Merge branch 'develop' into get_connections_develop

package/CHANGELOG

@@ -107,6 +107,7 @@ Enhancements
   * Added intra_bonds, intra_angles, intra_dihedrals etc. to return only
     the connections involving atoms within the AtomGroup, instead of
     including atoms outside the AtomGroup (Issue #1264, #2821, PR #3200)
+  * Added del_TopologyAttr function (PR #3069)
   * Switch GNMAnalysis to AnalysisBase (Issue #3243)
   * Adds python 3.9 support (Issue #2974, PR #3027, #3245)
   * Added an MDAnalysis shields.io badge to the README (Issue #3227, PR #3229)

package/MDAnalysis/core/groups.py

@@ -94,6 +94,7 @@
 import itertools
 import numbers
 import os
+import contextlib
 import warnings
 
 from .. import (_CONVERTERS,
@@ -255,6 +256,22 @@ def setter(self, values):
                     property(getter, setter, None, attr.singledoc))
             cls._SETATTR_WHITELIST.add(attr.singular)
 
+    @classmethod
+    def _del_prop(cls, attr):
+        """Remove `attr` from the namespace for this class.
+
+        Parameters
+        ----------
+        attr : A :class:`TopologyAttr` object
+        """
+        with contextlib.suppress(AttributeError):
+            delattr(cls, attr.attrname)
+        with contextlib.suppress(AttributeError):
+            delattr(cls, attr.singular)
+
+        cls._SETATTR_WHITELIST.discard(attr.attrname)
+        cls._SETATTR_WHITELIST.discard(attr.singular)
+
     def __setattr__(self, attr, value):
         # `ag.this = 42` calls setattr(ag, 'this', 42)
         if not (attr.startswith('_') or  # 'private' allowed

package/MDAnalysis/core/topology.py

@@ -56,6 +56,8 @@
 .. autofunction:: make_downshift_arrays
 
 """
+import contextlib
+
 import numpy as np
 
 from .topologyattrs import Atomindices, Resindices, Segindices
@@ -516,6 +518,21 @@ def add_TopologyAttr(self, topologyattr):
         topologyattr.top = self
         self.__setattr__(topologyattr.attrname, topologyattr)
 
+    def del_TopologyAttr(self, topologyattr):
+        """Remove a TopologyAttr from the Topology.
+
+        If it is not present, nothing happens.
+
+        Parameters
+        ----------
+        topologyattr : TopologyAttr
+
+
+        .. versionadded:: 2.0.0
+        """
+        self.__delattr__(topologyattr.attrname)
+        self.attrs.remove(topologyattr)
+
     @property
     def guessed_attributes(self):
         """A list of the guessed attributes in this topology"""

package/MDAnalysis/core/topologyobjects.py

@@ -899,21 +899,15 @@ def values(self, **kwargs):
         elif self.btype == 'improper':
             return self.dihedrals(**kwargs)
 
-    def _bondsSlow(self, pbc=False):  # pragma: no cover
-        """Slow version of bond (numpy implementation)"""
-        if not self.btype == 'bond':
-            return TypeError("TopologyGroup is not of type 'bond'")
-        else:
-            bond_dist = self._ags[0].positions - self._ags[1].positions
-            if pbc:
-                box = self._ags[0].dimensions
-                # orthogonal and divide by zero check
-                if (box[6:9] == 90.).all() and not (box[0:3] == 0).any():
-                    bond_dist -= np.rint(bond_dist / box[0:3]) * box[0:3]
-                else:
-                    raise ValueError("Only orthogonal boxes supported")
-
-            return np.array([mdamath.norm(a) for a in bond_dist])
+    def _calc_connection_values(self, func, *btypes, result=None, pbc=False):
+        if not any(self.btype == btype for btype in btypes):
+            strbtype = "' or '".join(btypes)
+            raise TypeError(f"TopologyGroup is not of type '{strbtype}'")
+        if not result:
+            result = np.zeros(len(self), np.float64)
+        box = None if not pbc else self._ags[0].dimensions
+        positions = [ag.positions for ag in self._ags]
+        return func(*positions, box=box, result=result)
 
     def bonds(self, pbc=False, result=None):
         """Calculates the distance between all bonds in this TopologyGroup
@@ -928,30 +922,8 @@ def bonds(self, pbc=False, result=None):
 
