PSFParser reads and converts string-Like residue number to the leading number (#4582)

* psf support string like resid

* add psf file with insertion code

* add changelog

* update doc and pep8

* add test for psf

Author: yuxuanzhuang

package/CHANGELOG

@@ -16,11 +16,14 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher
+         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
+         yuxuanzhuang
 
  * 2.8.0
 
 Fixes
+ * Fix PSFParser error when encoutering string-like resids
+ * (Issue #2053, Issue #4189 PR #4582)
  * Fix `MDAnalysis.analysis.align.AlignTraj` not accepting writer kwargs
    (Issue #4564, PR #4565)
  * Fix #4259 via removing argument `parallelizable` of `NoJump` transformation.

package/MDAnalysis/lib/util.py

@@ -205,6 +205,7 @@
 from functools import wraps
 import textwrap
 import weakref
+import itertools
 
 import mmtf
 import numpy as np
@@ -2560,3 +2561,34 @@ def no_copy_shim():
     else:
         copy = False
     return copy
+
+
+def atoi(s: str) -> int:
+    """Convert the leading number part of a string to an integer.
+
+    Parameters
+    ----------
+    s : str
+        The string to convert to an integer.
+
+    Returns
+    -------
+    number : int
+        The first numeric part of the string converted to an integer.
+        If the string does not start with a number, 0 is returned.
+
+    Examples
+    --------
+    >>> from MDAnalysis.lib.util import atoi
+    >>> atoi('34f4')
+    34
+    >>> atoi('foo')
+    0
+ 
+
+    .. versionadded:: 2.8.0
+    """
+    try:
+        return int(''.join(itertools.takewhile(str.isdigit, s.strip())))
+    except ValueError:
+        return 0

package/MDAnalysis/topology/PSFParser.py

@@ -48,7 +48,7 @@
 from math import ceil
 import numpy as np
 
-from ..lib.util import openany
+from ..lib.util import openany, atoi
 from . import guessers
 from .base import TopologyReaderBase, squash_by, change_squash
 from ..core.topologyattrs import (
@@ -89,6 +89,10 @@ class PSFParser(TopologyReaderBase):
     - impropers
 
     .. _PSF: http://www.charmm.org/documentation/c35b1/struct.html
+
+
+    .. versionchanged:: 2.8.0
+       PSFParser now reads string resids and converts them to integers.
     """
     format = 'PSF'
 
@@ -248,7 +252,8 @@ def _parseatoms(self, lines, atoms_per, numlines):
         }
         atom_parser = atom_parsers[self._format]
         # once partitioned, assigned each component the correct type
-        set_type = lambda x: (int(x[0]) - 1, x[1] or "SYSTEM", int(x[2]), x[3],
+        set_type = lambda x: (int(x[0]) - 1, x[1] or "SYSTEM",
+                              atoi(x[2]), x[3],
                               x[4], x[5], float(x[6]), float(x[7]))
 
         # Oli: I don't think that this is the correct OUTPUT format: