Removed instant selectors (Fixes Issue #1377) (#2535)

* Removed instant selectors (Fixes Issue #1377)

Author: richardjgowers

package/CHANGELOG

@@ -86,6 +86,8 @@ Enhancements
   * Improve the distance search in water bridge analysis with capped_distance (PR #2480)
 
 Changes
+  * Removed instant selectors on Universe and Group objects (e.g. AtomGroup.C,
+    Segment.r1, Universe.s4AKE).  Use select_atoms instead (Issue #1377)
   * Calling Universe() now raises a TypeError advising you to use Universe.empty.
     Universe.empty() now no longer has n_atoms=0 as default. (Issue #2527)
   * deprecated `start`, `stop`, and `step` keywords have been removed from `__init__` 

package/MDAnalysis/core/groups.py

@@ -2203,55 +2203,19 @@ class AtomGroup(GroupBase):
     :class:`AtomGroup` instances are always bound to a
     :class:`MDAnalysis.core.universe.Universe`. They cannot exist in isolation.
 
-    .. rubric:: Deprecated functionality
-
-    *Instant selectors* will be removed in the 1.0 release.  See issue `#1377
-    <https://github.com/MDAnalysis/mdanalysis/issues/1377>`_ for more details.
-
-    :class:`Atoms<Atom>` can also be accessed in a Pythonic fashion by using the
-    :class:`Atom` name as an attribute. For instance, ::
-
-        ag.CA
-
-    will provide an :class:`AtomGroup` of all CA :class:`Atoms<Atom>` in the
-    group. These *instant selector* attributes are auto-generated for
-    each atom name encountered in the group.
-
-    Notes
-    -----
-    The name-attribute instant selector access to :class:`Atoms<Atom>` is mainly
-    meant for quick interactive work. Thus it either returns a single
-    :class:`Atom` if there is only one matching :class:`Atom`, *or* a
-    new :class:`AtomGroup` for multiple matches.  This makes it difficult to use
-    the feature consistently in scripts.
-
 
     See Also
     --------
     :class:`MDAnalysis.core.universe.Universe`
 
-
     .. deprecated:: 0.16.2
        *Instant selectors* of :class:`AtomGroup` will be removed in the 1.0
-       release. See :ref:`Instant selectors <instance-selectors>` for details
-       and alternatives.
+       release.
+    .. versionchanged:: 1.0.0
+       Removed instant selectors, use select_atoms('name ...') to select
+       atoms by name.
     """
-    def __getitem__(self, item):
-        # DEPRECATED in 0.16.2
-        # REMOVE in 1.0
-        #
-        # u.atoms['HT1'] access, otherwise default
-        if isinstance(item, string_types):
-            try:
-                return self._get_named_atom(item)
-            except (AttributeError, selection.SelectionError):
-                pass
-        return super(AtomGroup, self).__getitem__(item)
-
     def __getattr__(self, attr):
-        # DEPRECATED in 0.16.2
-        # REMOVE in 1.0
-        #
         # is this a known attribute failure?
         # TODO: Generalise this to cover many attributes
         if attr in ('fragments', 'fragindices', 'n_fragments', 'unwrap'):
@@ -2260,12 +2224,6 @@ def __getattr__(self, attr):
             # raise NDE(_ATTR_ERRORS[attr])
             raise NoDataError("AtomGroup.{} not available; this requires Bonds"
                               "".format(attr))
-        elif hasattr(self.universe._topology, 'names'):
-            # Ugly hack to make multiple __getattr__s work
-            try:
-                return self._get_named_atom(attr)
-            except selection.SelectionError:
-                pass
         raise AttributeError("{cls} has no attribute {attr}".format(
             cls=self.__class__.__name__, attr=attr))
 
@@ -3256,8 +3214,8 @@ class ResidueGroup(GroupBase):
 
     .. deprecated:: 0.16.2
        *Instant selectors* of Segments will be removed in the 1.0 release.
-       See :ref:`Instant selectors <instance-selectors>` for details and
-       alternatives.
+    .. versionchanged:: 1.0.0
+       Removed instant selectors, use select_atoms instead
     """
 
     @property
@@ -3419,8 +3377,8 @@ class SegmentGroup(GroupBase):
 
     .. deprecated:: 0.16.2
        *Instant selectors* of Segments will be removed in the 1.0 release.
-       See :ref:`Instant selectors <instance-selectors>` for details and
-       alternatives.
+    .. versionchanged:: 1.0.0
+       Removed instant selectors, use select_atoms instead
     """
 
     @property
@@ -3841,8 +3799,11 @@ class Segment(ComponentBase):
 