         Uses cython implementation
         """
-        if not self.btype == 'bond':
-            raise TypeError("TopologyGroup is not of type 'bond'")
-        if not result:
-            result = np.zeros(len(self), np.float64)
-        if pbc:
-            return distances.calc_bonds(self._ags[0].positions,
-                                        self._ags[1].positions,
-                                        box=self._ags[0].dimensions,
-                                        result=result)
-        else:
-            return distances.calc_bonds(self._ags[0].positions,
-                                        self._ags[1].positions,
-                                        result=result)
-
-    def _anglesSlow(self):  # pragma: no cover
-        """Slow version of angle (numpy implementation)"""
-        if not self.btype == 'angle':
-            raise TypeError("TopologyGroup is not of type 'angle'")
-
-        vec1 = self._ags[0].positions - self._ags[1].positions
-        vec2 = self._ags[2].positions - self._ags[1].positions
-
-        angles = np.array([mdamath.angle(a, b) for a, b in zip(vec1, vec2)])
-        return angles
+        return self._calc_connection_values(distances.calc_bonds, "bond",
+                                            pbc=pbc, result=result)
 
     def angles(self, result=None, pbc=False):
         """Calculates the angle in radians formed between a bond
@@ -975,34 +947,8 @@ def angles(self, result=None, pbc=False):
            Added *pbc* option (default ``False``)
 
         """
-        if not self.btype == 'angle':
-            raise TypeError("TopologyGroup is not of type 'angle'")
-        if not result:
-            result = np.zeros(len(self), np.float64)
-        if pbc:
-            return distances.calc_angles(self._ags[0].positions,
-                                         self._ags[1].positions,
-                                         self._ags[2].positions,
-                                         box=self._ags[0].dimensions,
-                                         result=result)
-        else:
-            return distances.calc_angles(self._ags[0].positions,
-                                         self._ags[1].positions,
-                                         self._ags[2].positions,
-                                         result=result)
-
-    def _dihedralsSlow(self):  # pragma: no cover
-        """Slow version of dihedral (numpy implementation)"""
-        if self.btype not in ['dihedral', 'improper']:
-            raise TypeError("TopologyGroup is not of type 'dihedral' or "
-                            "'improper'")
-
-        ab = self._ags[0].positions - self._ags[1].positions
-        bc = self._ags[1].positions - self._ags[2].positions
-        cd = self._ags[2].positions - self._ags[3].positions
-
-        return np.array([mdamath.dihedral(a, b, c)
-                         for a, b, c in zip(ab, bc, cd)])
+        return self._calc_connection_values(distances.calc_angles, "angle",
+                                            pbc=pbc, result=result)
 
     def dihedrals(self, result=None, pbc=False):
         """Calculate the dihedral angle in radians for this topology
@@ -1028,21 +974,6 @@ def dihedrals(self, result=None, pbc=False):
         .. versionchanged:: 0.9.0
            Added *pbc* option (default ``False``)
         """
-        if self.btype not in ['dihedral', 'improper']:
-            raise TypeError("TopologyGroup is not of type 'dihedral' or "
-                            "'improper'")
-        if not result:
-            result = np.zeros(len(self), np.float64)
-        if pbc:
-            return distances.calc_dihedrals(self._ags[0].positions,
-                                            self._ags[1].positions,
-                                            self._ags[2].positions,
-                                            self._ags[3].positions,
-                                            box=self._ags[0].dimensions,
-                                            result=result)
-        else:
-            return distances.calc_dihedrals(self._ags[0].positions,
-                                            self._ags[1].positions,
-                                            self._ags[2].positions,
-                                            self._ags[3].positions,
-                                            result=result)
+        return self._calc_connection_values(distances.calc_dihedrals,
+                                            "dihedral", "improper",
+                                            pbc=pbc, result=result)

package/MDAnalysis/core/universe.py

@@ -58,6 +58,7 @@
 import logging
 import copy
 import warnings
+import contextlib
 import collections
 
 import MDAnalysis
@@ -786,6 +787,62 @@ def add_TopologyAttr(self, topologyattr, values=None):
         self._topology.add_TopologyAttr(topologyattr)
         self._process_attr(topologyattr)
 
