# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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.
# doi: 10.25080/majora-629e541a-00e
#
# 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
:class:`atoms<Atom>` 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. :class:`AtomGroup` instances
can be easily created (e.g., from an :meth:`AtomGroup.select_atoms` selection or
simply by slicing).
For convenience, chemically meaningful groups of :class:`Atoms<Atom>` 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 collections import namedtuple
import numpy as np
import functools
import itertools
import numbers
import os
import contextlib
import warnings
from .. import (_CONVERTERS,
_TOPOLOGY_ATTRS, _TOPOLOGY_TRANSPLANTS, _TOPOLOGY_ATTRNAMES)
from ..lib import util
from ..lib.util import (cached, warn_if_not_unique,
unique_int_1d, unique_int_1d_unsorted,
int_array_is_sorted
)
from ..lib import distances
from ..lib import transformations
from ..lib import mdamath
from .accessors import Accessor, ConverterWrapper
from ..selections import get_writer as get_selection_writer_for
from . import selection
from ..exceptions import NoDataError
from . import topologyobjects
from ._get_readers import get_writer_for, get_converter_for
def _unpickle(u, ix):
return u.atoms[ix]
# TODO 3.0: deprecate _unpickle in favor of _unpickle2.
def _unpickle2(u, ix, cls):
return cls(ix, u)
def _unpickle_uag(basepickle, selections, selstrs):
bfunc, bargs = basepickle[0], basepickle[1:][0]
basegroup = bfunc(*bargs)
return UpdatingAtomGroup(basegroup, selections, selstrs)
def make_classes():
r"""Make a fresh copy of all classes
Returns
-------
Two dictionaries. One with a set of :class:`_TopologyAttrContainer` classes
to serve as bases for :class:`~MDAnalysis.core.universe.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:`~MDAnalysis.core.topologyattrs.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:`~MDAnalysis.core.universe.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
(:class:`AtomGroup` etc.) and Components (:class:`Atom` etc.) in
internal methods when considering actions such as addition of
objects or adding
:class:`TopologyAttributes<MDAnalysis.core.topologyattrs.TopologyAttr>`
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, cls, other), {})
newcls._derived_class = newcls
return newcls
@classmethod
def _add_prop(cls, attr):
"""Add `attr` into the namespace for this class
Parameters
----------
attr : A :class:`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)
@classmethod
def _del_prop(cls, attr):
"""Remove `attr` from the namespace for this class.
Parameters
----------
attr : A :class:`TopologyAttr` object
"""
with contextlib.suppress(AttributeError):
delattr(cls, attr.attrname)
with contextlib.suppress(AttributeError):
delattr(cls, attr.singular)
cls._SETATTR_WHITELIST.discard(attr.attrname)
cls._SETATTR_WHITELIST.discard(attr.singular)
def __setattr__(self, attr, value):
# `ag.this = 42` calls setattr(ag, 'this', 42)
if not (attr.startswith('_') or # 'private' allowed
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:`~MDAnalysis.core.universe.Universe._classes`. If there is a cache
miss, a merged class is made
with a base from :attr:`~MDAnalysis.core.universe.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:
# older AtomGroup init method..
u = args[0][0].universe
except (TypeError, IndexError, AttributeError):
from .universe import Universe
# 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, (Universe, GroupBase,
ComponentBase)):
u = arg.universe
break
else:
errmsg = (
f"No universe, or universe-containing object "
f"passed to the initialization of {cls.__name__}")
raise TypeError(errmsg) from None
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:
errmsg = (f"Attempted to instantiate class '{cls.__name__}' "
f"but none of its parents are known to the universe."
f" Currently possible parent classes are: "
f"{str(sorted(u._class_bases.keys()))}")
raise TypeError(errmsg) from None
newcls = u._classes[cls] = parent_cls._mix(cls)
return object.__new__(newcls)
def __getattr__(self, attr):
selfcls = type(self).__name__
if attr in _TOPOLOGY_TRANSPLANTS:
topattr, meth, clstype = _TOPOLOGY_TRANSPLANTS[attr]
if isinstance(meth, property):
attrname = attr
attrtype = 'property'
else:
attrname = attr + '()'
attrtype = 'method'
# property of wrong group/component
if not isinstance(self, clstype):
mname = 'property' if isinstance(meth, property) else 'method'
err = '{attr} is a {method} of {clstype}, not {selfcls}'
clsname = clstype.__name__
if clsname == 'GroupBase':
clsname = selfcls + 'Group'
raise AttributeError(err.format(attr=attrname,
method=attrtype,
clstype=clsname,
selfcls=selfcls))
# missing required topologyattr
else:
err = ('{selfcls}.{attrname} not available; '
'this requires {topattr}')
raise NoDataError(err.format(selfcls=selfcls,
attrname=attrname,
topattr=topattr))
else:
clean = attr.lower().replace('_', '')
err = '{selfcls} has no attribute {attr}. '.format(selfcls=selfcls,
attr=attr)
if clean in _TOPOLOGY_ATTRNAMES:
match = _TOPOLOGY_ATTRNAMES[clean]
err += 'Did you mean {match}?'.format(match=match)
raise AttributeError(err)
def get_connections(self, typename, outside=True):
"""
Get bonded connections between atoms as a
:class:`~MDAnalysis.core.topologyobjects.TopologyGroup`.
Parameters
----------
typename : str
group name. One of {"bonds", "angles", "dihedrals",
"impropers", "ureybradleys", "cmaps"}
outside : bool (optional)
Whether to include connections involving atoms outside
this group.
Returns
-------
TopologyGroup
containing the bonded group of choice, i.e. bonds, angles,
dihedrals, impropers, ureybradleys or cmaps.
.. versionadded:: 1.1.0
"""
# AtomGroup has handy error messages for missing attributes
ugroup = getattr(self.universe.atoms, typename)
if not ugroup:
return ugroup
func = np.any if outside else np.all
try:
indices = self.atoms.ix_array
except AttributeError: # if self is an Atom
indices = self.ix_array
seen = [np.in1d(col, indices) for col in ugroup._bix.T]
mask = func(seen, axis=0)
return ugroup[mask]
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 _pbc_to_wrap(function):
"""Raises deprecation warning if 'pbc' is set and assigns value to 'wrap'"""
@functools.wraps(function)
def wrapped(group, *args, **kwargs):
if kwargs.get('pbc', None) is not None:
warnings.warn("The 'pbc' kwarg has been deprecated and will be "
"removed in version 3.0., "
"please use 'wrap' instead",
DeprecationWarning)
kwargs['wrap'] = kwargs.pop('pbc')
return function(group, *args, **kwargs)
return wrapped
def check_wrap_and_unwrap(function):
"""Raises ValueError when both 'wrap' and 'unwrap' are set to True"""
@functools.wraps(function)
def wrapped(group, *args, **kwargs):
if kwargs.get('wrap') and kwargs.get('unwrap'):
raise ValueError("both 'wrap' and 'unwrap' can not be set to true")
return function(group, *args, **kwargs)
return wrapped
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):
r"""Base class from which a :class:`<~MDAnalysis.core.universe.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):
try:
if len(args) == 1:
# 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
except (AttributeError, # couldn't find ix/universe
TypeError): # couldn't iterate the object we got
errmsg = (
"Can only initialise a Group from an iterable of Atom/Residue/"
"Segment objects eg: AtomGroup([Atom1, Atom2, Atom3]) "
"or an iterable of indices and a Universe reference "
"eg: AtomGroup([0, 5, 7, 8], u).")
raise TypeError(errmsg) from None
# 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 item is None:
raise TypeError('None cannot be used to index a group.')
elif 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 __getattr__(self, attr):
selfcls = type(self).__name__
if attr in _TOPOLOGY_ATTRS:
cls = _TOPOLOGY_ATTRS[attr]
if attr == cls.singular and attr != cls.attrname:
err = ('{selfcls} has no attribute {attr}. '
'Do you mean {plural}?')
raise AttributeError(err.format(selfcls=selfcls, attr=attr,
plural=cls.attrname))
else:
err = 'This Universe does not contain {singular} information'
raise NoDataError(err.format(singular=cls.singular))
else:
return super(GroupBase, self).__getattr__(attr)
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 :class:`Universes<MDAnalysis.core.universe.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):
"""The underlying :class:`~MDAnalysis.core.universe.Universe` the group
belongs to.
"""
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, :attr:`ix_array` is the same as :attr:`ix`. This method
gives a consistent API between components and groups.
See Also
--------
:attr:`ix`
"""
return self._ix
@property
def dimensions(self):
"""Obtain a copy of the dimensions of the currently loaded Timestep"""
dims = self.universe.trajectory.ts.dimensions
if dims is None:
return dims
else:
return dims.copy()
@dimensions.setter
def dimensions(self, dimensions):
self.universe.trajectory.ts.dimensions = dimensions
@property
@cached('sorted_unique')
def sorted_unique(self):
return self.asunique(sorted=True)
@property
@cached('unsorted_unique')
def unsorted_unique(self):
return self.asunique(sorted=False)
@property
@cached('issorted')
def issorted(self):
return int_array_is_sorted(self.ix)
@property
@cached('isunique')
def isunique(self):
"""Boolean indicating whether all components of the group are unique,
i.e., the group contains no duplicates.
Examples
--------
>>> ag = u.atoms[[2, 1, 2, 2, 1, 0]]
>>> ag
<AtomGroup with 6 atoms>
>>> ag.isunique
False
>>> ag2 = ag.unique
>>> ag2
<AtomGroup with 3 atoms>
>>> ag2.isunique
True
See Also
--------
asunique
.. versionadded:: 0.19.0
"""
if len(self) <= 1:
return True
return unique_int_1d(self.ix).shape[0] == self.ix.shape[0]
def _asunique(self, group, sorted=False, set_mask=False):
try:
name = 'sorted_unique' if sorted else 'unsorted_unique'
return self._cache[name]
except KeyError:
pass
if self.isunique:
if not sorted:
self._cache['unsorted_unique'] = self
return self
if self.issorted:
self._cache['unsorted_unique'] = self
self._cache['sorted_unique'] = self
return self
if sorted:
if set_mask:
unique_ix, restore_mask = np.unique(
self.ix, return_inverse=True)
self._unique_restore_mask = restore_mask
else:
unique_ix = unique_int_1d(self.ix)
_unique = group[unique_ix]
_unique._cache['isunique'] = True
_unique._cache['issorted'] = True
_unique._cache['sorted_unique'] = _unique
_unique._cache['unsorted_unique'] = _unique
self._cache['sorted_unique'] = _unique
return _unique
indices = unique_int_1d_unsorted(self.ix)
if set_mask:
mask = np.zeros_like(self.ix)
for i, x in enumerate(indices):
values = np.where(self.ix == x)[0]
mask[values] = i
self._unique_restore_mask = mask
issorted = int_array_is_sorted(indices)
if issorted and 'sorted_unique' in self._cache:
self._cache['unsorted_unique'] = self.sorted_unique
return self.sorted_unique
_unique = group[indices]
_unique._cache['isunique'] = True
_unique._cache['issorted'] = issorted
_unique._cache['unsorted_unique'] = _unique
self._cache['unsorted_unique'] = _unique
if issorted:
self._cache['sorted_unique'] = _unique
_unique._cache['sorted_unique'] = _unique
return _unique
def _get_compound_indices(self, compound):
if compound == 'residues':
compound_indices = self.atoms.resindices
elif compound == 'segments':
compound_indices = self.atoms.segindices
elif compound == 'molecules':
try:
compound_indices = self.atoms.molnums
except AttributeError:
errmsg = ("Cannot use compound='molecules': No molecule "
"information in topology.")
raise NoDataError(errmsg) from None
elif compound == 'fragments':
try:
compound_indices = self.atoms.fragindices
except NoDataError:
errmsg = ("Cannot use compound='fragments': No bond "
"information in topology.")
raise NoDataError(errmsg) from None
elif compound == 'group':
raise ValueError("This method does not accept compound='group'")
else:
raise ValueError("Unrecognized compound definition: {}\nPlease use"
" one of 'residues', 'segments', 'molecules',"
" or 'fragments'.".format(compound))
return compound_indices
def _split_by_compound_indices(self, compound, stable_sort=False):
"""Splits a group's compounds into groups of equal compound size.
Grouping equal sizes together facilitates subsequent vectorization.
For a 10-atom molecule with atoms organized into compounds C0 through
C2::
at.id: 0 1 2 3 4 5 6 7 8 9
compound: C0 C0 C0 C0 C1 C1 C2 C2 C2 C2
this function will yield an `atom_masks` list with two submasks: one
for compounds of size 2 and one for compounds of size 4:
[array([[4, 5]]),
array([[1, 2, 3, 0],
[8, 7, 6, 9]])]
(Note that atom order within component submasks may be lost unless a
`stable_sort` is requested)
These submasks can be used directly to fancy-index arrays of the same
length as self (including :class:`AtomGroups<AtomGroup>`).
This function also returns `compound_masks`, the boolean mapping of
each of the `atom_masks` submask into the original compound order::
[array([False, True, False]),
array([ True, False, True])]
Parameters
----------
compound : {'segments', 'residues', 'molecules', 'fragments'}
The compound type to base splitting on.
stable_sort : bool, optional
Whether to ensure that, when needed, sorting does not affect an
atom's order within a compound (at a cost to performance). E.g.,
for an unwrap operation it is important that the first atom of a
compound is always the same, whereas a center-of-geometry
computation wouldn't care.
Returns
-------
atom_masks : list of numpy.ndarray
Integer masks for fancy-indexing atoms/weights lists; masks are
already shaped as ``(number of compounds of a given size,
compound_size)``.
compound_masks : list of numpy.ndarray
1D boolean masks for fancy-indexing lists of compounds. Translate
the distribution of the compounds in each mask of `atom_masks` into
their original order.
n_compounds : int
The number of individual compounds.
"""
# Caching would help here, especially when repeating the operation
# over different frames, since these masks are coordinate-independent.
# However, cache must be invalidated whenever new compound indices are
# modified, which is not yet implemented.
# Also, should we include here the grouping for 'group', which is
# essentially a non-split?
compound_indices = self._get_compound_indices(compound)
compound_sizes = np.bincount(compound_indices)
size_per_atom = compound_sizes[compound_indices]
compound_sizes = compound_sizes[compound_sizes != 0]
unique_compound_sizes = unique_int_1d(compound_sizes)
# Are we already sorted? argsorting and fancy-indexing can be expensive
# so we do a quick pre-check.
needs_sorting = np.any(np.diff(compound_indices) < 0)
if needs_sorting:
# stable sort ensures reproducibility, especially concerning who
# gets to be a compound's atom[0] and be a reference for unwrap.
if stable_sort:
sort_indices = np.argsort(compound_indices, kind='stable')
else:
# Quicksort
sort_indices = np.argsort(compound_indices)
# We must sort size_per_atom accordingly (Issue #3352).
size_per_atom = size_per_atom[sort_indices]
compound_masks = []
atom_masks = []
for compound_size in unique_compound_sizes:
compound_masks.append(compound_sizes == compound_size)
if needs_sorting:
atom_masks.append(sort_indices[size_per_atom == compound_size]
.reshape(-1, compound_size))
else:
atom_masks.append(np.where(size_per_atom == compound_size)[0]
.reshape(-1, compound_size))
return atom_masks, compound_masks, len(compound_sizes)
@warn_if_not_unique
@_pbc_to_wrap
@check_wrap_and_unwrap
def center(self, weights, wrap=False, unwrap=False, compound='group'):
"""Weighted center of (compounds of) the group
Computes the weighted center of :class:`Atoms<Atom>` in the group.
Weighted centers per :class:`Residue`, :class:`Segment`, molecule, or
fragment can be obtained by setting the `compound` parameter
accordingly. If the weights of a compound sum up to zero, the
coordinates of that compound's weighted center will be ``nan`` (not a
number).
Parameters
----------
weights : array_like or None
Weights to be used. Setting `weights=None` is equivalent to passing
identical weights for all atoms of the group.
wrap : bool, optional
If ``True`` and `compound` is ``'group'``, move all atoms to the
primary unit cell before calculation.
If ``True`` and `compound` is not ``'group'`` the center of each
compound will be calculated without moving any
:class:`Atoms<Atom>` to keep the compounds intact. Instead, the
resulting position vectors will be moved to the primary unit cell
after calculation. Default [``False``].
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their
centers.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional
If ``'group'``, the weighted center of all atoms in the group will
be returned as a single position vector. Else, the weighted centers
of each :class:`Segment`, :class:`Residue`, molecule, or fragment
will be returned as an array of position vectors, i.e. a 2d array.
Note that, in any case, *only* the positions of :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
Returns
-------
center : numpy.ndarray
Position vector(s) of the weighted center(s) of the group.
If `compound` was set to ``'group'``, the output will be a single
position vector.
If `compound` was set to ``'segments'``, ``'residues'``,
``'molecules'``, or ``'fragments'``, the output will be a 2d array
of shape ``(n, 3)`` where ``n`` is the number of compounds.
Raises
------
ValueError
If `compound` is not one of ``'group'``, ``'segments'``,
``'residues'``, ``'molecules'``, or ``'fragments'``.
ValueError
If both 'wrap' and 'unwrap' set to true.
~MDAnalysis.exceptions.NoDataError
If `compound` is ``'molecule'`` but the topology doesn't
contain molecule information (molnums) or if `compound` is
``'fragments'`` but the topology doesn't contain bonds.
Examples
--------
To find the center of charge of a given :class:`AtomGroup`::
>>> sel = u.select_atoms('prop mass > 4.0')
>>> sel.center(sel.charges)
To find the centers of mass per residue of all CA :class:`Atoms<Atom>`::
>>> sel = u.select_atoms('name CA')
>>> sel.center(sel.masses, compound='residues')
.. versionchanged:: 0.19.0 Added `compound` parameter
.. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'``
compounds
.. versionchanged:: 0.20.0 Added `unwrap` parameter
.. versionchanged:: 1.0.0 Removed flags affecting default behaviour
.. versionchanged::
2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but
is deprecated and will be removed in version 3.0.
"""
atoms = self.atoms
# enforce calculations in double precision:
dtype = np.float64
comp = compound.lower()
if comp == 'group':
if wrap:
coords = atoms.pack_into_box(inplace=False)
elif unwrap:
coords = atoms.unwrap(
compound=comp, reference=None, inplace=False)
else:
coords = atoms.positions
# If there's no atom, return its (empty) coordinates unchanged.
if len(atoms) == 0:
return coords
if weights is None:
# promote coords to dtype if required:
coords = coords.astype(dtype, copy=False)
return coords.mean(axis=0)
# promote weights to dtype if required:
weights = weights.astype(dtype, copy=False)
return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
# When compound split caching gets implemented it will be clever to
# preempt at this point whether or not stable sorting will be needed
# later for unwrap (so that we don't split now with non-stable sort,
# only to have to re-split with stable sort if unwrap is requested).
(atom_masks,
compound_masks,
n_compounds) = self._split_by_compound_indices(comp)
# Unwrap Atoms
if unwrap:
coords = atoms.unwrap(compound=comp, reference=None, inplace=False)
else:
coords = atoms.positions
if weights is None:
coords = coords.astype(dtype, copy=False)
else:
weights = weights.astype(dtype, copy=False)
# Allocate output array:
centers = np.empty((n_compounds, 3), dtype=dtype)
# Compute centers per compound for each compound size:
for compound_mask, atom_mask in zip(compound_masks, atom_masks):
_coords = coords[atom_mask]
if weights is None:
_centers = _coords.mean(axis=1)
else:
_weights = weights[atom_mask]
_centers = np.einsum('ijk,ijk->ik',_coords,_weights[:, :, None])
_centers /= _weights.sum(axis=1)[:, None]
centers[compound_mask] = _centers
if wrap:
centers = distances.apply_PBC(centers, atoms.dimensions)
return centers
@warn_if_not_unique
@_pbc_to_wrap
@check_wrap_and_unwrap
def center_of_geometry(self, wrap=False, unwrap=False, compound='group'):
r"""Center of geometry of (compounds of) the group
.. math::
\boldsymbol R = \frac{\sum_i \boldsymbol r_i}{\sum_i 1}
where :math:`\boldsymbol r_i` of :class:`Atoms<Atom>` :math:`i`.
Centers of geometry per :class:`Residue` or per :class:`Segment` can
be obtained by setting the `compound` parameter accordingly.
Parameters
----------
wrap : bool, optional
If ``True`` and `compound` is ``'group'``, move all atoms to the
primary unit cell before calculation. If ``True`` and `compound` is
``'segments'`` or ``'residues'``, the center of each compound will
be calculated without moving any :class:`Atoms<Atom>` to keep the
compounds intact. Instead, the resulting position vectors will be
moved to the primary unit cell after calculation. Default False.
unwrap : bool, optional
If ``True``, compounds will be unwrapped before computing their
centers.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'}, optional
If ``'group'``, the center of geometry of all :class:`Atoms<Atom>`
in the group will be returned as a single position vector. Else,
the centers of geometry of each :class:`Segment` or
:class:`Residue` will be returned as an array of position vectors,
i.e. a 2d array. Note that, in any case, *only* the positions of
:class:`Atoms<Atom>` *belonging to the group* will be taken into
account.
Returns
-------
center : numpy.ndarray
Position vector(s) of the geometric center(s) of the group.
If `compound` was set to ``'group'``, the output will be a single
position vector.
If `compound` was set to ``'segments'`` or ``'residues'``, the
output will be a 2d array of shape ``(n, 3)`` where ``n`` is the
number of compounds.
.. versionchanged:: 0.8 Added `pbc` keyword
.. versionchanged:: 0.19.0 Added `compound` parameter
.. versionchanged:: 0.20.0 Added ``'molecules'`` and ``'fragments'``
compounds
.. versionchanged:: 0.20.0 Added `unwrap` parameter
.. versionchanged:: 1.0.0 Removed flags affecting default behaviour
.. versionchanged::
2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but
is deprecated and will be removed in version 3.0.
"""
return self.center(None, wrap=wrap, compound=compound, unwrap=unwrap)
centroid = center_of_geometry
@warn_if_not_unique
def accumulate(self, attribute, function=np.sum, compound='group'):
r"""Accumulates the attribute associated with (compounds of) the group.
Accumulates the attribute of :class:`Atoms<Atom>` in the group.
The accumulation per :class:`Residue`, :class:`Segment`, molecule,
or fragment can be obtained by setting the `compound` parameter
accordingly. By default, the method sums up all attributes per compound,
but any function that takes an array and returns an acuumulation over a
given axis can be used. For multi-dimensional input arrays, the
accumulation is performed along the first axis.
