fix Python >= 3.12 syntax warnings

prody/atomic/flags.py

@@ -493,7 +493,7 @@ def changeBackbone(flag, names):
 for resi in DEFAULTS['nucleoside']:
     __doc__ += PDBLIGSUM.format(resi)
 
-__doc__ += """
+__doc__ += r"""
 
 Heteros
 -------------------------------------------------------------------------------

prody/atomic/select.py

@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-"""This module defines a class for selecting subsets of atoms.  You can read
+r"""This module defines a class for selecting subsets of atoms.  You can read
 this page in interactive sessions using ``help(select)``.
 
 ProDy offers a fast and powerful atom selection class, :class:`.Select`.
@@ -755,7 +755,7 @@ def regularExpParseAction(sel, loc, token):
 PP_REGEXP.setParseAction(regularExpParseAction)
 
 _ = r'[-+]?\d+(\.\d*)?([eE]\d+)?'
-RE_NRANGE = re_compile(_ + '\ *(to|:)\ *' + _)
+RE_NRANGE = re_compile(_ + r'\ *(to|:)\ *' + _)
 
 PP_NRANGE = pp.Group(pp.Regex(RE_NRANGE.pattern) +
                      pp.Optional(pp.Regex(r'(\ *:\ *' + _ + ')')))

prody/dynamics/pca.py

@@ -56,7 +56,7 @@ def setCovariance(self, covariance, is3d=True):
         self._trace = self._cov.trace()
 
     def buildCovariance(self, coordsets, **kwargs):
-        """Build a covariance matrix for *coordsets* using mean coordinates
+        r"""Build a covariance matrix for *coordsets* using mean coordinates
         as the reference.  *coordsets* argument may be one of the following:
 
         * :class:`.Atomic`

prody/proteins/dssp.py

@@ -75,7 +75,7 @@ def execDSSP(pdb, outputname=None, outputdir=None, stderr=True):
 
 
 def parseDSSP(dssp, ag, parseall=False):
-    """Parse DSSP data from file *dssp* into :class:`.AtomGroup` instance
+    r"""Parse DSSP data from file *dssp* into :class:`.AtomGroup` instance
     *ag*.  DSSP output file must be in the new format used from July 1995
     and onwards.  When *dssp* file is parsed, following attributes are added
     to *ag*:

prody/sequence/analysis.py

@@ -167,7 +167,7 @@ def calcMSAOccupancy(msa, occ='res', count=False):
 
 
 def applyMutinfoNorm(mutinfo, entropy, norm='sument'):
-    """Apply one of the normalizations discussed in [MLC05]_ to *mutinfo*
+    r"""Apply one of the normalizations discussed in [MLC05]_ to *mutinfo*
     matrix.  *norm* can be one of the following:
 
       * ``'sument'``: :math:`H(X) + H(Y)`, sum of entropy of columns