     .. deprecated:: 0.16.2
        *Instant selectors* of :class:`Segments<Segment>` will be removed in the
-       1.0 release. See :ref:`Instant selectors <instance-selectors>` for
-       details and alternatives.
+       1.0 release.
+    .. versionchanged:: 1.0.0
+       Removed instant selectors, use either segment.residues[...] to select
+       residue by number, or segment.residues[segment.residue.resnames = ...]
+       to select by resname.
     """
     def __repr__(self):
         me = '<Segment'
@@ -3870,26 +3831,6 @@ def residues(self):
         rg._cache['unique'] = rg
         return rg
 
-    def __getattr__(self, attr):
-        # DEPRECATED in 0.16.2
-        # REMOVE in 1.0
-        #
-        # Segment.r1 access
-        if attr.startswith('r') and attr[1:].isdigit():
-            resnum = int(attr[1:])
-            rg = self.residues[resnum - 1]  # convert to 0 based
-            warnings.warn("Instant selectors Segment.r<N> will be removed in "
-                          "1.0. Use Segment.residues[N-1] instead.",
-                          DeprecationWarning)
-            return rg
-        # Resname accesss
-        if hasattr(self.residues, 'resnames'):
-            try:
-                return self.residues._get_named_residue(attr)
-            except selection.SelectionError:
-                pass
-        raise AttributeError("{cls} has no attribute {attr}"
-                             "".format(cls=self.__class__.__name__, attr=attr))
 
 # Accessing these attrs doesn't trigger an update. The class and instance
 # methods of UpdatingAtomGroup that are used during __init__ must all be

package/MDAnalysis/core/topologyattrs.py

@@ -45,7 +45,6 @@
 import numpy as np
 import warnings
 
-from numpy.lib.utils import deprecate
 
 from ..lib.util import (cached, convert_aa_code, iterable, warn_if_not_unique,
                         unique_int_1d)
@@ -481,63 +480,6 @@ class Atomnames(AtomAttr):
     def _gen_initial_values(na, nr, ns):
         return np.array(['' for _ in range(na)], dtype=object)
 
-    def getattr__(atomgroup, name):
-        try:
-            return atomgroup._get_named_atom(name)
-        except selection.SelectionError:
-            six.raise_from(
-                AttributeError("'{0}' object has no attribute '{1}'".format(
-                    atomgroup.__class__.__name__, name)),
-                None)
-
-    def _get_named_atom(group, name):
-        """Get all atoms with name *name* in the current AtomGroup.
-
-        For more than one atom it returns a list of :class:`Atom`
-        instance. A single :class:`Atom` is returned just as such. If
-        no atoms are found, a :exc:`SelectionError` is raised.
-
-        .. versionadded:: 0.9.2
-
-        .. deprecated:: 0.16.2
-           *Instant selectors* will be removed in the 1.0 release.
-           Use ``AtomGroup.select_atoms('name <name>')`` instead.
-           See issue `#1377
-           <https://github.com/MDAnalysis/mdanalysis/issues/1377>`_ for
-           more details.
-
-        """
-        # There can be more than one atom with the same name
-        atomlist = group.atoms.unique[group.atoms.unique.names == name]
-        if len(atomlist) == 0:
-            raise selection.SelectionError(
-                "No atoms with name '{0}'".format(name))
-        elif len(atomlist) == 1:
-            # XXX: keep this, makes more sense for names
-            atomlist = atomlist[0]
-        warnings.warn("Instant selector AtomGroup['<name>'] or AtomGroup.<name> "
-                      "is deprecated and will be removed in 1.0. "
-                      "Use AtomGroup.select_atoms('name <name>') instead.",
-                      DeprecationWarning)
-        return atomlist
-
-    # AtomGroup already has a getattr
-#    transplants[AtomGroup].append(
-#        ('__getattr__', getattr__))
-
-    transplants[Residue].append(
-        ('__getattr__', getattr__))
-
-    # this is also getitem for a residue
-    transplants[Residue].append(
-        ('__getitem__', getattr__))
-
-    transplants[AtomGroup].append(
-        ('_get_named_atom', _get_named_atom))
-
-    transplants[Residue].append(
-        ('_get_named_atom', _get_named_atom))
-
     def phi_selection(residue):
         """AtomGroup corresponding to the phi protein backbone dihedral
         C'-N-CA-C.
@@ -1383,63 +1325,6 @@ class Resnames(ResidueAttr):
     def _gen_initial_values(na, nr, ns):
         return np.array(['' for _ in range(nr)], dtype=object)
 
