[fmt] Selections

package/MDAnalysis/selections/__init__.py

@@ -84,6 +84,8 @@ def get_writer(filename: str, defaultformat: str) -> base.SelectionWriterBase:
     try:
         return _SELECTION_WRITERS[format]
     except KeyError:
-        errmsg = (f"Writing as {format} is not implemented; only "
-                  f"{ _SELECTION_WRITERS.keys()} will work.")
+        errmsg = (
+            f"Writing as {format} is not implemented; only "
+            f"{ _SELECTION_WRITERS.keys()} will work."
+        )
         raise NotImplementedError(errmsg) from None

package/MDAnalysis/selections/base.py

@@ -60,7 +60,7 @@
     def __init__(cls, name, bases, classdict):
         type.__init__(type, name, bases, classdict)
         try:
-            fmt = util.asiterable(classdict['format'])
+            fmt = util.asiterable(classdict["format"])
         except KeyError:
             pass
         else:
@@ -97,17 +97,20 @@
        and closed with the :meth:`close` method or when exiting the `with`
        statement.
     """
+
     #: Name of the format.
     format = None
     #: Extension of output files.
     ext = None
     #: Special character to continue a line across a newline.
-    continuation = ''
+    continuation = ""
     #: Comment format string; should contain '%s' or ``None`` for no comments.
     commentfmt = None
     default_numterms = 8
 
-    def __init__(self, filename, mode="w", numterms=None, preamble=None, **kwargs):
+    def __init__(
+        self, filename, mode="w", numterms=None, preamble=None, **kwargs
+    ):
         """Set up for writing to *filename*.
 
         Parameters
@@ -126,8 +129,10 @@
             use as defaults for :meth:`write`
         """
         self.filename = util.filename(filename, ext=self.ext)
-        if not mode in ('a', 'w'):
-            raise ValueError("mode must be one of 'w', 'a', not {0!r}".format(mode))
+        if not mode in ("a", "w"):
+            raise ValueError(
+                "mode must be one of 'w', 'a', not {0!r}".format(mode)
+            )
         self.mode = mode
         self._current_mode = mode[0]
         if numterms is None or numterms < 0:
@@ -154,8 +159,8 @@
         A newline is appended to non-empty strings.
         """
         if self.commentfmt is None:
-            return ''
-        return self.commentfmt % s + '\n'
+            return ""
+        return self.commentfmt % s + "\n"
 
     def write_preamble(self):
         """Write a header, depending on the file format."""
@@ -188,7 +193,7 @@
                 frame = u.trajectory.ts.frame
             except AttributeError:
                 frame = 1  # should catch cases when we are analyzing a single PDB (?)
-        name = name or self.otherargs.get('name', None)
+        name = name or self.otherargs.get("name", None)
         if name is None:
             if number is None:
                 self.number += 1
@@ -203,13 +208,15 @@
         out = self._outfile
         self._write_head(out, name=name)
         for iatom in range(0, len(selection.atoms), step):
-            line = selection_terms[iatom:iatom + step]
+            line = selection_terms[iatom : iatom + step]
             out.write(" ".join(line))
             if len(line) == step and not iatom + step == len(selection.atoms):
-                out.write(' ' + self.continuation + '\n')
-        out.write(' ')  # safe so that we don't have to put a space at the start of tail
+                out.write(" " + self.continuation + "\n")
+        out.write(
+            " "
+        )  # safe so that we don't have to put a space at the start of tail
         self._write_tail(out)
-        out.write('\n')  # always terminate with newline
+        out.write("\n")  # always terminate with newline
 
     def close(self):
         """Close the file
@@ -234,11 +241,11 @@
 
     def _write_head(self, out, **kwargs):
         """Initial output to open file object *out*."""
-        pass # pylint: disable=unnecessary-pass
+        pass  # pylint: disable=unnecessary-pass
 
     def _write_tail(self, out, **kwargs):
         """Last output to open file object *out*."""
-        pass # pylint: disable=unnecessary-pass
+        pass  # pylint: disable=unnecessary-pass
 
