Source code for MDAnalysis.core.groups

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#

"""\
==========================================================
Core objects: Containers --- :mod:`MDAnalysis.core.groups`
==========================================================

The :class:`~MDAnalysis.core.universe.Universe` instance contains all
the particles in the system (which MDAnalysis calls
:class:`Atom`). Groups of atoms are handled as :class:`AtomGroup`
instances. The :class:`AtomGroup` is probably the most important
object in MDAnalysis because virtually everything can be accessed
through it. `AtomGroup` instances can be easily created (e.g., from a
:meth:`AtomGroup.select_atoms` selection or just by slicing).

For convenience, chemically meaningful groups of atoms such as a
:class:`Residue` or a :class:`Segment` (typically a whole molecule or
all of the solvent) also exist as containers, as well as groups of
these units ((:class:`ResidueGroup`, :class:`SegmentGroup`).


Classes
=======

Collections
-----------

.. autoclass:: AtomGroup
   :members:
   :inherited-members:
.. autoclass:: ResidueGroup
   :members:
   :inherited-members:
.. autoclass:: SegmentGroup
   :members:
   :inherited-members:
.. autoclass:: UpdatingAtomGroup
   :members:

Chemical units
--------------

.. autoclass:: Atom
   :members:
   :inherited-members:
.. autoclass:: Residue
   :members:
   :inherited-members:
.. autoclass:: Segment
   :members:
   :inherited-members:

Levels
------

Each of the above classes has a level attribute.  This can be used to
verify that two objects are of the same level, or to access a particular
class::

   u = mda.Universe()

   ag = u.atoms[:10]
   at = u.atoms[11]

   ag.level == at.level  # Returns True

   ag.level.singular  # Returns Atom class
   at.level.plural  # Returns AtomGroup class


"""
from __future__ import absolute_import
from six.moves import zip
from six import string_types

from collections import namedtuple
import numpy as np
import functools
import itertools
import numbers
import os
import warnings

from numpy.lib.utils import deprecate

import MDAnalysis
from .. import _ANCHOR_UNIVERSES
from ..lib import util
from ..lib import distances
from ..lib import transformations
from ..selections import get_writer as get_selection_writer_for
from . import selection
from . import flags
from ..exceptions import NoDataError
from . import topologyobjects
from ._get_readers import get_writer_for


def _unpickle(uhash, ix):
    try:
        u = _ANCHOR_UNIVERSES[uhash]
    except KeyError:
        # doesn't provide as nice an error message as before as only hash of universe is stored
        # maybe if we pickled the filename too we could do better...
        raise RuntimeError(
            "Couldn't find a suitable Universe to unpickle AtomGroup onto "
            "with Universe hash '{}'.  Available hashes: {}"
            "".format(uhash, ', '.join([str(k)
                                        for k in _ANCHOR_UNIVERSES.keys()])))
    return u.atoms[ix]

def _unpickle_uag(basepickle, selections, selstrs):
    bfunc, bargs = basepickle[0], basepickle[1:][0]
    basegroup = bfunc(*bargs)
    return UpdatingAtomGroup(basegroup, selections, selstrs)


def make_classes():
    """Make a fresh copy of all Classes

    Returns
    -------
    Two dictionaries. One with a set of :class:`_TopologyAttrContainer` classes
    to serve as bases for universe-specific MDA container classes. Another with
    the final merged versions of those classes. The classes themselves are used
    as hashing keys.

    """
    bases = {}
    classes = {}
    groups = (AtomGroup, ResidueGroup, SegmentGroup)
    components = (Atom, Residue, Segment)

    # The 'GBase' middle man is needed so that a single topologyattr
    #  patching applies automatically to all groups.
    GBase = bases[GroupBase] = _TopologyAttrContainer._subclass(is_group=True)
    for cls in groups:
        bases[cls] = GBase._subclass(is_group=True)
    # CBase for patching all components
    CBase = bases[ComponentBase] = _TopologyAttrContainer._subclass(
        is_group=False)
    for cls in components:
        bases[cls] = CBase._subclass(is_group=False)

    # Initializes the class cache.
    for cls in groups + components:
        classes[cls] = bases[cls]._mix(cls)

    return bases, classes


class _TopologyAttrContainer(object):
    """Class factory for receiving sets of :class:`TopologyAttr` objects.

    :class:`_TopologyAttrContainer` is a convenience class to encapsulate the
    functions that deal with:
    * the import and namespace transplant of :class:`TopologyAttr` objects;
    * the copying (subclassing) of itself to create distinct bases for the
      different container classes (:class:`AtomGroup`, :class:`ResidueGroup`,
      :class:`SegmentGroup`, :class:`Atom`, :class:`Residue`, :class:`Segment`,
      and subclasses thereof);
    * the mixing (subclassing and co-inheritance) with the container classes.
      The mixed subclasses become the final container classes specific to each
      :class:`Universe`.
    """
    @classmethod
    def _subclass(cls, is_group):
        """Factory method returning :class:`_TopologyAttrContainer` subclasses.

        Parameters
        ----------
        is_group : bool
            The :attr:`_is_group` of the returned class will be set to
            *is_group*. This is used to distinguish between Groups (AtomGroup
            etc.) and Components (Atom etc.) in internal methods when
            considering actions such as addition between objects, adding
            TopologyAttributes to them.

        Returns
        -------
        type
            A subclass of :class:`_TopologyAttrContainer`, with the same name.
        """
        newcls = type(cls.__name__, (cls,), {'_is_group': bool(is_group)})
        if is_group:
            newcls._SETATTR_WHITELIST = {
                'positions', 'velocities', 'forces', 'dimensions',
                'atoms', 'residue', 'residues', 'segment', 'segments',
            }
        else:
            newcls._SETATTR_WHITELIST = {
                'position', 'velocity', 'force', 'dimensions',
                'atoms', 'residue', 'residues', 'segment',
            }

        return newcls

    @classmethod
    def _mix(cls, other):
        """Creates a subclass with ourselves and another class as parents.

        Classes mixed at this point override :meth:`__new__`, causing further
        instantiations to shortcut to :meth:`~object.__new__` (skipping the
        cache-fetch process for :class:`_MutableBase` subclasses).

        The new class will have an attribute `_derived_class` added, pointing
        to itself. This pointer instructs which class to use when
        slicing/adding instances of the new class. At initialization time the
        new class may choose to point `_derived_class` to another class (as is
        done in the initialization of :class:`UpdatingAtomGroup`).

        Parameters
        ----------
        other : type
            The class to mix with ourselves.

        Returns
        -------
        type
            A class of parents :class:`_ImmutableBase`, *other* and this class.
            Its name is the same as *other*'s.
        """
        newcls = type(other.__name__, (_ImmutableBase, other, cls), {})
        newcls._derived_class = newcls
        return newcls

    @classmethod
    def _add_prop(cls, attr):
        """Add attr into the namespace for this class

        Parameters
        ----------
        attr : A TopologyAttr object
        """
        def getter(self):
            return attr.__getitem__(self)

        def setter(self, values):
            return attr.__setitem__(self, values)

        if cls._is_group:
            setattr(cls, attr.attrname,
                    property(getter, setter, None, attr.groupdoc))
            cls._SETATTR_WHITELIST.add(attr.attrname)
        else:
            setattr(cls, attr.singular,
                    property(getter, setter, None, attr.singledoc))
            cls._SETATTR_WHITELIST.add(attr.singular)

    def __setattr__(self, attr, value):
        # `ag.this = 42` calls setattr(ag, 'this', 42)
        if not (attr.startswith('_') or  # 'private' allowed
                attr in self._SETATTR_WHITELIST or  # known attributes allowed
                hasattr(self, attr)):  # preexisting (eg properties) allowed
            raise AttributeError(
                "Cannot set arbitrary attributes to a {}".format(
                    'Group' if self._is_group else 'Component'))
        # if it is, we allow the setattr to proceed by deferring to the super
        # behaviour (ie do it)
        super(_TopologyAttrContainer, self).__setattr__(attr, value)


class _MutableBase(object):
    """
    Base class that merges appropriate :class:`_TopologyAttrContainer` classes.

    Implements :meth:`__new__`. In it the instantiating class is fetched from
    :attr:`Universe._classes`. If there is a cache miss, a merged class is made
    with a base from :attr:`Universe._class_bases` and cached.

    The classes themselves are used as the cache dictionary keys for simplcity
    in cache retrieval.

    """
    def __new__(cls, *args, **kwargs):
        # This pre-initialization wrapper must be pretty generic to
        # allow for different initialization schemes of the possible classes.
        # All we really need here is to fish a universe out of the arg list.
        # The AtomGroup cases get priority and are fished out first.
        try:
            u = args[-1].universe
        except (IndexError, AttributeError):
            try:
                # deprecated AtomGroup init method..
                u = args[0][0].universe
            except (IndexError, AttributeError):
                # Let's be generic and get the first argument that's either a
                # Universe, a Group, or a Component, and go from there.
                # This is where the UpdatingAtomGroup args get matched.
                for arg in args+tuple(kwargs.values()):
                    if isinstance(arg, (MDAnalysis.Universe, GroupBase,
                                        ComponentBase)):
                        u = arg.universe
                        break
                else:
                    raise TypeError("No universe, or universe-containing "
                                   "object passed to the initialization of "
                                    "{}".format(cls.__name__))
        try:
            return object.__new__(u._classes[cls])
        except KeyError:
            # Cache miss. Let's find which kind of class this is and merge.
            try:
                parent_cls = next(u._class_bases[parent]
                                  for parent in cls.mro()
                                  if parent in u._class_bases)
            except StopIteration:
                raise TypeError("Attempted to instantiate class '{}' but "
                                "none of its parents are known to the "
                                "universe. Currently possible parent "
                                "classes are: {}".format(cls.__name__,
                                    str(sorted(u._class_bases.keys()))))
            newcls = u._classes[cls] = parent_cls._mix(cls)
            return object.__new__(newcls)


class _ImmutableBase(object):
    """Class used to shortcut :meth:`__new__` to :meth:`object.__new__`.