Parameters
----------
attribute : str or array_like
Attribute or array of values to accumulate.
If a :class:`numpy.ndarray` (or compatible) is provided, its first
dimension must have the same length as the total number of atoms in
the group.
function : callable, optional
The function performing the accumulation. It must take the array of
attribute values to accumulate as its only positional argument and
accept an (optional) keyword argument ``axis`` allowing to specify
the axis along which the accumulation is performed.
compound : {'group', 'segments', 'residues', 'molecules', 'fragments'},\
optional
If ``'group'``, the accumulation of all attributes associated with
atoms in the group will be returned as a single value. Otherwise,
the accumulation of the attributes per :class:`Segment`,
:class:`Residue`, molecule, or fragment will be returned as a 1d
array. Note that, in any case, *only* the :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
Returns
-------
float or numpy.ndarray
Acuumulation of the `attribute`.
If `compound` is set to ``'group'``, the first dimension of the
`attribute` array will be contracted to a single value.
If `compound` is set to ``'segments'``, ``'residues'``,
``'molecules'``, or ``'fragments'``, the length of the first
dimension will correspond to the number of compounds. In all cases,
the other dimensions of the returned array will be of the original
shape (without the first dimension).
Raises
------
ValueError
If the length of a provided `attribute` array does not correspond to
the number of atoms in the group.
ValueError
If `compound` is not one of ``'group'``, ``'segments'``,
``'residues'``, ``'molecules'``, or ``'fragments'``.
~MDAnalysis.exceptions.NoDataError
If `compound` is ``'molecule'`` but the topology doesn't
contain molecule information (molnums), or if `compound` is
``'fragments'`` but the topology doesn't contain bonds.
Examples
--------
To find the total charge of a given :class:`AtomGroup`::
>>> sel = u.select_atoms('prop mass > 4.0')
>>> sel.accumulate('charges')
To find the total mass per residue of all CA :class:`Atoms<Atom>`::
>>> sel = u.select_atoms('name CA')
>>> sel.accumulate('masses', compound='residues')
To find the maximum atomic charge per fragment of a given
:class:`AtomGroup`::
>>> sel.accumulate('charges', compound="fragments", function=np.max)
.. versionadded:: 0.20.0
"""
atoms = self.atoms
if isinstance(attribute, str):
attribute_values = getattr(atoms, attribute)
else:
attribute_values = np.asarray(attribute)
if len(attribute_values) != len(atoms):
raise ValueError("The input array length ({}) does not match "
"the number of atoms ({}) in the group."
"".format(len(attribute_values), len(atoms)))
comp = compound.lower()
if comp == 'group':
return function(attribute_values, axis=0)
(atom_masks,
compound_masks,
n_compounds) = self._split_by_compound_indices(comp)
higher_dims = list(attribute_values.shape[1:])
# Allocate output array:
# (what dtype should this be?)
accumulation = np.empty([n_compounds] + higher_dims)
# Apply the accumulation function per compound for each compound size:
for compound_mask, atom_mask in zip(compound_masks, atom_masks):
_elements = attribute_values[atom_mask]
_accumulation = function(_elements, axis=1)
accumulation[compound_mask] = _accumulation
return accumulation
@_pbc_to_wrap
def bbox(self, wrap=False):
"""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
----------
wrap : bool, optional
If ``True``, move all :class:`Atoms<Atom>` to the primary unit cell
before calculation. [``False``]
Returns
-------
corners : numpy.ndarray
2x3 array giving corners of bounding box as
``[[xmin, ymin, zmin], [xmax, ymax, zmax]]``.
.. versionadded:: 0.7.2
.. versionchanged:: 0.8 Added *pbc* keyword
.. versionchanged:: 1.0.0 Removed flags affecting default behaviour
.. versionchanged::
2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but
is deprecated and will be removed in version 3.0.
"""
# TODO: Add unwrap/compounds treatment
atomgroup = self.atoms
if wrap:
x = atomgroup.pack_into_box(inplace=False)
else:
x = atomgroup.positions
return np.array([x.min(axis=0), x.max(axis=0)])
@_pbc_to_wrap
def bsphere(self, wrap=False):
"""Return the bounding sphere of the selection.
The sphere is calculated relative to the
:meth:`center of geometry<center_of_geometry>`.
Parameters
----------
wrap : bool, optional
If ``True``, move all atoms to the primary unit cell before
calculation. [``False``]
Returns
-------
R : float
Radius of the bounding sphere.
center : numpy.ndarray
Coordinates of the sphere center as ``[xcen, ycen, zcen]``.
.. versionadded:: 0.7.3
.. versionchanged:: 0.8 Added *pbc* keyword
.. versionchanged::
2.1.0 Renamed `pbc` kwarg to `wrap`. `pbc` is still accepted but
is deprecated and will be removed in version 3.0.
"""
atomgroup = self.atoms.unsorted_unique
if wrap:
x = atomgroup.pack_into_box(inplace=False)
centroid = atomgroup.center_of_geometry(wrap=True)
else:
x = atomgroup.positions
centroid = atomgroup.center_of_geometry(wrap=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.
:class:`Atom` coordinates are rotated and translated in-place.
Parameters
----------
M : array_like
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 about the origin and is applied
before the translation :math:`\mathbf{t}`:
.. math::
\mathbf{x}' = \mathsf{R}\mathbf{x} + \mathbf{t}
"""
M = np.asarray(M)
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.
:class:`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.unsorted_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}
:class:`Atom` coordinates are rotated in-place.
Parameters
----------
R : array_like
3x3 rotation matrix
point : array_like, optional
Center of rotation
Returns
-------
self
Notes
-----
By default, rotates about the origin ``point=(0, 0, 0)``. To rotate
a group ``g`` around its center of geometry, use
``g.rotate(R, point=g.center_of_geometry())``.
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)
atomgroup = self.atoms.unsorted_unique
require_translation = bool(np.count_nonzero(point))
if require_translation:
atomgroup.translate(-point)
x = atomgroup.universe.trajectory.ts.positions
idx = atomgroup.indices
x[idx] = np.dot(x[idx], R.T)
if require_translation:
atomgroup.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
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)
if point is None:
point = self.center_of_geometry()
point = np.asarray(point)
M = transformations.rotation_matrix(alpha, axis, point=point)
return self.transform(M)
def pack_into_box(self, box=None, inplace=True):
r"""Shift all :class:`Atoms<Atom>` in this group to 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.timestep.Timestep.dimensions`,
``[lx, ly, lz, alpha, beta, gamma]``. If ``None``, uses these
timestep dimensions.
inplace : bool
``True`` to change coordinates in place.
Returns
-------
coords : numpy.ndarray
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.timestep.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.
.. note::
:meth:`pack_into_box` is identical to :meth:`wrap` with all default
keywords.
.. note::
:meth:`AtomGroup.pack_into_box` is currently faster than
:meth:`ResidueGroup.pack_into_box` or
:meth:`SegmentGroup.pack_into_box`.
.. versionadded:: 0.8
"""
return self.wrap(box=box, inplace=inplace)
def wrap(self, compound="atoms", center="com", box=None, inplace=True):
r"""Shift the contents of this group back into the primary unit cell
according to periodic boundary conditions.
Specifying a `compound` will keep the :class:`Atoms<Atom>` in each
compound together during the process. If `compound` is different from
``'atoms'``, each compound as a whole will be shifted so that its
`center` lies within the primary unit cell.
Parameters
----------
compound : {'atoms', 'group', 'segments', 'residues', 'molecules', \
'fragments'}, optional
Which type of compound to keep together during wrapping. Note that,
in any case, *only* the positions of :class:`Atoms<Atom>`
*belonging to the group* will be taken into account.
center : {'com', 'cog'}
How to define the center of a given group of atoms. If `compound` is
``'atoms'``, this parameter is meaningless and therefore ignored.
box : array_like, optional
The unitcell dimensions of the system, which can be orthogonal or
triclinic and must be provided in the same format as returned by
:attr:`MDAnalysis.coordinates.timestep.Timestep.dimensions`:
``[lx, ly, lz, alpha, beta, gamma]``.
If ``None``, uses the
dimensions of the current time step.
inplace: bool, optional
If ``True``, coordinates will be changed in place.
Returns
-------
numpy.ndarray
Array of wrapped atom coordinates of dtype `np.float32` and shape
``(len(self.atoms.n_atoms), 3)``
Raises
------
ValueError
If `compound` is not one of ``'atoms'``, ``'group'``,
``'segments'``, ``'residues'``, ``'molecules'``, or ``'fragments'``.
~MDAnalysis.exceptions.NoDataError
If `compound` is ``'molecule'`` but the topology doesn't
contain molecule information (molnums) or if `compound` is
``'fragments'`` but the topology doesn't contain bonds or if
`center` is ``'com'`` but the topology doesn't contain masses.
Notes
-----
All atoms of the group will be moved so that the centers of its
compounds lie within the primary periodic image. For orthorhombic unit
cells, the primary periodic image is defined as the half-open interval
:math:`[0,L_i)` between :math:`0` and boxlength :math:`L_i` in all
dimensions :math:`i\in\{x,y,z\}`, i.e., the origin of the of the
simulation box is taken to be at the origin :math:`(0,0,0)` of the
euclidian coordinate system. A compound center residing at position
:math:`x_i` in dimension :math:`i` will be shifted to :math:`x_i'`
according to
.. math::
x_i' = x_i - \left\lfloor\frac{x_i}{L_i}\right\rfloor\,.
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 not all atoms of a compound will be
inside the unit cell after wrapping, but rather will be the center of
the compound.
Be aware of the fact that only atoms *belonging to the group* will be
taken into account!
`center` allows to define how the center of each group is computed.
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, the :attr:`~MDAnalysis.coordinates.timestep.Timestep.dimensions`
information from the current
:class:`~MDAnalysis.coordinates.timestep.Timestep` will be used.
.. note::
:meth:`AtomGroup.wrap` is currently faster than
:meth:`ResidueGroup.wrap` or :meth:`SegmentGroup.wrap`.
See Also
--------
:meth:`pack_into_box`
:meth:`unwrap`
:meth:`MDAnalysis.lib.distances.apply_PBC`
.. versionadded:: 0.9.2
.. versionchanged:: 0.20.0
The method only acts on atoms *belonging to the group* and returns
the wrapped positions as a :class:`numpy.ndarray`.
Added optional argument `inplace`.
"""
# Try and auto detect box dimensions:
if box is None:
box = self.dimensions
if box is None:
raise ValueError("No dimensions information in Universe. "
" Either use the 'box' argument or"
" set the '.dimensions' attribute")
else:
box = np.asarray(box, dtype=np.float32)
if not np.all(box > 0.0) or box.shape != (6,):
raise ValueError("Invalid box: Box has invalid shape or not all "
"box dimensions are positive. You can specify a "
"valid box using the 'box' argument.")
# no matter what kind of group we have, we need to work on its (unique)
# atoms:
atoms = self.atoms
if not self.isunique:
_atoms = atoms.unsorted_unique
restore_mask = atoms._unique_restore_mask
atoms = _atoms
comp = compound.lower()
if comp not in ('atoms', 'group', 'segments', 'residues', 'molecules',
'fragments'):
raise ValueError("Unrecognized compound definition '{}'. "
"Please use one of 'atoms', 'group', 'segments', "
"'residues', 'molecules', or 'fragments'."
"".format(compound))
if len(atoms) == 0:
return np.zeros((0, 3), dtype=np.float32)
if comp == "atoms" or len(atoms) == 1:
positions = distances.apply_PBC(atoms.positions, box)
else:
ctr = center.lower()
if ctr == 'com':
# Don't use hasattr(self, 'masses') because that's incredibly
# slow for ResidueGroups or SegmentGroups
if not hasattr(self._u._topology, 'masses'):
raise NoDataError("Cannot perform wrap with center='com', "
"this requires masses.")
elif ctr != 'cog':
raise ValueError("Unrecognized center definition '{}'. Please "
"use one of 'com' or 'cog'.".format(center))
positions = atoms.positions
# compute and apply required shift:
if ctr == 'com':
ctrpos = atoms.center_of_mass(wrap=False, compound=comp)
if np.any(np.isnan(ctrpos)):
specifier = 'the' if comp == 'group' else 'one of the'
raise ValueError("Cannot use compound='{0}' with "
"center='com' because {1} {0}\'s total "
"mass is zero.".format(comp, specifier))
else: # ctr == 'cog'
ctrpos = atoms.center_of_geometry(wrap=False, compound=comp)
ctrpos = ctrpos.astype(np.float32, copy=False)
target = distances.apply_PBC(ctrpos, box)
shifts = target - ctrpos
if comp == 'group':
positions += shifts
else:
compound_indices = atoms._get_compound_indices(comp)
# apply the shifts:
unique_compound_indices = unique_int_1d(compound_indices)
shift_idx = 0
for i in unique_compound_indices:
mask = np.where(compound_indices == i)
positions[mask] += shifts[shift_idx]
shift_idx += 1
if inplace:
atoms.positions = positions
if not self.isunique:
positions = positions[restore_mask]
return positions
def unwrap(self, compound='fragments', reference='com', inplace=True):
r"""Move atoms of this group so that bonds within the
group's compounds aren't split across periodic boundaries.
This function is most useful when atoms have been packed into the
primary unit cell, causing breaks mid-molecule, with the molecule then
appearing on either side of the unit cell. This is problematic for
operations such as calculating the center of mass of the molecule. ::
+-----------+ +-----------+
| | | |
| 6 3 | | 3 | 6
| ! ! | | ! | !
|-5-8 1-2-| ==> | 1-2-|-5-8
| ! ! | | ! | !
| 7 4 | | 4 | 7
| | | |
+-----------+ +-----------+
Parameters
----------
compound : {'group', 'segments', 'residues', 'molecules', \
'fragments'}, optional
Which type of compound to unwrap. Note that, in any case, all
atoms within each compound must be interconnected by bonds, i.e.,
compounds must correspond to (parts of) molecules.
reference : {'com', 'cog', None}, optional
If ``'com'`` (center of mass) or ``'cog'`` (center of geometry), the
unwrapped compounds will be shifted so that their individual
reference point lies within the primary unit cell.
If ``None``, no such shift is performed.
inplace : bool, optional
If ``True``, coordinates are modified in place.
Returns
-------
coords : numpy.ndarray
Unwrapped atom coordinate array of shape ``(n, 3)``.
Raises
------
NoDataError
If `compound` is ``'molecules'`` but the underlying topology does
not contain molecule information, or if `reference` is ``'com'``
but the topology does not contain masses.
ValueError
If `reference` is not one of ``'com'``, ``'cog'``, or ``None``, or
if `reference` is ``'com'`` and the total mass of any `compound` is
zero.
Note
----
Be aware of the fact that only atoms *belonging to the group* will
be unwrapped! If you want entire molecules to be unwrapped, make sure
that all atoms of these molecules are part of the group.
An AtomGroup containing all atoms of all fragments in the group ``ag``
can be created with::
all_frag_atoms = sum(ag.fragments)
See Also
--------
:func:`~MDAnalysis.lib.mdamath.make_whole`,
:meth:`wrap`,
:meth:`pack_into_box`,
:func:`~MDanalysis.lib.distances.apply_PBC`
.. versionadded:: 0.20.0
"""
atoms = self.atoms
# bail out early if no bonds in topology:
if not hasattr(atoms, 'bonds'):
raise NoDataError("{}.unwrap() not available; this requires Bonds"
"".format(self.__class__.__name__))
unique_atoms = atoms.unsorted_unique
# Parameter sanity checking
if reference is not None:
try:
reference = reference.lower()
if reference not in ('cog', 'com'):
raise ValueError
except (AttributeError, ValueError):
raise ValueError("Unrecognized reference '{}'. Please use one "
"of 'com', 'cog', or None.".format(reference))
# Don't use hasattr(self, 'masses') because that's incredibly slow for
# ResidueGroups or SegmentGroups
if reference == 'com' and not hasattr(unique_atoms, 'masses'):
raise NoDataError("Cannot perform unwrap with reference='com', "
"this requires masses.")
# Sanity checking of the compound parameter is done downstream in
# _split_by_compound_indices
comp = compound.lower()
# The 'group' needs no splitting:
# There is a lot of code duplication with the multi-compound split
# case below. Both code paths could be merged, but 'group' can be done
# unidimensionally whereas the general multi-compound case involves
# more indexing and is therefore slower. Leaving separate for now.
if comp == 'group':
positions = mdamath.make_whole(unique_atoms, inplace=False)
# Apply reference shift if required:
if reference is not None and len(positions) > 0:
if reference == 'com':
masses = unique_atoms.masses
total_mass = masses.sum()
if np.isclose(total_mass, 0.0):
raise ValueError("Cannot perform unwrap with "
"reference='com' because the total "
"mass of the group is zero.")
refpos = np.einsum('ij,ij->j',positions,masses[:, None])
refpos /= total_mass
else: # reference == 'cog'
refpos = positions.mean(axis=0)
refpos = refpos.astype(np.float32, copy=False)
target = distances.apply_PBC(refpos, self.dimensions)
positions += target - refpos
else: # We need to split the group into compounds
# When unwrapping and not shifting with a cog/com reference we
# need to make sure that the first atom of each compound is stable
# regarding sorting.
atom_masks = unique_atoms._split_by_compound_indices(comp,
stable_sort=reference is None)[0]
positions = unique_atoms.positions
for atom_mask in atom_masks:
for mask in atom_mask:
positions[mask] = mdamath.make_whole(unique_atoms[mask],
inplace=False)
# Apply reference shift if required:
if reference is not None:
if reference == 'com':
masses = unique_atoms.masses[atom_mask]
total_mass = masses.sum(axis=1)
if np.any(np.isclose(total_mass, 0.0)):
raise ValueError("Cannot perform unwrap with "
"reference='com' because the "
"total mass of at least one of "
"the {} is zero.".format(comp))
refpos = np.einsum('ijk,ijk->ik',positions[atom_mask],
masses[:, :, None])
refpos /= total_mass[:, None]
else: # reference == 'cog'
refpos = positions[atom_mask].mean(axis=1)
refpos = refpos.astype(np.float32, copy=False)
target = distances.apply_PBC(refpos, self.dimensions)
positions[atom_mask] += (target[:, None, :]
- refpos[:, None, :])
if inplace:
unique_atoms.positions = positions
if not atoms.isunique:
positions = positions[atoms._unique_restore_mask]
return positions
def copy(self):
"""Get another group identical to this one.
.. versionadded:: 0.19.0
"""
group = self[:]
group._set_unique_caches_from(self)
return group
def _set_unique_caches_from(self, other):
# Try to fill the copied group's uniqueness caches:
try:
self._cache['isunique'] = other._cache['isunique']
except KeyError:
pass
else:
if self.isunique:
self._cache['unsorted_unique'] = self
try:
self._cache['issorted'] = other._cache['issorted']
except KeyError:
pass
else:
if self.issorted:
if self._cache.get('isunique'):
self._cache['sorted_unique'] = self
def groupby(self, topattrs):
"""Group together items in this group according to values of *topattr*
Parameters
----------
topattrs: str or list
One or more topology attributes to group components by.
Single arguments are passed as a string. Multiple arguments
are passed as a list.
Returns
-------
dict
Unique values of the multiple combinations of topology attributes
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>}
To group atoms with the same residue name and mass together:
>>> ag.groupby(['resnames', 'masses'])
{('ALA', 1.008): <AtomGroup with 95 atoms>,
('ALA', 12.011): <AtomGroup with 57 atoms>,
('ALA', 14.007): <AtomGroup with 19 atoms>,
('ALA', 15.999): <AtomGroup with 19 atoms>},
('ARG', 1.008): <AtomGroup with 169 atoms>,
...}
>>> ag.groupby(['resnames', 'masses'])('ALA', 15.999)
<AtomGroup with 19 atoms>
.. versionadded:: 0.16.0
.. versionchanged:: 0.18.0 The function accepts multiple attributes
"""
res = dict()
if isinstance(topattrs, (str, bytes)):
attr = topattrs
if isinstance(topattrs, bytes):
attr = topattrs.decode('utf-8')
ta = getattr(self, attr)
return {i: self[ta == i] for i in set(ta)}
else:
attr = topattrs[0]
ta = getattr(self, attr)
for i in set(ta):
if len(topattrs) == 1:
res[i] = self[ta == i]
else:
res[i] = self[ta == i].groupby(topattrs[1:])
return util.flatten_dict(res)
@_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:
>>> shell1 = u.select_atoms('resname SOL and around 4.0 segid 1')
>>> shell2 = u.select_atoms('resname SOL and 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):
"""An ordered array of atoms.
Can be initiated from an iterable of :class:`Atoms<Atom>`::
ag = AtomGroup([Atom1, Atom2, Atom3])
Or from providing a list of indices and the
:class:`~MDAnalysis.core.universe.Universe` it should belong to::
ag = AtomGroup([72, 14, 25], u)
Alternatively, an :class:`AtomGroup` is generated by indexing/slicing
another :class:`AtomGroup`, such as the group of all :class:`Atoms<Atom>` in
the :class:`~MDAnalysis.core.universe.Universe` at
:attr:`MDAnalysis.core.universe.Universe.atoms`.
An :class:`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 :class:`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 :class:`AtomGroup` of :class:`Atoms<Atom>` with those
indices in the old :class:`AtomGroup`.
Finally, :class:`AtomGroups<AtomGroup>` can be created from a selection.
See :meth:`select_atoms`.
.. note::
:class:`AtomGroups<AtomGroup>` originating from a selection are sorted
and duplicate elements are removed. This is not true for
:class:`AtomGroups<AtomGroup>` produced by slicing. Thus, slicing can be
used when the order of atoms is crucial (for instance, in order to
define angles or dihedrals).
:class:`AtomGroups<AtomGroup>` can be compared and combined using group
operators. For instance, :class:`AtomGroups<AtomGroup>` 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 :class:`Atoms<Atom>` is
conserved. If :class:`Atoms<Atom>` 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 :class:`AtomGroups<AtomGroup>`
as sets so that duplicates are removed from the resulting group, and
:class:`Atoms<Atom>` 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 :class:`Atoms<Atom>` of the group
that are not in a given other group; the order of the :class:`Atoms<Atom>`
is kept, and so are 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 :class:`Atoms<Atom>`.
+-------------------------------+------------+----------------------------+
| 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 as well as duplicates.
+-------------------------------+------------+----------------------------+
| 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
:class:`AtomGroup`.
:class:`AtomGroup` instances are always bound to a
:class:`MDAnalysis.core.universe.Universe`. They cannot exist in isolation.
During serialization, :class:`AtomGroup` will be pickled with its bound
:class:`MDAnalysis.core.universe.Universe` which means after unpickling,
a new :class:`MDAnalysis.core.universe.Universe` will be created and
be attached by the new :class:`AtomGroup`. If the Universe is serialized
with its :class:`AtomGroup`, they will still be bound together afterwards:
.. code-block:: python
>>> u = mda.Universe(PSF, DCD)
>>> g = u.atoms
>>> g_pickled = pickle.loads(pickle.dumps(g))
>>> print("g_pickled.universe is u: ", u is g_pickled.universe)
g_pickled.universe is u: False
>>> g_pickled, u_pickled = pickle.load(pickle.dumps(g, u))
>>> print("g_pickled.universe is u_pickled: ",
>>> u_pickle is g_pickled.universe)
g_pickled.universe is u_pickled: True
If multiple :class:`AtomGroup` are bound to the same
:class:`MDAnalysis.core.universe.Universe`, they will bound to the same one
after serialization:
.. code-block:: python
>>> u = mda.Universe(PSF, DCD)
>>> g = u.atoms
>>> h = u.atoms
>>> g_pickled = pickle.loads(pickle.dumps(g))
>>> h_pickled = pickle.loads(pickle.dumps(h))
>>> print("g_pickled.universe is h_pickled.universe : ",
>>> g_pickled.universe is h_pickled.universe)
g_pickled.universe is h_pickled.universe: False
>>> g_pickled, h_pickled = pickle.load(pickle.dumps(g, h))
>>> print("g_pickled.universe is h_pickled.universe: ",
>>> g_pickle.universe is h_pickled.universe)
g_pickled.universe is h_pickled.universe: True
The aforementioned two cases are useful for implementation of parallel
analysis base classes. First, you always get an independent
:class:`MDAnalysis.core.universe.Universe`
in the new process; you don't have to worry about detaching and reattaching
Universe with :class:`AtomGroup`. It also means the state of the
new pickled AtomGroup will not be changed with the old Universe,
So either the Universe has to pickled together with the AtomGroup
(e.g. as a tuple, or as attributes of the object to be pickled), or the
implicit new Universe (`AtomGroup.Universe`) needs to be used.
Second, When multiple AtomGroup need to be pickled, they will recognize if
they belong to the same Univese or not.
Also keep in mind that they need to be pickled together.
See Also
--------
:class:`MDAnalysis.core.universe.Universe`
.. deprecated:: 0.16.2
*Instant selectors* of :class:`AtomGroup` will be removed in the 1.0
release.
.. versionchanged:: 1.0.0
Removed instant selectors, use select_atoms('name ...') to select
atoms by name.
.. versionchanged:: 2.0.0
:class:`AtomGroup` can always be pickled with or without its universe,
instead of failing when not finding its anchored universe.
.. versionchanged:: 2.1.0
Indexing an AtomGroup with ``None`` raises a ``TypeError``.
"""
def __getattr__(self, attr):
# special-case timestep info
if attr in ('velocities', 'forces'):
raise NoDataError('This Timestep has no ' + attr)
elif attr == 'positions':
raise NoDataError('This Universe has no coordinates')
return super(AtomGroup, self).__getattr__(attr)
def __reduce__(self):
return (_unpickle, (self.universe, self.ix))
@property
def atoms(self):
"""The :class:`AtomGroup` itself.
See Also
--------
copy : return a true copy of the :class:`AtomGroup`
.. versionchanged:: 0.19.0
In previous versions, this returned a copy, but now
the :class:`AtomGroup` itself is returned. This should
not affect any code but only speed up calculations.
"""
return self
@property
def n_atoms(self):
"""Number of atoms in the :class:`AtomGroup`.
Equivalent to ``len(self)``.
"""
return len(self)
@property
def residues(self):
"""A sorted :class:`ResidueGroup` of the unique
:class:`Residues<Residue>` present in the :class:`AtomGroup`.
"""
rg = self.universe.residues[unique_int_1d(self.resindices)]
rg._cache['isunique'] = True
rg._cache['issorted'] = True
rg._cache['sorted_unique'] = rg
rg._cache['unsorted_unique'] = rg
return rg
@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:
errmsg = ("Can only set AtomGroup residues to Residue "
"or ResidueGroup not {}".format(
', '.join(type(r) for r in new
if not isinstance(r, Residue))))
raise TypeError(errmsg) from None
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 :class:`Residues<Residue>` present in the
:class:`AtomGroup`.
Equivalent to ``len(self.residues)``.
"""
return len(self.residues)
@property
def segments(self):
"""A sorted :class:`SegmentGroup` of the unique segments present in the
:class:`AtomGroup`.
"""
sg = self.universe.segments[unique_int_1d(self.segindices)]
sg._cache['isunique'] = True
sg._cache['issorted'] = True
sg._cache['sorted_unique'] = sg
sg._cache['unsorted_unique'] = sg
return sg
@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 present in the :class:`AtomGroup`.
Equivalent to ``len(self.segments)``.
"""
return len(self.segments)
@property
@cached('unique_restore_mask')
def _unique_restore_mask(self):
# The _unique_restore_mask property's cache is populated whenever the
# AtomGroup.unique property of a *non-unique* AtomGroup is accessed.
# If _unique_restore_mask is not cached, it is *definitely* used in the
# wrong place, so we raise an exception here. In principle, the
# exception should be an AttributeError, but the error message would
# then be replaced by the __getattr__() error message. To prevent the
# message from being overridden, we raise a RuntimeError instead.
if self.isunique:
msg = ("{0}._unique_restore_mask is not available if the {0} is "
"unique. ".format(self.__class__.__name__))
else:
msg = ("{0}._unique_restore_mask is only available after "
"accessing {0}.unique. ".format(self.__class__.__name__))
msg += ("If you see this error message in an unmodified release "
"version of MDAnalysis, this is almost certainly a bug!")
raise RuntimeError(msg)
@_unique_restore_mask.setter
def _unique_restore_mask(self, mask):
self._cache['unique_restore_mask'] = mask
@property
def unique(self):
"""An :class:`AtomGroup` containing sorted and unique
:class:`Atoms<Atom>` only.
Examples
--------
>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
>>> ag = u.atoms[[2, 1, 2, 2, 1, 0]]
>>> ag
<AtomGroup with 6 atoms>
>>> ag.ix
array([2, 1, 2, 2, 1, 0], dtype=int64)
>>> ag2 = ag.unique
>>> ag2
<AtomGroup with 3 atoms>
>>> ag2.ix
array([0, 1, 2], dtype=int64)
>>> ag2.unique is ag2
False
See Also
--------
asunique
.. versionadded:: 0.16.0
.. versionchanged:: 0.19.0 If the :class:`AtomGroup` is already unique,
:attr:`AtomGroup.unique` now returns the group itself instead of a
copy.
.. versionchanged:: 2.0.0
This function now always returns a copy.
"""
group = self.sorted_unique[:]
group._cache['isunique'] = True
group._cache['issorted'] = True
group._cache['sorted_unique'] = group
group._cache['unsorted_unique'] = group
return group
[docs] def asunique(self, sorted=False):
"""Return a :class:`AtomGroup` containing unique
:class:`Atoms<Atom>` only, with optional sorting.
If the :class:`AtomGroup` is unique, this is the group itself.
Parameters
----------
sorted: bool (optional)
Whether or not the returned AtomGroup should be sorted
by index.