     # Context manager support to match Coordinate writers
     # all file handles use a with block in their write method, so these do nothing special

package/MDAnalysis/selections/charmm.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
@@ -45,20 +45,26 @@
 class SelectionWriter(base.SelectionWriterBase):
     format = ["CHARMM", "str"]
     ext = "str"
-    continuation = '-'
+    continuation = "-"
     commentfmt = "! %s"
-    default_numterms = 4  # be conservative because CHARMM only reads 72 columns
+    default_numterms = (
+        4  # be conservative because CHARMM only reads 72 columns
+    )
 
     def _translate(self, atoms, **kwargs):
         # CHARMM index is 1-based
         def _index(atom):
             return "BYNUM {0:d}".format((atom.index + 1))
 
-        return base.join(atoms, ' .or.', _index)
+        return base.join(atoms, " .or.", _index)
 
     def _write_head(self, out, **kwargs):
         out.write(self.comment("MDAnalysis CHARMM selection"))
-        out.write("DEFINE {name!s} SELECT ".format(**kwargs) + self.continuation + '\n')
+        out.write(
+            "DEFINE {name!s} SELECT ".format(**kwargs)
+            + self.continuation
+            + "\n"
+        )
 
     def _write_tail(self, out, **kwargs):
         out.write("END")

package/MDAnalysis/selections/gromacs.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors

package/MDAnalysis/selections/jmol.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
@@ -46,14 +46,14 @@ class SelectionWriter(base.SelectionWriterBase):
     format = ["Jmol", "spt"]
     ext = "spt"
     default_numterms = None
-    commentfmt = '#'
+    commentfmt = "#"
 
     def _translate(self, atoms, **kwargs):
         # Jmol indexing is 0 based when using atom bitsets
         def _index(atom):
             return str(atom.index)
 
-        return base.join(atoms, ' ', _index)
+        return base.join(atoms, " ", _index)
 
     def _write_head(self, out, **kwargs):
         out.write("@~{name!s} ({{".format(**kwargs))

package/MDAnalysis/selections/pymol.py

@@ -1,5 +1,5 @@
 # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
-# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #
 # MDAnalysis --- https://www.mdanalysis.org
 # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
@@ -46,7 +46,7 @@
 class SelectionWriter(base.SelectionWriterBase):
     format = ["PyMol", "pml"]
     ext = "pml"
-    continuation = '\\'  # quoted backslash!
+    continuation = "\\"  # quoted backslash!
     commentfmt = "# %s"
     default_numterms = 6
 
@@ -55,8 +55,10 @@ def _translate(self, atoms, **kwargs):
         def _index(atom):
             return "index {0:d}".format((atom.index + 1))
 
-        return base.join(atoms, ' |', _index)
+        return base.join(atoms, " |", _index)
 
     def _write_head(self, out, **kwargs):
         out.write(self.comment("MDAnalysis PyMol selection"))
-        out.write("select {name!s}, ".format(**kwargs) + self.continuation + '\n')
+        out.write(
+            "select {name!s}, ".format(**kwargs) + self.continuation + "\n"
+        )

package/MDAnalysis/selections/vmd.py

@@ -53,7 +53,7 @@
 class SelectionWriter(base.SelectionWriterBase):
     format = "VMD"
     ext = "vmd"
-    continuation = '\\'
+    continuation = "\\"
     commentfmt = "# %s"
 
     def _write_head(self, out, **kwargs):

package/pyproject.toml

@@ -136,6 +136,7 @@ tables\.py
 | MDAnalysis/lib/.*\.py^
 | MDAnalysis/transformations/.*\.py
 | MDAnalysis/converters/.*\.py
+| MDAnalysis/selections/.*\.py
 )
 '''
 extend-exclude = '''