    """
    # When mixed via _TopologyAttrContainer._mix this class has MRO priority.
    #  Setting __new__ like this will avoid having to go through the
    #  cache lookup if the class is reused (as in ag._derived_class(...)).
    __new__ = object.__new__



def _only_same_level(function):
    @functools.wraps(function)
    def wrapped(self, other):
        if not isinstance(other, (ComponentBase, GroupBase)):  # sanity check
            raise TypeError("Can't perform '{}' between objects:"
                            " '{}' and '{}'".format(
                                function.__name__,
                                type(self).__name__,
                                type(other).__name__))
        if self.level != other.level:
            raise TypeError("Can't perform '{}' on different level objects"
                            "".format(function.__name__))
        if self.universe is not other.universe:
            raise ValueError(
                "Can't operate on objects from different Universes")
        return function(self, other)
    return wrapped


class GroupBase(_MutableBase):
    """Base class from which a Universe's Group class is built.

    Instances of :class:`GroupBase` provide the following operations that
    conserve element repetitions and order:

    +-------------------------------+------------+----------------------------+
    | Operation                     | Equivalent | Result                     |
    +===============================+============+============================+
    | ``len(s)``                    |            | number of elements (atoms, |
    |                               |            | residues or segment) in    |
    |                               |            | the group                  |
    +-------------------------------+------------+----------------------------+
    | ``s == t``                    |            | test if ``s`` and ``t``    |
    |                               |            | contain the same elements  |
    |                               |            | in the same order          |
    +-------------------------------+------------+----------------------------+
    | ``x in s``                    |            | test if component ``x`` is |
    |                               |            | part of group ``s``        |
    +-------------------------------+------------+----------------------------+
    | ``s.concatenate(t)``          | ``s + t``  | new Group with elements    |
    |                               |            | from ``s`` and from ``t``  |
    +-------------------------------+------------+----------------------------+
    | ``s.subtract(t)``             |            | new Group with elements    |
    |                               |            | from ``s`` that are not    |
    |                               |            | in ``t``                   |
    +-------------------------------+------------+----------------------------+

    The following operations treat the Group as set. Any result will have any
    duplicate entries removed and the Group will be sorted.

    +-------------------------------+------------+----------------------------+
    | Operation                     | Equivalent | Result                     |
    +===============================+============+============================+
    | ``s.isdisjoint(t)``           |            | ``True`` if ``s`` and      |
    |                               |            | ``t`` do not share         |
    |                               |            | elements                   |
    +-------------------------------+------------+----------------------------+
    | ``s.issubset(t)``             |            | test if all elements of    |
    |                               |            | ``s`` are part of ``t``    |
    +-------------------------------+------------+----------------------------+
    | ``s.is_strict_subset(t)``     |            | test if all elements of    |
    |                               |            | ``s`` are part of ``t``,   |
    |                               |            | and ``s != t``             |
    +-------------------------------+------------+----------------------------+
    | ``s.issuperset(t)``           |            | test if all elements of    |
    |                               |            | ``t`` are part of ``s``    |
    +-------------------------------+------------+----------------------------+
    | ``s.is_strict_superset(t)``   |            | test if all elements of    |
    |                               |            | ``t`` are part of ``s``,   |
    |                               |            | and ``s != t``             |
    +-------------------------------+------------+----------------------------+
    | ``s.union(t)``                | ``s | t``  | new Group with elements    |
    |                               |            | from both ``s`` and ``t``  |
    +-------------------------------+------------+----------------------------+
    | ``s.intersection(t)``         | ``s & t``  | new Group with elements    |
    |                               |            | common to ``s`` and ``t``  |
    +-------------------------------+------------+----------------------------+
    | ``s.difference(t)``           | ``s - t``  | new Group with elements of |
    |                               |            | ``s`` that are not in ``t``|
    +-------------------------------+------------+----------------------------+
    | ``s.symmetric_difference(t)`` | ``s ^ t``  | new Group with elements    |
    |                               |            | that are part of ``s`` or  |
    |                               |            | ``t`` but not both         |
    +-------------------------------+------------+----------------------------+
    """
    def __init__(self, *args):
        if len(args) == 1:
            warnings.warn("Using deprecated init method for Group. "
                          "In the future use `Group(indices, universe)`. "
                          "This init method will be removed in version 1.0.",
                          DeprecationWarning)
            # list of atoms/res/segs, old init method
            ix = [at.ix for at in args[0]]
            u = args[0][0].universe
        else:
            # current/new init method
            ix, u = args

        # indices for the objects I hold
        self._ix = np.asarray(ix, dtype=np.intp)
        self._u = u
        self._cache = dict()

    def __hash__(self):
        return hash((self._u, self.__class__, tuple(self.ix.tolist())))

    def __len__(self):
        return len(self.ix)

    def __getitem__(self, item):
        # supports
        # - integer access
        # - boolean slicing
        # - fancy indexing
        # because our _ix attribute is a numpy array
        # it can be sliced by all of these already,
        # so just return ourselves sliced by the item
        if isinstance(item, numbers.Integral):
            return self.level.singular(self.ix[item], self.universe)
        else:
            if isinstance(item, list) and item:  # check for empty list
                # hack to make lists into numpy arrays
                # important for boolean slicing
                item = np.array(item)
            # We specify _derived_class instead of self.__class__ to allow
            # subclasses, such as UpdatingAtomGroup, to control the class
            # resulting from slicing.
            return self._derived_class(self.ix[item], self.universe)

    def __repr__(self):
        name = self.level.name
        return ("<{}Group with {} {}{}>"
                "".format(name.capitalize(), len(self), name,
                "s"[len(self)==1:])) # Shorthand for a conditional plural 's'.

    def __str__(self):
        name = self.level.name
        if len(self) <= 10:
            return '<{}Group {}>'.format(name.capitalize(), repr(list(self)))
        else:
            return '<{}Group {}, ..., {}>'.format(name.capitalize(),
                                                  repr(list(self)[:3])[:-1],
                                                  repr(list(self)[-3:])[1:])

    def __add__(self, other):
        """Concatenate the Group with another Group or Component of the same
        level.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with elements of `self` and `other` concatenated

        """
        return self.concatenate(other)

    def __radd__(self, other):
        """Using built-in sum requires supporting 0 + self. If other is
        anything other 0, an exception will be raised.

        Parameters
        ----------
        other : int
            Other should be 0, or else an exception will be raised.

        Returns
        -------
        self
            Group with elements of `self` reproduced

        """
        if other == 0:
            return self._derived_class(self.ix, self.universe)
        else:
            raise TypeError("unsupported operand type(s) for +:"
                            " '{}' and '{}'".format(type(self).__name__,
                                                    type(other).__name__))
    def __sub__(self, other):
        return self.difference(other)

    @_only_same_level
    def __eq__(self, other):
        """Test group equality.

        Two groups are equal if they contain the same indices in
        the same order. Groups that are not at the same level or that belong
        to different universe cannot be compared.
        """
        o_ix = other.ix
        return np.array_equal(self.ix, o_ix)

    def __contains__(self, other):
        if not other.level == self.level:
            # maybe raise TypeError instead?
            # eq method raises Error for wrong comparisons
            return False
        return other.ix in self.ix

    def __or__(self, other):
        return self.union(other)

    def __and__(self, other):
        return self.intersection(other)

    def __xor__(self, other):
        return self.symmetric_difference(other)

    @property
    def universe(self):
        return self._u

    @property
    def ix(self):
        """Unique indices of the components in the Group.

        - If this Group is an :class:`AtomGroup`, these are the
          indices of the :class:`Atom` instances.
        - If it is a :class:`ResidueGroup`, these are the indices of
          the :class:`Residue` instances.
        - If it is a :class:`SegmentGroup`, these are the indices of
          the :class:`Segment` instances.

        """
        return self._ix

    @property
    def ix_array(self):
        """Unique indices of the components in the Group.

        For a Group, ix_array is the same as ix. This method gives a
        consistent API between components and groups.

        See Also
        --------
        ix
        """
        return self._ix

    @property
    def dimensions(self):
        """Obtain a copy of the dimensions of the currently loaded Timestep"""
        return self.universe.trajectory.ts.dimensions.copy()

    @dimensions.setter
    def dimensions(self, dimensions):
        self.universe.trajectory.ts.dimensions = dimensions

    def center(self, weights, pbc=None):
        """Calculate center of group given some weights

        Parameters
        ----------
        weights : array_like
            weights to be used
        pbc : boolean, optional
            ``True``: Move all atoms within the primary unit cell
            before calculation [``False``]

        Returns
        -------
        center : ndarray
            weighted center of group

        Examples
        --------

        To find the charge weighted center of a given Atomgroup::

            >>> sel = u.select_atoms('prop mass > 4.0')
            >>> sel.center(sel.charges)


        Notes
        -----
        If the :class:`MDAnalysis.core.flags` flag *use_pbc* is set to
        ``True`` then the `pbc` keyword is used by default.

        """
        atoms = self.atoms
        if pbc is None:
            pbc = flags['use_pbc']
        if pbc:
            xyz = atoms.pack_into_box(inplace=False)
        else:
            xyz = atoms.positions

        return np.average(xyz, weights=weights, axis=0)

    def center_of_geometry(self, pbc=None):
        """Center of geometry (also known as centroid) of the selection.

        Parameters
        ----------
        pbc : boolean, optional
            ``True``: Move all atoms within the primary unit cell
            before calculation [``False``]

        Returns
        -------
        center : ndarray
            geometric center of group

        Notes
        -----
        If the :class:`MDAnalysis.core.flags` flag *use_pbc* is set to
        ``True`` then the `pbc` keyword is used by default.


        .. versionchanged:: 0.8 Added `pbc` keyword
        """
        return self.center(None, pbc=pbc)

    centroid = center_of_geometry

    def bbox(self, **kwargs):
        """Return the bounding box of the selection.

        The lengths A,B,C of the orthorhombic enclosing box are ::

          L = AtomGroup.bbox()
          A,B,C = L[1] - L[0]

        Parameters
        ----------
        pbc : bool, optional
            If ``True``, move all atoms within the primary unit cell before
            calculation. [``False``]

        Returns
        -------
         corners : array
            2x3 array giving corners of bounding box as
            [[xmin, ymin, zmin], [xmax, ymax, zmax]].

        Note
        ----
        The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
        ``True`` allows the *pbc* flag to be used by default.


        .. versionadded:: 0.7.2
        .. versionchanged:: 0.8 Added *pbc* keyword
        """
        atomgroup = self.atoms
        pbc = kwargs.pop('pbc', MDAnalysis.core.flags['use_pbc'])

        if pbc:
            x = atomgroup.pack_into_box(inplace=False)
        else:
            x = atomgroup.positions

        return np.array([x.min(axis=0), x.max(axis=0)])

    def bsphere(self, **kwargs):
        """Return the bounding sphere of the selection.

        The sphere is calculated relative to the centre of geometry.

        Parameters
        ----------
        pbc : bool, optional
            If ``True``, move all atoms within the primary unit cell before
            calculation. [``False``]

        Returns
        -------
        R : float
            Radius of bounding sphere.
        center : array
            Coordinates of sphere center as ``[xcen,ycen,zcen]``.

        Note
        ----
        The :class:`MDAnalysis.core.flags` flag *use_pbc* when set to
        ``True`` allows the *pbc* flag to be used by default.


        .. versionadded:: 0.7.3
        .. versionchanged:: 0.8 Added *pbc* keyword
        """
        atomgroup = self.atoms
        pbc = kwargs.pop('pbc', MDAnalysis.core.flags['use_pbc'])

        if pbc:
            x = atomgroup.pack_into_box(inplace=False)
            centroid = atomgroup.center_of_geometry(pbc=True)
        else:
            x = atomgroup.positions
            centroid = atomgroup.center_of_geometry(pbc=False)

        R = np.sqrt(np.max(np.sum(np.square(x - centroid), axis=1)))

        return R, centroid

    def transform(self, M):
        r"""Apply homogenous transformation matrix `M` to the coordinates.

        Parameters
        ----------
        M : array
            4x4 matrix, with the rotation in ``R = M[:3,:3]`` and the
            translation in ``t = M[:3,3]``.

        Returns
        -------
        self

        See Also
        --------
        MDAnalysis.lib.transformations : module of all coordinate transforms

        Notes
        -----
        The rotation :math:`\mathsf{R}` is applied before the translation
        :math:`\mathbf{t}`:

        .. math::

           \mathbf{x}' = \mathsf{R}\mathbf{x} + \mathbf{t}

        """
        R = M[:3, :3]
        t = M[:3, 3]
        return self.rotate(R, [0, 0, 0]).translate(t)

    def translate(self, t):
        r"""Apply translation vector `t` to the selection's coordinates.

        Atom coordinates are translated in-place.

        Parameters
        ----------
        t : array_like
            vector to translate coordinates with

        Returns
        -------
        self

        See Also
        --------
        MDAnalysis.lib.transformations : module of all coordinate transforms

        Notes
        -----
        The method applies a translation to the :class:`AtomGroup`
        from current coordinates :math:`\mathbf{x}` to new coordinates
        :math:`\mathbf{x}'`:

        .. math::

            \mathbf{x}' = \mathbf{x} + \mathbf{t}

        """
        atomgroup = self.atoms.unique
        vector = np.asarray(t)
        # changes the coordinates in place
        atomgroup.universe.trajectory.ts.positions[atomgroup.indices] += vector
        return self

    def rotate(self, R, point=(0, 0, 0)):
        r"""Apply a rotation matrix `R` to the selection's coordinates.
        :math:`\mathsf{R}` is a 3x3 orthogonal matrix that transforms a vector
        :math:`\mathbf{x} \rightarrow \mathbf{x}'`:

        .. math::

            \mathbf{x}' = \mathsf{R}\mathbf{x}

        Parameters
        ----------
        R : array_like
            3x3 rotation matrix to use for applying rotation.
        point : array_like, optional
            Center of rotation

        Returns
        -------
        self : AtomGroup

        Notes
        -----
        By default rotates around center of origin ``point=(0, 0, 0)``. To
        rotate around center of geometry of the atomgroup use ``ag.rotate(R,
        point=ag.centroid)``.

        See Also
        --------
        rotateby : rotate around given axis and angle
        MDAnalysis.lib.transformations : module of all coordinate transforms

        """
        R = np.asarray(R)
        point = np.asarray(point)

        # changes the coordinates (in place)
        if not np.allclose(point, np.zeros(3)):
            self.translate(-point)
        x = self.atoms.unique.universe.trajectory.ts.positions
        idx = self.atoms.unique.indices
        x[idx] = np.dot(x[idx], R.T)
        if not np.allclose(point, np.zeros(3)):
            self.translate(point)

        return self

    def rotateby(self, angle, axis, point=None):
        r"""Apply a rotation to the selection's coordinates.

        Parameters
        ----------
        angle : float
            Rotation angle in degrees.
        axis : array_like
            Rotation axis vector.
        point : array_like, optional
            Center of rotation. If ``None`` then the center of geometry of this
            group is used.

        Returns
        -------
        self : AtomGroup

        Notes
        -----
        The transformation from current coordinates :math:`\mathbf{x}`
        to new coordinates :math:`\mathbf{x}'` is

        .. math::

          \mathbf{x}' = \mathsf{R}\,(\mathbf{x}-\mathbf{p}) + \mathbf{p}

        where :math:`\mathsf{R}` is the rotation by `angle` around the
        `axis` going through `point` :math:`\mathbf{p}`.

        See Also
        --------
        MDAnalysis.lib.transformations.rotation_matrix : calculate :math:`\mathsf{R}`

        """
        alpha = np.radians(angle)
        axis = np.asarray(axis)
        point = np.asarray(point) if point is not None else self.centroid()
        M = transformations.rotation_matrix(alpha, axis, point=point)
        return self.transform(M)

    def pack_into_box(self, box=None, inplace=True):
        r"""Shift all atoms in this group to be within the primary unit cell.

        Parameters
        ----------
        box : array_like
            Box dimensions, can be either orthogonal or triclinic information.
            Cell dimensions must be in an identical to format to those returned
            by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`,
            ``[lx, ly, lz, alpha, beta, gamma]``. If ``None``, uses these
            timestep dimensions.
        inplace : bool
            ``True`` to change coordinates in place.

        Returns
        -------
        coords : array
            Shifted atom coordinates.

        Notes
        -----
        All atoms will be moved so that they lie between 0 and boxlength
        :math:`L_i` in all dimensions, i.e. the lower left corner of the
        simulation box is taken to be at (0,0,0):

        .. math::

           x_i' = x_i - \left\lfloor\frac{x_i}{L_i}\right\rfloor

        The default is to take unit cell information from the underlying
        :class:`~MDAnalysis.coordinates.base.Timestep` instance. The optional
        argument `box` can be used to provide alternative unit cell information
        (in the MDAnalysis standard format ``[Lx, Ly, Lz, alpha, beta,
        gamma]``).

        Works with either orthogonal or triclinic box types.


        .. versionadded:: 0.8

        """
        atomgroup = self.atoms.unique
        if box is None:  # Try and auto detect box dimensions
            box = atomgroup.dimensions  # Can accept any box

        if box.shape == (3, 3):
            # for a vector representation, diagonal cannot be zero
            if (box.diagonal() == 0.0).any():
                raise ValueError("One or more box dimensions is zero."
                                 "  You can specify a boxsize with 'box ='")
        else:
            if (box == 0).any():  # Check that a box dimension isn't zero
                raise ValueError("One or more box dimensions is zero."
                                 "  You can specify a boxsize with 'box='")

        coords = atomgroup.universe.coord.positions[atomgroup.indices]
        if not inplace:
            return distances.apply_PBC(coords, box)

        atomgroup.universe.coord.positions[atomgroup.indices] = distances.apply_PBC(coords, box)

        return atomgroup.universe.coord.positions[atomgroup.indices]

    def wrap(self, compound="atoms", center="com", box=None):
        """Shift the contents of this Group back into the unit cell.

        This is a more powerful version of :meth:`pack_into_box`, allowing
        groups of atoms to be kept together through the process.

        Parameters
        ----------
        compound : {'atoms', 'group', 'residues', 'segments', 'fragments'}
            The group which will be kept together through the shifting process.
        center : {'com', 'cog'}
            How to define the center of a given group of atoms.
        box : array
            Box dimensions, can be either orthogonal or triclinic information.
            Cell dimensions must be in an identical to format to those returned
            by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`,
            ``[lx, ly, lz, alpha, beta, gamma]``. If ``None``, uses these
            timestep dimensions.

        Notes
        -----
        When specifying a `compound`, the translation is calculated based on
        each compound. The same translation is applied to all atoms
        within this compound, meaning it will not be broken by the shift.
        This might however mean that all atoms from the compound are not
        inside the unit cell, but rather the center of the compound is.

        `center` allows the definition of the center of each group to be
        specified. This can be either 'com' for center of mass, or 'cog' for
        center of geometry.

        `box` allows a unit cell to be given for the transformation. If not
        specified, an the dimensions information from the current Timestep will
        be used.

        .. note::
           wrap with all default keywords is identical to :meth:`pack_into_box`


        .. versionadded:: 0.9.2
        """
        atomgroup = self.atoms.unique
        if compound.lower() == "atoms":
            return atomgroup.pack_into_box(box=box)

        if compound.lower() == 'group':
            objects = [atomgroup.atoms]
        elif compound.lower() == 'residues':
            objects = atomgroup.residues
        elif compound.lower() == 'segments':
            objects = atomgroup.segments
        elif compound.lower() == 'fragments':
            objects = atomgroup.fragments
        else:
            raise ValueError("Unrecognised compound definition: {0}"
                             "Please use one of 'group' 'residues' 'segments'"
                             "or 'fragments'".format(compound))

        # TODO: ADD TRY-EXCEPT FOR MASSES PRESENCE
        if center.lower() in ('com', 'centerofmass'):
            centers = np.vstack([o.atoms.center_of_mass() for o in objects])
        elif center.lower() in ('cog', 'centroid', 'centerofgeometry'):
            centers = np.vstack([o.atoms.center_of_geometry() for o in objects])
        else:
            raise ValueError("Unrecognised center definition: {0}"
                             "Please use one of 'com' or 'cog'".format(center))
        centers = centers.astype(np.float32)

        if box is None:
            box = atomgroup.dimensions

        # calculate shift per object center
        dests = distances.apply_PBC(centers, box=box)
        shifts = dests - centers

        for o, s in zip(objects, shifts):
            # Save some needless shifts
            if not all(s == 0.0):
                o.atoms.translate(s)

    def groupby(self, topattr):
        """Group together items in this group according to values of *topattr*

        Parameters
        ----------
        topattr: str
           Topology attribute to group components by.

        Returns
        -------
        dict
            Unique values of the topology attribute as keys, Groups as values.

        Example
        -------
        To group atoms with the same mass together::

          >>> ag.groupby('masses')
          {12.010999999999999: <AtomGroup with 462 atoms>,
          14.007: <AtomGroup with 116 atoms>,
          15.999000000000001: <AtomGroup with 134 atoms>}

        .. versionadded:: 0.16.0
        """
        ta = getattr(self, topattr)
        return {i: self[ta == i] for i in set(ta)}

    @_only_same_level
    def concatenate(self, other):
        """Concatenate with another Group or Component of the same level.

        Duplicate entries and original order is preserved. It is synomymous to
        the `+` operator.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with elements of `self` and `other` concatenated

        Example
        -------
        The order of the original contents (including duplicates)
        are preserved when performing a concatenation.

        >>> ag1 = u.select_atoms('name O')
        >>> ag2 = u.select_atoms('name N')
        >>> ag3 = ag1 + ag2  # or ag1.concatenate(ag2)
        >>> ag3[:3].names
        array(['O', 'O', 'O'], dtype=object)
        >>> ag3[-3:].names
        array(['N', 'N', 'N'], dtype=object)

        .. versionadded:: 0.16.0
        """
        o_ix = other.ix_array
        return self._derived_class(np.concatenate([self.ix, o_ix]),
                                   self.universe)

    @_only_same_level
    def union(self, other):
        """Group of elements either in this Group or another

        On the contrary to concatenation, this method sort the elements and
        removes duplicate ones. It is synomymous to the `|` operator.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with the combined elements of `self` and `other`, without
            duplicate elements

        Example
        -------
        In contrast to :meth:`concatenate`, any duplicates are dropped
        and the result is sorted.

        >>> ag1 = u.select_atoms('name O')
        >>> ag2 = u.select_atoms('name N')
        >>> ag3 = ag1 | ag2  # or ag1.union(ag2)
        >>> ag3[:3].names
        array(['N', 'O', 'N'], dtype=object)

        See Also
        --------
        concatenate, intersection

        .. versionadded:: 0.16
        """
        o_ix = other.ix_array
        return self._derived_class(np.union1d(self.ix, o_ix), self.universe)

    @_only_same_level
    def intersection(self, other):
        """Group of elements which are in both this Group and another

        This method removes duplicate elements and sorts the result. It is
        synomymous to the `&` operator.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with the common elements of `self` and `other`, without
            duplicate elements

        Example
        -------
        Intersections can be used when the select atoms string would
        become too complicated.  For example to find the water atoms
        which are within 4.0A of two segments:

        >>> water = u.select_atoms('resname SOL')
        >>> shell1 = water.select_atoms('around 4.0 segid 1')
        >>> shell2 = water.select_atoms('around 4.0 segid 2')
        >>> common = shell1 & shell2  # or shell1.intersection(shell2)

        See Also
        --------
        union

        .. versionadded:: 0.16
        """
        o_ix = other.ix_array
        return self._derived_class(np.intersect1d(self.ix, o_ix), self.universe)

    @_only_same_level
    def subtract(self, other):
        """Group with elements from this Group that don't appear in other

        The original order of this group is kept, as well as any duplicate
        elements. If an element of this Group is duplicated and appears in
        the other Group or Component, then all the occurences of that element
        are removed from the returned Group.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with the elements of `self` that are not in  `other`,
            conserves order and duplicates.

        Example
        -------
        Unlike :meth:`difference` this method will not sort or remove
        duplicates.

        >>> ag1 = u.atoms[[3, 3, 2, 2, 1, 1]]
        >>> ag2 = u.atoms[2]
        >>> ag3 = ag1 - ag2  # or ag1.subtract(ag2)
        >>> ag1.indices
        array([3, 3, 1, 1])

        See Also
        --------
        concatenate, difference

        .. versionadded:: 0.16
        """
        o_ix = other.ix_array
        in_other = np.in1d(self.ix, o_ix)  # mask of in self.ix AND other
        return self[~in_other]  # ie inverse of previous mask

    @_only_same_level
    def difference(self, other):
        """Elements from this Group that do not appear in another

        This method removes duplicate elements and sorts the result. As such,
        it is different from :meth:`subtract`. :meth:`difference` is synomymous
        to the `-` operator.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with the elements of `self` that are not in  `other`, without
            duplicate elements

        See Also
        --------
        subtract, symmetric_difference

        .. versionadded:: 0.16
        """
        o_ix = other.ix_array
        return self._derived_class(np.setdiff1d(self._ix, o_ix), self._u)

    @_only_same_level
    def symmetric_difference(self, other):
        """Group of elements which are only in one of this Group or another

        This method removes duplicate elements and the result is sorted. It is
        synomym to the `^` operator.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Group
            Group with the elements that are in `self` or in `other` but not in
            both, without duplicate elements

        Example
        -------

        >>> ag1 = u.atoms[[0, 1, 5, 3, 3, 2]]
        >>> ag2 = u.atoms[[4, 4, 6, 2, 3, 5]]
        >>> ag3 = ag1 ^ ag2  # or ag1.symmetric_difference(ag2)
        >>> ag3.indices  # 0 and 1 are only in ag1, 4 and 6 are only in ag2
        [0, 1, 4, 6]

        See Also
        --------
        difference

        .. versionadded:: 0.16
        """
        o_ix = other.ix_array
        return self._derived_class(np.setxor1d(self._ix, o_ix), self._u)

    def isdisjoint(self, other):
        """If the Group has no elements in common with the other Group

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Bool
            True if the two Groups do not have common elements

        .. versionadded:: 0.16
        """
        return len(self.intersection(other)) == 0

    @_only_same_level
    def issubset(self, other):
        """If all elements of this Group are part of another Group

        Note that an empty group is a subset of any group of the same level.

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Bool
            True if this Group is a subset of the other one

        .. versionadded:: 0.16
        """
        o_ix = set(other.ix_array)
        s_ix = set(self.ix)
        return s_ix.issubset(o_ix)

    def is_strict_subset(self, other):
        """If this Group is a subset of another Group but not identical

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Bool
            True if this Group is a strict subset of the other one

        .. versionadded:: 0.16
        """
        return self.issubset(other) and not self == other

    @_only_same_level
    def issuperset(self, other):
        """If all elements of another Group are part of this Group

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Bool
            True if this Group is a subset of the other one

        .. versionadded:: 0.16
        """
        o_ix = set(other.ix_array)
        s_ix = set(self.ix)
        return s_ix.issuperset(o_ix)

    def is_strict_superset(self, other):
        """If this Group is a superset of another Group but not identical

        Parameters
        ----------
        other : Group or Component
            Group or Component with `other.level` same as `self.level`

        Returns
        -------
        Bool
            True if this Group is a strict superset of the other one

        .. versionadded:: 0.16
        """
        return self.issuperset(other) and not self == other


[docs]class AtomGroup(GroupBase): """A group of atoms. An :class:`AtomGroup` is an ordered collection of atoms. Typically, an :class:`AtomGroup` is generated from a selection, or by indexing/slicing the :class:`AtomGroup` of all atoms in the :class:`Universe` at :attr:`MDAnalysis.core.universe.Universe.atoms`. An AtomGroup can be indexed and sliced like a list:: ag[0], ag[-1] will return the first and the last :class:`Atom` in the group whereas the slice :: ag[0:6:2] returns an AtomGroup of every second element, corresponding to indices 0, 2, and 4. It also supports "advanced slicing" when the argument is a :class:`numpy.ndarray` or a :class:`list`:: aslice = [0, 3, -1, 10, 3] ag[aslice] will return a new AtomGroup of atoms with those indices in the old AtomGroup. .. note:: AtomGroups originating from a selection are sorted and duplicate elements are removed. This is not true for AtomGroups produced by slicing. Thus slicing can be used when the order of atoms is crucial (for instance, in order to define angles or dihedrals). AtomGroups can be compared and combined using group operators. For instance, AtomGroups can be concatenated using `+` or :meth:`concatenate`:: ag_concat = ag1 + ag2 # or ag_concat = ag1.concatenate(ag2) When groups are concatenated, the order of the atoms is conserved. If atoms appear several times in one of the groups, the duplicates are kept in the resulting group. On the contrary to :meth:`concatenate`, :meth:`union` treats the AtomGroups as sets, duplicates are removed from the resulting group, and atoms are ordered. The `|` operator is synomymous to :meth:`union`:: ag_union = ag1 | ag2 # or ag_union = ag1.union(ag2) The opposite operation to :meth:`concatenate` is :meth:`subtract`. This method creates a new group with all the atoms of the group that are not in a given other group; the order of the atoms is kept, so as duplicates. :meth:`difference` is the set version of :meth:`subtract`. The resulting group is sorted and deduplicated. All set methods are listed in the table below. These methods treat the groups as sorted and deduplicated sets of atoms. +-------------------------------+------------+----------------------------+ | Operation | Equivalent | Result | +===============================+============+============================+ | ``s.isdisjoint(t)`` | | ``True`` if ``s`` and | | | | ``t`` do not share | | | | elements | +-------------------------------+------------+----------------------------+ | ``s.issubset(t)`` | | test if all elements of | | | | ``s`` are part of ``t`` | +-------------------------------+------------+----------------------------+ | ``s.is_strict_subset(t)`` | | test if all elements of | | | | ``s`` are part of ``t``, | | | | and ``s != t`` | +-------------------------------+------------+----------------------------+ | ``s.issuperset(t)`` | | test if all elements of | | | | ``t`` are part of ``s`` | +-------------------------------+------------+----------------------------+ | ``s.is_strict_superset(t)`` | | test if all elements of | | | | ``t`` are part of ``s``, | | | | and ``s != t`` | +-------------------------------+------------+----------------------------+ | ``s.union(t)`` | ``s | t`` | new Group with elements | | | | from both ``s`` and ``t`` | +-------------------------------+------------+----------------------------+ | ``s.intersection(t)`` | ``s & t`` | new Group with elements | | | | common to ``s`` and ``t`` | +-------------------------------+------------+----------------------------+ | ``s.difference(t)`` | ``s - t`` | new Group with elements of | | | | ``s`` that are not in ``t``| +-------------------------------+------------+----------------------------+ | ``s.symmetric_difference(t)`` | ``s ^ t`` | new Group with elements | | | | that are part of ``s`` or | | | | ``t`` but not both | +-------------------------------+------------+----------------------------+ The following methods keep the order of the atoms, and keep duplicated atoms. +-------------------------------+------------+----------------------------+ | Operation | Equivalent | Result | +===============================+============+============================+ | ``len(s)`` | | number of elements (atoms, | | | | residues or segment) in | | | | the group | +-------------------------------+------------+----------------------------+ | ``s == t`` | | test if ``s`` and ``t`` | | | | contain the same elements | | | | in the same order | +-------------------------------+------------+----------------------------+ | ``s.concatenate(t)`` | ``s + t`` | new Group with elements | | | | from ``s`` and from ``t`` | +-------------------------------+------------+----------------------------+ | ``s.subtract(t)`` | | new Group with elements | | | | from ``s`` that are not | | | | in ``t`` | +-------------------------------+------------+----------------------------+ The `in` operator allows to test if an :class:`Atom` is in the AtomGroup. 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. Atoms can also be accessed in a Pythonic fashion by using the atom name as an attribute. For instance, :: ag.CA will provide a :class:`AtomGroup` of all CA atoms 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 atoms is mainly meant for quick interactive work. Thus it either returns a single :class:`Atom` if there is only one matching 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 AtomGroup will be removed in the 1.0 release. See :ref:`Instant selectors <instance-selectors>` for details and alternatives. """ 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? if attr in ('fragments',): # TODO: Generalise this to cover many attributes # eg: # if attr in _ATTR_ERRORS: # raise NDE(_ATTR_ERRORS[attr]) raise NoDataError("AtomGroup has no fragments; this requires Bonds") 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)) def __reduce__(self): return (_unpickle, (self.universe.anchor_name, self.ix)) @property def atoms(self): """Get another AtomGroup identical to this one.""" return self.universe.atoms[self.ix] @property def n_atoms(self): """Number of atoms in AtomGroup. Equivalent to ``len(self)``.""" return len(self) @property def residues(self): """Get sorted :class:`ResidueGroup` of the (unique) residues represented in the AtomGroup.""" return self.universe.residues[np.unique(self.resindices)] @residues.setter def residues(self, new): # Can set with Res, ResGroup or list/tuple of Res if isinstance(new, Residue): r_ix = itertools.cycle((new.resindex,)) elif isinstance(new, ResidueGroup): r_ix = new.resindices else: try: r_ix = [r.resindex for r in new] except AttributeError: raise TypeError("Can only set AtomGroup residues to Residue " "or ResidueGroup not {}".format( ', '.join(type(r) for r in new if not isinstance(r, Residue)) )) if not isinstance(r_ix, itertools.cycle) and len(r_ix) != len(self): raise ValueError("Incorrect size: {} for AtomGroup of size: {}" "".format(len(new), len(self))) # Optimisation TODO: # This currently rebuilds the tt len(self) times # Ideally all changes would happen and *afterwards* tables are built # Alternatively, if the changes didn't rebuild table, this list # comprehension isn't terrible. for at, r in zip(self, r_ix): self.universe._topology.tt.move_atom(at.ix, r) @property def n_residues(self): """Number of unique residues represented in the AtomGroup. Equivalent to ``len(self.residues)``. """ return len(self.residues) @property def segments(self): """Get sorted :class:`SegmentGroup` of the (unique) segments represented in the AtomGroup.""" return self.universe.segments[np.unique(self.segindices)] @segments.setter def segments(self, new): raise NotImplementedError("Cannot assign Segments to AtomGroup. " "Segments are assigned to Residues") @property def n_segments(self): """Number of unique segments represented in the AtomGroup. Equivalent to ``len(self.segments)``. """ return len(self.segments) @property def unique(self): """Return an AtomGroup containing sorted and unique atoms only. Examples -------- >>> ag = u.atoms[[2, 1, 2, 2, 1, 0]] >>> ag <AtomGroup with 6 atoms> >>> ag.ix array([2, 1, 2, 2, 1, 0]) >>> ag2 = ag.unique >>> ag2 <AtomGroup with 3 atoms> >>> ag2.ix array([0, 1, 2]) .. versionadded:: 0.16.0 """ return self.universe.atoms[np.unique(self.ix)] @property def positions(self): """Coordinates of the atoms in the AtomGroup. The positions can be changed by assigning an array of the appropriate shape, i.e. either Nx3 to assign individual coordinates or 3, to assign the *same* coordinate to all atoms (e.g. ``ag.positions = array([0,0,0])`` will move all particles to the origin). .. note:: Changing the position is not reflected in any files; reading any frame from the trajectory will replace the change with that from the file *except* if the trajectory is held in memory, e.g., when the :class:`~MDAnalysis.core.universe.Universe.transfer_to_memory` method was used. """ return self.universe.trajectory.ts.positions[self.ix] @positions.setter def positions(self, values): ts = self.universe.trajectory.ts ts.positions[self.ix, :] = values @property def velocities(self): """Velocities of the atoms in the AtomGroup. The velocities can be changed by assigning an array of the appropriate shape, i.e. either Nx3 to assign individual velocities or 3 to assign the *same* velocity to all atoms (e.g. ``ag.velocity = array([0,0,0])`` will give all particles zero velocity). Raises a :exc:`NoDataError` if the underlying :class:`~MDAnalysis.coordinates.base.Timestep` does not contain :attr:`~MDAnalysis.coordinates.base.Timestep.velocities`. """ ts = self.universe.trajectory.ts try: return np.array(ts.velocities[self.ix]) except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain velocities") @velocities.setter def velocities(self, values): ts = self.universe.trajectory.ts try: ts.velocities[self.ix, :] = values except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain velocities") @property def forces(self): """Forces on each atom in the AtomGroup. The velocities can be changed by assigning an array of the appropriate shape, i.e. either Nx3 to assign individual velocities or 3 to assign the *same* velocity to all atoms (e.g. ``ag.velocity = array([0,0,0])`` will give all particles zero velocity). """ ts = self.universe.trajectory.ts try: return ts.forces[self.ix] except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain forces") @forces.setter def forces(self, values): ts = self.universe.trajectory.ts try: ts.forces[self.ix, :] = values except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain forces") @property def ts(self): """Temporary Timestep that contains the selection coordinates. A :class:`~MDAnalysis.coordinates.base.Timestep` instance, which can be passed to a trajectory writer. If :attr:`~AtomGroup.ts` is modified then these modifications will be present until the frame number changes (which typically happens when the underlying trajectory frame changes). It is not possible to assign a new :class:`~MDAnalysis.coordinates.base.Timestep` to the :attr:`AtomGroup.ts` attribute; change attributes of the object. """ trj_ts = self.universe.trajectory.ts # original time step return trj_ts.copy_slice(self.indices) # As with universe.select_atoms, needing to fish out specific kwargs # (namely, 'updating') doesn't allow a very clean signature.
