 
     DonorEmi = open(D_Emi, "r")

scripts/propka.py

@@ -1,4 +1,4 @@
-'''
+r'''
 Described at PyMOL wiki:
 http://www.pymolwiki.org/index.php/propka
 
@@ -222,7 +222,7 @@ def getpropka(PDB="NIL", chain="*", resi="0", resn="NIL", source="upload", PDBID
     assert version in ['v2.0', 'v3.0', 'v3.1'], "'version' has to be either: 'v2.0', 'v3.0', 'v3.1'"
     assert source in ['ID', 'upload', 'addr', 'input_file'], "'source' has to be either: 'ID', 'upload', 'addr', 'input_file'"
     if source == "upload":
-        assert PDB not in ['NIL'], "You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
+        assert PDB not in ['NIL'], r"You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
     if source == "ID":
         assert len(PDBID) == 4, "PDBID has to be 4 characters"
     # To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
@@ -517,7 +517,7 @@ def importpropkabonds(result_pka_pkafile):
 
 def createdirs():
     if platform.system() == 'Windows':
-        Newdir = os.getcwd() + "\Results_propka\\"
+        Newdir = os.getcwd() + "\\Results_propka\\"
     if platform.system() == 'Linux':
         Newdir = os.getcwd() + "/Results_propka/"
     if not os.path.exists(Newdir):

scripts/transformations.py

@@ -30,7 +30,7 @@
 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 # POSSIBILITY OF SUCH DAMAGE.
 
-"""Homogeneous Transformation Matrices and Quaternions.
+r"""Homogeneous Transformation Matrices and Quaternions.
 
 A library for calculating 4x4 matrices for translating, rotating, reflecting,
 scaling, shearing, projecting, orthogonalizing, and superimposing arrays of
@@ -883,7 +883,7 @@ def orthogonalization_matrix(lengths, angles):
 
 
 def affine_matrix_from_points(v0, v1, shear=True, scale=True, usesvd=True):
-    """Return affine transform matrix to register two point sets.
+    r"""Return affine transform matrix to register two point sets.
 
     v0 and v1 are shape (ndims, \*) arrays of at least ndims non-homogeneous
     coordinates, where ndims is the dimensionality of the coordinate space.
@@ -992,7 +992,7 @@ def affine_matrix_from_points(v0, v1, shear=True, scale=True, usesvd=True):
 
 
 def superimposition_matrix(v0, v1, scale=False, usesvd=True):
-    """Return matrix to transform given 3D point set into second point set.
+    r"""Return matrix to transform given 3D point set into second point set.
 
     v0 and v1 are shape (3, \*) or (4, \*) arrays of at least 3 points.
 

scripts/wfmesh.py

@@ -42,7 +42,7 @@ def readOBJ(self, file):
         if os.path.exists(file):
             input = open(file, 'r')
             for line in input:
-                dat = re.split("\s+", line)
+                dat = re.split(r"\s+", line)
 
                 # Find vertex line
                 if line[0] == 'v' and line[1] != 't' and line[1] != 'n':