+    def del_TopologyAttr(self, topologyattr):
+        """Remove a topology attribute from the Universe
+
+        Removing a TopologyAttribute from the Universe makes it unavailable to
+        all AtomGroups etc throughout the Universe.
+
+        Parameters
+        ----------
+        topologyattr: TopologyAttr or string
+          Either a MDAnalysis TopologyAttr object or the name of a possible
+          topology attribute.
+
+        Example
+        -------
+        For example to remove bfactors to a Universe:
+
+        >>> u.del_TopologyAttr('bfactors')
+        >>> hasattr(u.atoms[:3], 'bfactors')
+        False
+
+
+        .. versionadded:: 2.0.0
+        """
+
+        if not isinstance(topologyattr, str):
+            try:
+                topologyattr = topologyattr.attrname
+            except AttributeError:
+                # either TopologyGroup or not valid
+                try:
+                    # this may not end well
+                    # e.g. matrix -> matrices
+                    topologyattr = topologyattr.btype + "s"
+                except AttributeError:
+                    raise ValueError("Topology attribute must be str or "
+                                     "TopologyAttr object or class. "
+                                     f"Given: {type(topologyattr)}") from None
+
+        try:
+            topologyattr = _TOPOLOGY_ATTRS[topologyattr].attrname
+        except KeyError:
+            attrs = ', '.join(sorted(_TOPOLOGY_ATTRS))
+            errmsg = (f"Unrecognised topology attribute: '{topologyattr}'."
+                      f"  Possible values: '{attrs}'\n"
+                      "To raise an issue go to: "
+                      "https://github.com/MDAnalysis/mdanalysis/issues")
+            raise ValueError(errmsg) from None
+
+        try:
+            topattr = getattr(self._topology, topologyattr)
+        except AttributeError:
+            raise ValueError(f"Topology attribute {topologyattr} "
+                             "not in Universe.") from None
+        self._topology.del_TopologyAttr(topattr)
+        self._unprocess_attr(topattr)
+
     def _process_attr(self, attr):
         """Squeeze a topologyattr for its information
 
@@ -820,6 +877,24 @@ def _process_attr(self, attr):
         for funcname, meth in attr.transplants['Universe']:
             setattr(self.__class__, funcname, meth)
 
+    def _unprocess_attr(self, attr):
+        """
+        Undo all the stuff in _process_attr.
+
+        If the topology attribute is not present, nothing happens
+        (silent fail).
+        """
+        for cls in attr.target_classes:
+            self._class_bases[cls]._del_prop(attr)
+
+        # Universe transplants
+        for funcname, _ in attr.transplants.pop("Universe", []):
+            delattr(self.__class__, funcname)
+        # Group transplants
+        for cls, transplants in attr.transplants.items():
+            for funcname, _ in transplants:
+                delattr(self._class_bases[cls], funcname)
+
     def add_Residue(self, segment=None, **attrs):
         """Add a new Residue to this Universe
 

package/setup.py

@@ -610,15 +610,19 @@ def long_description(readme):
                        'trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber.'),
           long_description=LONG_DESCRIPTION,
           long_description_content_type='text/x-rst',
-          author='Naveen Michaud-Agrawal',
-          author_email='naveen.michaudagrawal@gmail.com',
-          maintainer='Richard Gowers',
-          maintainer_email='mdnalysis-discussion@googlegroups.com',
+          author='MDAnalysis Development Team',
+          author_email='mdanalysis@numfocus.org',
+          maintainer='MDAnalysis Core Developers',
+          maintainer_email='mdanalysis@numfocus.org',
           url='https://www.mdanalysis.org',
           download_url='https://github.com/MDAnalysis/mdanalysis/releases',
-          project_urls={'Documentation': 'https://www.mdanalysis.org/docs/',
+          project_urls={'Documentation': 'https://docs.mdanalysis.org/',
+                        'User Guide': 'https://userguide.mdanalysis.org/',
                         'Issue Tracker': 'https://github.com/mdanalysis/mdanalysis/issues',
-                        'User Group': 'https://groups.google.com/forum/#!forum/mdnalysis-discussion',
+                        'User Group': 'https://groups.google.com/g/mdnalysis-discussion/',
+                        'Discord': 'https://discord.com/channels/807348386012987462/',
+                        'Blog': 'https://www.mdanalysis.org/blog/',
+                        'Twitter': 'https://twitter.com/mdanalysis',
                         'Source': 'https://github.com/mdanalysis/mdanalysis',
                         },
           license='GPL 2',