[docs] def select_atoms(self, sel, *othersel, **selgroups): """Select atoms using a selection string. Returns an :class:`AtomGroup` with atoms sorted according to their index in the topology (this is to ensure that there are not any duplicates, which can happen with complicated selections). Examples -------- All simple selection listed below support multiple arguments which are implicitly combined with an or operator. For example >>> sel = universe.select_atoms('resname MET GLY') is equivalent to >>> sel = universe.select_atoms('resname MET or resname GLY') Will select all atoms with a residue name of either MET or GLY. Subselections can be grouped with parentheses. >>> sel = universe.select_atoms("segid DMPC and not ( name H* O* )") >>> sel <AtomGroup with 3420 atoms> Existing :class:`AtomGroup` objects can be passed as named arguments, which will then be available to the selection parser. >>> universe.select_atoms("around 10 group notHO", notHO=sel) <AtomGroup with 1250 atoms> Selections can be set to update automatically on frame change, by setting the `updating` keyword argument to `True`. This will return a :class:`UpdatingAtomGroup` which can represent the solvation shell around another object. >>> universe.select_atoms("resname SOL and around 2.0 protein", updating=True) <Updating AtomGroup with 100 atoms> Notes ----- If exact ordering of atoms is required (for instance, for :meth:`~AtomGroup.angle` or :meth:`~AtomGroup.dihedral` calculations) then one supplies selections *separately* in the required order. Also, when multiple :class:`AtomGroup` instances are concatenated with the ``+`` operator then the order of :class:`Atom` instances is preserved and duplicates are not removed. See Also -------- :ref:`selection-commands-label` for further details and examples. .. rubric:: Selection syntax The selection parser understands the following CASE SENSITIVE *keywords*: **Simple selections** protein, backbone, nucleic, nucleicbackbone selects all atoms that belong to a standard set of residues; a protein is identfied by a hard-coded set of residue names so it may not work for esoteric residues. segid *seg-name* select by segid (as given in the topology), e.g. ``segid 4AKE`` or ``segid DMPC`` resid *residue-number-range* resid can take a single residue number or a range of numbers. A range consists of two numbers separated by a colon (inclusive) such as ``resid 1:5``. A residue number ("resid") is taken directly from the topology. If icodes are present in the topology, then these will be taken into account. Ie 'resid 163B' will only select resid 163 with icode B while 'resid 163' will select only residue 163. Range selections will also respect icodes, so 'resid 162-163B' will select all residues in 162 and those in 163 up to icode B. resnum *resnum-number-range* resnum is the canonical residue number; typically it is set to the residue id in the original PDB structure. resname *residue-name* select by residue name, e.g. ``resname LYS`` name *atom-name* select by atom name (as given in the topology). Often, this is force field dependent. Example: ``name CA`` (for C&alpha; atoms) or ``name OW`` (for SPC water oxygen) type *atom-type* select by atom type; this is either a string or a number and depends on the force field; it is read from the topology file (e.g. the CHARMM PSF file contains numeric atom types). It has non-sensical values when a PDB or GRO file is used as a topology atom *seg-name* *residue-number* *atom-name* a selector for a single atom consisting of segid resid atomname, e.g. ``DMPC 1 C2`` selects the C2 carbon of the first residue of the DMPC segment altloc *alternative-location* a selection for atoms where alternative locations are available, which is often the case with high-resolution crystal structures e.g. `resid 4 and resname ALA and altloc B` selects only the atoms of ALA-4 that have an altloc B record. moltype *molecule-type* select by molecule type, e.g. ``moltype Protein_A``. At the moment, only the TPR format defines the molecule type. **Boolean** not all atoms not in the selection, e.g. ``not protein`` selects all atoms that aren't part of a protein and, or combine two selections according to the rules of boolean algebra, e.g. ``protein and not resname ALA LYS`` selects all atoms that belong to a protein, but are not in a lysine or alanine residue **Geometric** around *distance* *selection* selects all atoms a certain cutoff away from another selection, e.g. ``around 3.5 protein`` selects all atoms not belonging to protein that are within 3.5 Angstroms from the protein point *x* *y* *z* *distance* selects all atoms within a cutoff of a point in space, make sure coordinate is separated by spaces, e.g. ``point 5.0 5.0 5.0 3.5`` selects all atoms within 3.5 Angstroms of the coordinate (5.0, 5.0, 5.0) prop [abs] *property* *operator* *value* selects atoms based on position, using *property* **x**, **y**, or **z** coordinate. Supports the **abs** keyword (for absolute value) and the following *operators*: **<, >, <=, >=, ==, !=**. For example, ``prop z >= 5.0`` selects all atoms with z coordinate greater than 5.0; ``prop abs z <= 5.0`` selects all atoms within -5.0 <= z <= 5.0. sphzone *radius* *selection* Selects all atoms that are within *radius* of the center of geometry of *selection* sphlayer *inner radius* *outer radius* *selection* Similar to sphzone, but also excludes atoms that are within *inner radius* of the selection COG cyzone *externalRadius* *zMax* *zMin* *selection* selects all atoms within a cylindric zone centered in the center of geometry (COG) of a given selection, e.g. ``cyzone 15 4 -8 protein and resid 42`` selects the center of geometry of protein and resid 42, and creates a cylinder of external radius 15 centered on the COG. In z, the cylinder extends from 4 above the COG to 8 below. Positive values for *zMin*, or negative ones for *zMax*, are allowed. cylayer *innerRadius* *externalRadius* *zMax* *zMin* *selection* selects all atoms within a cylindric layer centered in the center of geometry (COG) of a given selection, e.g. ``cylayer 5 10 10 -8 protein`` selects the center of geometry of protein, and creates a cylindrical layer of inner radius 5, external radius 10 centered on the COG. In z, the cylinder extends from 10 above the COG to 8 below. Positive values for *zMin*, or negative ones for *zMax*, are allowed. **Connectivity** byres *selection* selects all atoms that are in the same segment and residue as selection, e.g. specify the subselection after the byres keyword bonded *selection* selects all atoms that are bonded to selection eg: ``select name H and bonded name O`` selects only hydrogens bonded to oxygens **Index** bynum *index-range* selects all atoms within a range of (1-based) inclusive indices, e.g. ``bynum 1`` selects the first atom in the universe; ``bynum 5:10`` selects atoms 5 through 10 inclusive. All atoms in the :class:`MDAnalysis.Universe` are consecutively numbered, and the index runs from 1 up to the total number of atoms. **Preexisting selections** group `group-name` selects the atoms in the :class:`AtomGroup` passed to the function as an argument named `group-name`. Only the atoms common to `group-name` and the instance :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` was called from will be considered, unless ``group`` is preceded by the ``global`` keyword. `group-name` will be included in the parsing just by comparison of atom indices. This means that it is up to the user to make sure the `group-name` group was defined in an appropriate :class:`Universe`. global *selection* by default, when issuing :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` from an :class:`~MDAnalysis.core.groups.AtomGroup`, selections and subselections are returned intersected with the atoms of that instance. Prefixing a selection term with ``global`` causes its selection to be returned in its entirety. As an example, the ``global`` keyword allows for ``lipids.select_atoms("around 10 global protein")`` --- where ``lipids`` is a group that does not contain any proteins. Were ``global`` absent, the result would be an empty selection since the ``protein`` subselection would itself be empty. When issuing :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` from a :class:`~MDAnalysis.core.universe.Universe`, ``global`` is ignored. **Dynamic selections** If :meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` is invoked with named argument `updating` set to `True`, an :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` instance will be returned, instead of a regular :class:`~MDAnalysis.core.groups.AtomGroup`. It behaves just like the latter, with the difference that the selection expressions are re-evaluated every time the trajectory frame changes (this happens lazily, only when the :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` is accessed so that there is no redundant updating going on). Issuing an updating selection from an already updating group will cause later updates to also reflect the updating of the base group. A non-updating selection or a slicing operation made on an :class:`~MDAnalysis.core.groups.UpdatingAtomGroup` will return a static :class:`~MDAnalysis.core.groups.AtomGroup`, which will no longer update across frames. .. versionchanged:: 0.7.4 Added *resnum* selection. .. versionchanged:: 0.8.1 Added *group* and *fullgroup* selections. .. deprecated:: 0.11 The use of ``fullgroup`` has been deprecated in favor of the equivalent ``global group``. .. versionchanged:: 0.13.0 Added *bonded* selection .. versionchanged:: 0.16.0 Resid selection now takes icodes into account where present. .. versionadded:: 0.16.0 Updating selections now possible by setting the ``updating`` argument. .. versionadded:: 0.17.0 Added *moltype* and *molnum* selections. """ updating = selgroups.pop('updating', False) sel_strs = (sel,) + othersel selections = tuple((selection.Parser.parse(s, selgroups) for s in sel_strs)) if updating: atomgrp = UpdatingAtomGroup(self, selections, sel_strs) else: # Apply the first selection and sum to it atomgrp = sum([sel.apply(self) for sel in selections[1:]], selections[0].apply(self))
return atomgrp
[docs] def split(self, level): """Split AtomGroup into a list of atomgroups by `level`. Parameters ---------- level : {'atom', 'residue', 'molecule', 'segment'} .. versionadded:: 0.9.0 .. versionchanged:: 0.17.0 Added the 'molecule' level. """ accessors = {'segment': 'segindices', 'residue': 'resindices', 'molecule': 'molnums'} if level == "atom": return [self.universe.atoms[[a.ix]] for a in self] # higher level groupings try: levelindices = getattr(self, accessors[level]) except AttributeError: raise AttributeError('This universe does not have {} ' 'information. Maybe it is not provided in the ' 'topology format in use.'.format(level)) except KeyError: raise ValueError("level = '{0}' not supported, " "must be one of {1}".format(level, accessors.keys())) return [self[levelindices == index] for index in
np.unique(levelindices)]
[docs] def guess_bonds(self, vdwradii=None): """Guess bonds that exist within this AtomGroup and add to Universe Parameters ---------- vdwradii : dict, optional Dict relating atom type: vdw radii See Also -------- :func:`MDAnalysis.topology.guessers.guess_bonds` .. versionadded:: 0.10.0 """ from ..topology.core import guess_bonds, guess_angles, guess_dihedrals from .topologyattrs import Bonds, Angles, Dihedrals def get_TopAttr(u, name, cls): """either get *name* or create one from *cls*""" try: return getattr(u._topology, name) except AttributeError: attr = cls([]) u.add_TopologyAttr(attr) return attr # indices of bonds b = guess_bonds(self.atoms, self.atoms.positions, vdwradii=vdwradii) bondattr = get_TopAttr(self.universe, 'bonds', Bonds) bondattr.add_bonds(b, guessed=True) a = guess_angles(self.bonds) angleattr = get_TopAttr(self.universe, 'angles', Angles) angleattr.add_bonds(a, guessed=True) d = guess_dihedrals(self.angles) diheattr = get_TopAttr(self.universe, 'dihedrals', Dihedrals)