-    def getattr__(residuegroup, resname):
-        try:
-            return residuegroup._get_named_residue(resname)
-        except selection.SelectionError:
-            six.raise_from(
-                AttributeError("'{0}' object has no attribute '{1}'".format(
-                    residuegroup.__class__.__name__, resname)),
-                    None)
-
-    transplants[ResidueGroup].append(('__getattr__', getattr__))
-    # This transplant is hardcoded for now to allow for multiple getattr things
-    #transplants[Segment].append(('__getattr__', getattr__))
-
-    def _get_named_residue(group, resname):
-        """Get all residues with name *resname* in the current ResidueGroup
-        or Segment.
-
-        For more than one residue it returns a
-        :class:`MDAnalysis.core.groups.ResidueGroup` instance. A single
-        :class:`MDAnalysis.core.group.Residue` is returned for a single match.
-        If no residues are found, a :exc:`SelectionError` is raised.
-
-        .. versionadded:: 0.9.2
-
-        .. deprecated:: 0.16.2
-           *Instant selectors* will be removed in the 1.0 release.
-           Use ``ResidueGroup[ResidueGroup.resnames == '<name>']``
-           or ``Segment.residues[Segment.residues == '<name>']``
-           instead.
-           See issue `#1377
-           <https://github.com/MDAnalysis/mdanalysis/issues/1377>`_ for
-           more details.
-
-        """
-        # There can be more than one residue with the same name
-        residues = group.residues.unique[
-                group.residues.unique.resnames == resname]
-        if len(residues) == 0:
-            raise selection.SelectionError(
-                "No residues with resname '{0}'".format(resname))
-        warnings.warn("Instant selector ResidueGroup.<name> "
-                      "or Segment.<name> "
-                      "is deprecated and will be removed in 1.0. "
-                      "Use ResidueGroup[ResidueGroup.resnames == '<name>'] "
-                      "or Segment.residues[Segment.residues == '<name>'] "
-                      "instead.",
-                      DeprecationWarning)
-        if len(residues) == 1:
-            # XXX: keep this, makes more sense for names
-            return residues[0]
-        else:
-            # XXX: but inconsistent (see residues and Issue 47)
-            return residues
-
-    transplants[ResidueGroup].append(
-        ('_get_named_residue', _get_named_residue))
-
     def sequence(self, **kwargs):
         """Returns the amino acid sequence.
 
@@ -1627,60 +1512,6 @@ class Segids(SegmentAttr):
     def _gen_initial_values(na, nr, ns):
         return np.array(['' for _ in range(ns)], dtype=object)
 
-    def getattr__(segmentgroup, segid):
-        try:
-            return segmentgroup._get_named_segment(segid)
-        except selection.SelectionError:
-            six.raise_from(
-                AttributeError("'{0}' object has no attribute '{1}'".format(
-                    segmentgroup.__class__.__name__, segid)),
-                None)
-
-    transplants[SegmentGroup].append(
-        ('__getattr__', getattr__))
-
-    def _get_named_segment(group, segid):
-        """Get all segments with name *segid* in the current SegmentGroup.
-
-        For more than one residue it returns a
-        :class:`MDAnalysis.core.groups.SegmentGroup` instance. A single
-        :class:`MDAnalysis.core.group.Segment` is returned for a single match.
-        If no residues are found, a :exc:`SelectionError` is raised.
-
-        .. versionadded:: 0.9.2
-
-        .. deprecated:: 0.16.2
-           *Instant selectors* will be removed in the 1.0 release.
-           Use ``SegmentGroup[SegmentGroup.segids == '<name>']`` instead.
-           See issue `#1377
-           <https://github.com/MDAnalysis/mdanalysis/issues/1377>`_ for
-           more details.
-
-        """
-        # Undo adding 's' if segid started with digit
-        if segid.startswith('s') and len(segid) >= 2 and segid[1].isdigit():
-            segid = segid[1:]
-
-        # There can be more than one segment with the same name
-        segments = group.segments.unique[
-                group.segments.unique.segids == segid]
-        if len(segments) == 0:
-            raise selection.SelectionError(
-                "No segments with segid '{0}'".format(segid))
-        warnings.warn("Instant selector SegmentGroup.<name> "
-                      "is deprecated and will be removed in 1.0. "
-                      "Use SegmentGroup[SegmentGroup.segids == '<name>'] "
-                      "instead.",
-                      DeprecationWarning)
-        if len(segments) == 1:
-            # XXX: keep this, makes more sense for names
-            return segments[0]
-        else:
-            # XXX: but inconsistent (see residues and Issue 47)
-            return segments
-
-    transplants[SegmentGroup].append(
-        ('_get_named_segment', _get_named_segment))
 
 def _check_connection_values(func):
     """