diheattr.add_bonds(d) @property def bond(self): """This AtomGroup represented as a Bond object Returns ------- A :class:`MDAnalysis.core.topologyobjects.Bond` object Raises ------ `ValueError` if the AtomGroup is not length 2 .. versionadded:: 0.11.0 """ if len(self) != 2: raise ValueError( "bond only makes sense for a group with exactly 2 atoms") return topologyobjects.Bond(self.ix, self.universe) @property def angle(self): """This AtomGroup represented as an Angle object Returns ------- A :class:`MDAnalysis.core.topologyobjects.Angle` object Raises ------ `ValueError` if the AtomGroup is not length 3 .. versionadded:: 0.11.0 """ if len(self) != 3: raise ValueError( "angle only makes sense for a group with exactly 3 atoms") return topologyobjects.Angle(self.ix, self.universe) @property def dihedral(self): """This AtomGroup represented as a Dihedral object Returns ------- A :class:`MDAnalysis.core.topologyobjects.Dihedral` object Raises ------ `ValueError` if the AtomGroup is not length 4 .. versionadded:: 0.11.0 """ if len(self) != 4: raise ValueError( "dihedral only makes sense for a group with exactly 4 atoms") return topologyobjects.Dihedral(self.ix, self.universe) @property def improper(self): """This AtomGroup represented as an ImproperDihedral object Returns ------- A :class:`MDAnalysis.core.topologyobjects.ImproperDihedral` object Raises ------ `ValueError` if the AtomGroup is not length 4 .. versionadded:: 0.11.0 """ if len(self) != 4: raise ValueError( "improper only makes sense for a group with exactly 4 atoms") return topologyobjects.ImproperDihedral(self.ix, self.universe)
[docs] def write(self, filename=None, file_format="PDB", filenamefmt="{trjname}_{frame}", **kwargs): """Write `AtomGroup` to a file. The output can either be a coordinate file or a selection, depending on the `format`. Only single-frame coordinate files are supported. If you need to write out a trajectory, see :mod:`MDAnalysis.coordinates`. Parameters ---------- filename : str, optional ``None``: create TRJNAME_FRAME.FORMAT from filenamefmt [``None``] file_format : str, optional PDB, CRD, GRO, VMD (tcl), PyMol (pml), Gromacs (ndx) CHARMM (str) Jmol (spt); case-insensitive and can also be supplied as the filename extension [PDB] filenamefmt : str, optional format string for default filename; use substitution tokens 'trjname' and 'frame' ["%(trjname)s_%(frame)d"] bonds : str, optional how to handle bond information, especially relevant for PDBs. ``"conect"``: write only the CONECT records defined in the original file. ``"all"``: write out all bonds, both the original defined and those guessed by MDAnalysis. ``None``: do not write out bonds. Default os ``"conect"``. .. versionchanged:: 0.9.0 Merged with write_selection. This method can now write both selections out. """ # check that AtomGroup actually has any atoms (Issue #434) if len(self.atoms) == 0: raise IndexError("Cannot write an AtomGroup with 0 atoms") trj = self.universe.trajectory # unified trajectory API if trj.n_frames == 1: kwargs.setdefault("multiframe", False) if filename is None: trjname, ext = os.path.splitext(os.path.basename(trj.filename)) filename = filenamefmt.format(trjname=trjname, frame=trj.frame) filename = util.filename(filename, ext=file_format.lower(), keep=True) # From the following blocks, one must pass. # Both can't pass as the extensions don't overlap. # Try and select a Class using get_ methods (becomes `writer`) # Once (and if!) class is selected, use it in with block try: # format keyword works differently in get_writer and get_selection_writer # here it overrides everything, in get_sel it is just a default # apply sparingly here! format = os.path.splitext(filename)[1][1:] # strip initial dot! format = format or file_format format = format.strip().upper() multiframe = kwargs.pop('multiframe', None) writer = get_writer_for(filename, format=format, multiframe=multiframe) #MDAnalysis.coordinates.writer(filename, **kwargs) coords = True except (ValueError, TypeError): coords = False try: # here `file_format` is only used as default, # anything pulled off `filename` will be used preferentially writer = get_selection_writer_for(filename, file_format) selection = True except (TypeError, NotImplementedError): selection = False if not (coords or selection): raise ValueError("No writer found for format: {}".format(filename)) else: with writer(filename, n_atoms=self.n_atoms, **kwargs) as w:
w.write(self.atoms)
[docs]class ResidueGroup(GroupBase): """ResidueGroup base class. This class is used by a :class:`Universe` for generating its Topology-specific :class:`ResidueGroup` class. All the :class:`TopologyAttr` components are obtained from :class:`GroupBase`, so this class only includes ad-hoc methods specific to ResidueGroups. ResidueGroups can be compared and combined using group operators. See the list of these operators on :class:`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. """ @property def atoms(self): """Get an :class:`AtomGroup` of atoms represented in this :class:`ResidueGroup`. The atoms are ordered locally by residue in the :class:`ResidueGroup`. No duplicates are removed. """ return self.universe.atoms[np.concatenate(self.indices)] @property def n_atoms(self): """Number of atoms represented in :class:`ResidueGroup`, including duplicate residues. Equivalent to ``len(self.atoms)``. """ return len(self.atoms) @property def residues(self): """Get another :class:`ResidueGroup` identical to this one. """ return self.universe.residues[self.ix] @property def n_residues(self): """Number of residues in ResidueGroup. Equivalent to ``len(self)``. """ return len(self) @property def segments(self): """Get sorted SegmentGroup of the (unique) segments represented in the ResidueGroup. """ return self.universe.segments[np.unique(self.segindices)] @segments.setter def segments(self, new): # Can set with Seg, SegGroup or list/tuple of Seg if isinstance(new, Segment): s_ix = itertools.cycle((new.segindex,)) elif isinstance(new, SegmentGroup): s_ix = new.segindices else: try: s_ix = [s.segindex for s in new] except AttributeError: raise TypeError("Can only set ResidueGroup residues to Segment " "or ResidueGroup not {}".format( ', '.join(type(r) for r in new if not isinstance(r, Segment)) )) if not isinstance(s_ix, itertools.cycle) and len(s_ix) != len(self): raise ValueError("Incorrect size: {} for ResidueGroup of size: {}" "".format(len(new), len(self))) # Optimisation TODO: # This currently rebuilds the tt len(self) times # Ideally all changes would happen and *afterwards* tables are built # Alternatively, if the changes didn't rebuild table, this list # comprehension isn't terrible. for r, s in zip(self, s_ix): self.universe._topology.tt.move_residue(r.ix, s) @property def n_segments(self): """Number of unique segments represented in the ResidueGroup. Equivalent to ``len(self.segments)``. """ return len(self.segments) @property def unique(self): """Return a ResidueGroup containing sorted and unique residues only. Examples -------- >>> rg = u.residues[[2, 1, 2, 2, 1, 0]] >>> rg <ResidueGroup with 6 residues> >>> rg.ix array([2, 1, 2, 2, 1, 0]) >>> rg2 = rg.unique >>> rg2 <ResidueGroup with 3 residues> >>> rg2.ix array([0, 1, 2]) .. versionadded:: 0.16.0 """
return self.universe.residues[np.unique(self.ix)]
[docs]class SegmentGroup(GroupBase): """SegmentGroup base class. This class is used by a Universe for generating its Topology-specific SegmentGroup class. All the TopologyAttr components are obtained from GroupBase, so this class only includes ad-hoc methods specific to SegmentGroups. SegmentGroups can be compared and combined using group operators. See the list of these operators on :class:`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. """ @property def atoms(self): """Get an AtomGroup of atoms represented in this SegmentGroup. The atoms are ordered locally by residue, which are further ordered by segment in the SegmentGroup. No duplicates are removed. """ return self.universe.atoms[np.concatenate(self.indices)] @property def n_atoms(self): """Number of atoms represented in SegmentGroup, including duplicate segments. Equivalent to ``len(self.atoms)``. """ return len(self.atoms) @property def residues(self): """Get a ResidueGroup of residues represented in this SegmentGroup. The residues are ordered locally by segment in the SegmentGroup. No duplicates are removed. """ return self.universe.residues[np.concatenate(self.resindices)] @property def n_residues(self): """Number of residues represented in SegmentGroup, including duplicate segments. Equivalent to ``len(self.residues)``. """ return len(self.residues) @property def segments(self): """Get another SegmentGroup identical to this one. """ return self.universe.segments[self.ix] @property def n_segments(self): """Number of segments in SegmentGroup. Equivalent to ``len(self)``. """ return len(self) @property def unique(self): """Return a SegmentGroup containing sorted and unique segments only. Examples -------- >>> sg = u.segments[[2, 1, 2, 2, 1, 0]] >>> sg <SegmentGroup with 6 segments> >>> sg.ix array([2, 1, 2, 2, 1, 0]) >>> sg2 = sg.unique >>> sg2 <SegmentGroup with 3 segments> >>> sg2.ix array([0, 1, 2]) .. versionadded:: 0.16.0 """
return self.universe.segments[np.unique(self.ix)] @functools.total_ordering class ComponentBase(_MutableBase): """Base class from which a Universe's Component class is built. Components are the individual objects that are found in Groups. """ def __init__(self, ix, u): # index of component self._ix = ix self._u = u def __lt__(self, other): if self.level != other.level: raise TypeError("Can't compare different level objects") return self.ix < other.ix def __eq__(self, other): if self.level != other.level: raise TypeError("Can't compare different level objects") return self.ix == other.ix def __ne__(self, other): return not self == other def __hash__(self): return hash(self.ix) @_only_same_level def __add__(self, other): """Concatenate the Component with another Component or Group of the same level. Parameters ---------- other : Component or Group Component or Group with `other.level` same as `self.level` Returns ------- Group Group with elements of `self` and `other` concatenated """ o_ix = other.ix_array return self.level.plural( np.concatenate([self.ix_array, o_ix]), self.universe) def __radd__(self, other): """Using built-in sum requires supporting 0 + self. If other is anything other 0, an exception will be raised. Parameters ---------- other : int Other should be 0, or else an exception will be raised. Returns ------- self Group with elements of `self` reproduced """ if other == 0: return self.level.plural(self.ix_array, self.universe) else: raise TypeError("unsupported operand type(s) for +:" " '{}' and '{}'".format(type(self).__name__, type(other).__name__)) @property def universe(self): return self._u @property def ix(self): """Unique index of this component. If this component is an Atom, this is the index of the atom. If it is a Residue, this is the index of the residue. If it is a Segment, this is the index of the segment. """ return self._ix @property def ix_array(self): """Unique index of this component as an array. This method gives a consistent API between components and groups. See Also -------- ix """ return np.array([self.ix], dtype=np.intp)
[docs]class Atom(ComponentBase): """Atom base class. This class is used by a Universe for generating its Topology-specific Atom class. All the TopologyAttr components are obtained from ComponentBase, so this class only includes ad-hoc methods specific to Atoms. """ def __getattr__(self, attr): """Try and catch known attributes and give better error message""" if attr in ('fragment',): raise NoDataError("Atom has no fragment data, this requires Bonds") else: raise AttributeError("{cls} has no attribute {attr}".format( cls=self.__class__.__name__, attr=attr)) def __repr__(self): me = '<Atom {}:'.format(self.ix + 1) if hasattr(self, 'name'): me += ' {}'.format(self.name) if hasattr(self, 'type'): me += ' of type {}'.format(self.type) if hasattr(self, 'resname'): me += ' of resname {},'.format(self.resname) if hasattr(self, 'resid'): me += ' resid {}'.format(self.resid) if hasattr(self, 'segid'): me += ' and segid {}'.format(self.segid) if hasattr(self, 'altLoc'): me += ' and altLoc {}'.format(self.altLoc) return me + '>' @property def residue(self): return self.universe.residues[self.universe._topology.resindices[self]] @residue.setter def residue(self, new): if not isinstance(new, Residue): raise TypeError( "Can only set Atom residue to Residue, not {}".format(type(new))) self.universe._topology.tt.move_atom(self.ix, new.resindex) @property def segment(self): return self.universe.segments[self.universe._topology.segindices[self]] @segment.setter def segment(self, new): raise NotImplementedError("Cannot set atom segment. " "Segments are assigned to Residues") @property def position(self): """Coordinates of the atom. The position can be changed by assigning an array of length (3,). .. note:: changing the position is not reflected in any files; reading any frame from the trajectory will replace the change with that from the file """ return self.universe.trajectory.ts.positions[self.ix].copy() @position.setter def position(self, values): self.universe.trajectory.ts.positions[self.ix, :] = values @property def velocity(self): """Velocity of the atom. The velocity can be changed by assigning an array of shape (3,). .. note:: changing the velocity is not reflected in any files; reading any frame from the trajectory will replace the change with that from the file A :exc:`~MDAnalysis.NoDataError` is raised if the trajectory does not contain velocities. """ ts = self.universe.trajectory.ts try: return ts.velocities[self.ix].copy() except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain velocities") @velocity.setter def velocity(self, values): ts = self.universe.trajectory.ts try: ts.velocities[self.ix, :] = values except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain velocities") @property def force(self): """Force on the atom. The force can be changed by assigning an array of shape (3,). .. note:: changing the force is not reflected in any files; reading any frame from the trajectory will replace the change with that from the file A :exc:`~MDAnalysis.NoDataError` is raised if the trajectory does not contain forces. """ ts = self.universe.trajectory.ts try: return ts.forces[self.ix].copy() except (AttributeError, NoDataError): raise NoDataError("Timestep does not contain forces") @force.setter def force(self, values): ts = self.universe.trajectory.ts try: ts.forces[self.ix, :] = values except (AttributeError, NoDataError):
raise NoDataError("Timestep does not contain forces")
[docs]class Residue(ComponentBase): """Residue base class. This class is used by a Universe for generating its Topology-specific Residue class. All the TopologyAttr components are obtained from ComponentBase, so this class only includes ad-hoc methods specific to Residues. """ def __repr__(self): me = '<Residue' if hasattr(self, 'resname'): me += ' {},'.format(self.resname) if hasattr(self, 'resid'): me += ' {}'.format(self.resid) return me + '>' @property def atoms(self): return self.universe.atoms[self.universe._topology.indices[self][0]] @property def segment(self): return self.universe.segments[self.universe._topology.segindices[self]] @segment.setter def segment(self, new): if not isinstance(new, Segment): raise TypeError( "Can only set Residue segment to Segment, not {}".format(type(new)))
self.universe._topology.tt.move_residue(self.ix, new.segindex)
[docs]class Segment(ComponentBase): """Segment base class. This class is used by a Universe for generating its Topology-specific Segment class. All the TopologyAttr components are obtained from ComponentBase, so this class only includes ad-hoc methods specific to Segments. .. 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. """ def __repr__(self): me = '<Segment' if hasattr(self, 'segid'): me += ' {}'.format(self.segid) return me + '>' @property def atoms(self): return self.universe.atoms[self.universe._topology.indices[self][0]] @property def residues(self): return self.universe.residues[self.universe._topology.resindices[self][0]] 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 # here, otherwise we get __getattribute__ infinite loops. _UAG_SHORTCUT_ATTRS = { # Class information of the UAG "__class__", "_derived_class", # Metadata of the UAG "_base_group", "_selections", "_lastupdate", "level", "_u", "universe", # Methods of the UAG "_ensure_updated", "is_uptodate", "update_selection", }
[docs]class UpdatingAtomGroup(AtomGroup): """:class:`AtomGroup` subclass that dynamically updates its selected atoms. Accessing any attribute/method of an :class:`UpdatingAtomGroup` instance triggers a check for the last frame the group was updated. If the last frame matches the current trajectory frame, the attribute is returned normally; otherwise the group is updated (the stored selections are re-applied), and only then is the attribute returned. .. versionadded:: 0.16.0 """ # WARNING: This class has __getattribute__ and __getattr__ methods (the # latter inherited from AtomGroup). Because of this bugs introduced in the # class that cause an AttributeError may be very hard to diagnose and # debug: the most obvious symptom is an infinite loop going through both # __getattribute__ and __getattr__, and a solution might be to add said # attribute to _UAG_SHORTCUT_ATTRS. def __init__(self, base_group, selections, strings): """ Parameters ---------- base_group : :class:`AtomGroup` group on which *selections* are to be applied. selections : a tuple of :class:`~MDAnalysis.core.selection.Selection` instances selections ready to be applied to *base_group*. """ # Because we're implementing __getattribute__, which needs _u for # its check, no self.attribute access can be made before this line self._u = base_group.universe self._selections = selections self._selection_strings = strings self._base_group = base_group self._lastupdate = None self._derived_class = base_group._derived_class if self._selections: # Allows the creation of a cheap placeholder UpdatingAtomGroup # by passing an empty selection tuple. self._ensure_updated()
[docs] def update_selection(self): """ Forces the reevaluation and application of the group's selection(s). This method is triggered automatically when accessing attributes, if the last update occurred under a different trajectory frame. """ bg = self._base_group sels = self._selections if sels: # As with select_atoms, we select the first sel and then sum to it. ix = sum([sel.apply(bg) for sel in sels[1:]], sels[0].apply(bg)).ix else: ix = np.array([], dtype=np.intp) # Run back through AtomGroup init with this information to remake ourselves super(UpdatingAtomGroup, self).__init__(ix, self.universe)
self.is_uptodate = True @property def is_uptodate(self): """ Checks whether the selection needs updating based on frame number only. Modifications to the coordinate data that render selections stale are not caught, and in those cases :attr:`is_uptodate` may return an erroneous value. Returns ------- bool `True` if the group's selection is up-to-date, `False` otherwise. """ try: return self.universe.trajectory.frame == self._lastupdate except AttributeError: # self.universe has no trajectory return self._lastupdate == -1 @is_uptodate.setter def is_uptodate(self, value): if value: try: self._lastupdate = self.universe.trajectory.frame except AttributeError: # self.universe has no trajectory self._lastupdate = -1 else: # This always marks the selection as outdated self._lastupdate = None def _ensure_updated(self): """ Checks whether the selection needs updating and updates it, if needed. Returns ------- bool `True` if the group was already up-to-date, `False` otherwise. """ status = self.is_uptodate if not status: self.update_selection() return status def __getattribute__(self, name): # ALL attribute access goes through here # If the requested attribute is public (not starting with '_') and # isn't in the shortcut list, update ourselves if not (name.startswith('_') or name in _UAG_SHORTCUT_ATTRS): self._ensure_updated() # Going via object.__getattribute__ then bypasses this check stage return object.__getattribute__(self, name) def __reduce__(self): # strategy for unpickling is: # - unpickle base group # - recreate UAG as created through select_atoms (basegroup and selstrs) # even if base_group is a UAG this will work through recursion return (_unpickle_uag, (self._base_group.__reduce__(), self._selections, self._selection_strings)) def __repr__(self): basestr = super(UpdatingAtomGroup, self).__repr__() if not self._selection_strings: return basestr sels = "'{}'".format("' + '".join(self._selection_strings)) # Cheap comparison. Might fail for corner cases but this is # mostly cosmetic. if self._base_group is self.universe.atoms: basegrp = "the entire Universe." else: basegrp = "another AtomGroup." # With a shorthand to conditionally append the 's' in 'selections'. return "{}, with selection{} {} on {}>".format(basestr[:-1],
"s"[len(self._selection_strings)==1:], sels, basegrp) # Define relationships between these classes # with Level objects _Level = namedtuple('Level', ['name', 'singular', 'plural']) ATOMLEVEL = _Level('atom', Atom, AtomGroup) RESIDUELEVEL = _Level('residue', Residue, ResidueGroup) SEGMENTLEVEL = _Level('segment', Segment, SegmentGroup) Atom.level = ATOMLEVEL AtomGroup.level = ATOMLEVEL Residue.level = RESIDUELEVEL ResidueGroup.level = RESIDUELEVEL Segment.level = SEGMENTLEVEL SegmentGroup.level = SEGMENTLEVEL def requires(*attrs): """Decorator to check if all AtomGroup arguments have certain attributes Example ------- When used to wrap a function, will check all AtomGroup arguments for the listed requirements @requires('masses', 'charges') def mass_times_charge(atomgroup): return atomgroup.masses * atomgroup.charges """ def require_dec(func): @functools.wraps(func) def check_args(*args, **kwargs): for a in args: # for each argument if isinstance(a, AtomGroup): # Make list of missing attributes missing = [attr for attr in attrs if not hasattr(a, attr)] if missing: raise NoDataError( "{funcname} failed. " "AtomGroup is missing the following required " "attributes: {attrs}".format( funcname=func.__name__, attrs=', '.join(missing))) return func(*args, **kwargs) return check_args return require_dec