Returns
-------
:class:`AtomGroup`
Unique ``AtomGroup``
Examples
--------
>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
>>> ag = u.atoms[[2, 1, 0]]
>>> ag2 = ag.asunique(sorted=False)
>>> ag2 is ag
True
>>> ag2.ix
array([2, 1, 0], dtype=int64)
>>> ag3 = ag.asunique(sorted=True)
>>> ag3 is ag
False
>>> ag3.ix
array([0, 1, 2], dtype=int64)
>>> u.atoms[[2, 1, 1, 0, 1]].asunique(sorted=False).ix
array([2, 1, 0], dtype=int64)
.. versionadded:: 2.0.0
"""
return self._asunique(sorted=sorted, group=self.universe.atoms,
set_mask=True)
@property
def positions(self):
r"""Coordinates of the :class:`Atoms<Atom>` in the :class:`AtomGroup`.
A :class:`numpy.ndarray` with
:attr:`~numpy.ndarray.shape`\ ``=(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)``
and :attr:`~numpy.ndarray.dtype`\ ``=numpy.float32``.
The positions can be changed by assigning an array of the appropriate
shape, i.e., either ``(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)`` to
assign individual coordinates, or ``(3,)`` to assign the *same*
coordinate to all :class:`Atoms<Atom>` (e.g.,
``ag.positions = array([0,0,0])`` will move all :class:`Atoms<Atom>`
to the origin).
.. note:: Changing positions is not reflected in any files; reading any
frame from the
:attr:`~MDAnalysis.core.universe.Universe.trajectory` will
replace the change with that from the file *except* if the
:attr:`~MDAnalysis.core.universe.Universe.trajectory` is held
in memory, e.g., when the
:meth:`~MDAnalysis.core.universe.Universe.transfer_to_memory`
method was used.
Raises
------
~MDAnalysis.exceptions.NoDataError
If the underlying :class:`~MDAnalysis.coordinates.timestep.Timestep`
does not contain
:attr:`~MDAnalysis.coordinates.timestep.Timestep.positions`.
"""
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):
r"""Velocities of the :class:`Atoms<Atom>` in the :class:`AtomGroup`.
A :class:`numpy.ndarray` with
:attr:`~numpy.ndarray.shape`\ ``=(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)``
and :attr:`~numpy.ndarray.dtype`\ ``=numpy.float32``.
The velocities can be changed by assigning an array of the appropriate
shape, i.e. either ``(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)`` to assign
individual velocities or ``(3,)`` to assign the *same* velocity to all
:class:`Atoms<Atom>` (e.g. ``ag.velocities = array([0,0,0])`` will give
all :class:`Atoms<Atom>` zero :attr:`~Atom.velocity`).
Raises
------
~MDAnalysis.exceptions.NoDataError
If the underlying :class:`~MDAnalysis.coordinates.timestep.Timestep`
does not contain
:attr:`~MDAnalysis.coordinates.timestep.Timestep.velocities`.
"""
ts = self.universe.trajectory.ts
return np.array(ts.velocities[self.ix])
@velocities.setter
def velocities(self, values):
ts = self.universe.trajectory.ts
ts.velocities[self.ix, :] = values
@property
def forces(self):
r"""Forces on each :class:`Atom` in the :class:`AtomGroup`.
A :class:`numpy.ndarray` with
:attr:`~numpy.ndarray.shape`\ ``=(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)``
and :attr:`~numpy.ndarray.dtype`\ ``=numpy.float32``.
The forces can be changed by assigning an array of the appropriate
shape, i.e. either ``(``\ :attr:`~AtomGroup.n_atoms`\ ``, 3)`` to assign
individual forces or ``(3,)`` to assign the *same* force to all
:class:`Atoms<Atom>` (e.g. ``ag.forces = array([0,0,0])`` will give all
:class:`Atoms<Atom>` a zero :attr:`~Atom.force`).
Raises
------
~MDAnalysis.exceptions.NoDataError
If the :class:`~MDAnalysis.coordinates.timestep.Timestep` does not
contain :attr:`~MDAnalysis.coordinates.timestep.Timestep.forces`.
"""
ts = self.universe.trajectory.ts
return ts.forces[self.ix]
@forces.setter
def forces(self, values):
ts = self.universe.trajectory.ts
ts.forces[self.ix, :] = values
@property
def ts(self):
"""Temporary Timestep that contains the selection coordinates.
A :class:`~MDAnalysis.coordinates.timestep.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
:attr:`~MDAnalysis.core.universe.Universe.trajectory` frame changes).
It is not possible to assign a new
:class:`~MDAnalysis.coordinates.timestep.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, periodic=True, rtol=1e-05,
atol=1e-08, updating=False, sorted=True,
rdkit_kwargs=None, smarts_kwargs=None, **selgroups):
"""Select atoms from within this Group using a selection string.
Returns an :class:`AtomGroup` sorted according to their index in the
topology (this is to ensure that there are no duplicates, which can
happen with complicated selections).
Parameters
----------
sel : str
string of the selection, eg "name Ca", see below for possibilities.
othersel : iterable of str
further selections to perform. The results of these selections
will be appended onto the results of the first.
periodic : bool (optional)
for geometric selections, whether to account for atoms in different
periodic images when searching
atol : float, optional
The absolute tolerance parameter for float comparisons.
Passed to :func:``numpy.isclose``.
rtol : float, optional
The relative tolerance parameter for float comparisons.
Passed to :func:``numpy.isclose``.
updating : bool (optional)
force the selection to be re evaluated each time the Timestep of the
trajectory is changed. See section on **Dynamic selections** below.
[``True``]
sorted: bool, optional
Whether to sort the output AtomGroup by index.
rdkit_kwargs : dict (optional)
Arguments passed to the
:class:`~MDAnalysis.converters.RDKit.RDKitConverter` when using
selection based on SMARTS queries
smarts_kwargs : dict (optional)
Arguments passed internally to RDKit's `GetSubstructMatches
<https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol.GetSubstructMatches>`_.
**selgroups : keyword arguments of str: AtomGroup (optional)
when using the "group" keyword in selections, groups are defined by
passing them as keyword arguments. See section on **preexisting
selections** below.
Raises
------
TypeError
If the arbitrary groups passed are not of type
:class:`MDAnalysis.core.groups.AtomGroup`
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 Cα 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.
record_type *record_type*
for selecting either ATOM or HETATM from PDB-like files.
e.g. ``select_atoms('name CA and not record_type HETATM')``
smarts *SMARTS-query*
select atoms using Daylight's SMARTS queries, e.g. ``smarts
[#7;R]`` to find nitrogen atoms in rings. Requires RDKit.
All matches are combined as a single unique match. The `smarts`
selection accepts two sets of key word arguments from
`select_atoms()`: the ``rdkit_kwargs`` are passed internally to
`RDKitConverter.convert()` and the ``smarts_kwargs`` are passed to
RDKit's `GetSubstructMatches
<https://www.rdkit.org/docs/source/rdkit.Chem.rdchem.html#rdkit.Chem.rdchem.Mol.GetSubstructMatches>`_.
By default, the `useChirality` kwarg in ``rdkit_kwargs`` is set to true
and maxMatches in ``smarts_kwargs`` is
``max(1000, 10 * n_atoms)``, where ``n_atoms`` is either
``len(AtomGroup)`` or ``len(Universe.atoms)``, whichever is
applicable. Note that the number of matches can occasionally
exceed the default value of maxMatches, causing too few atoms
to be returned. If this occurs, a warning will be issued. The
problem can be fixed by increasing the value of maxMatches.
This behavior may be updated in the future.
>>> universe.select_atoms("C", smarts_kwargs={"maxMatches": 100})
<AtomGroup with 100 atoms>
chiral *R | S*
select a particular stereocenter. e.g. ``name C and chirality
S`` to select only S-chiral carbon atoms. Only ``R`` and
``S`` will be possible options but other values will not raise
an error.
formalcharge *formal-charge*
select atoms based on their formal charge, e.g.
``name O and formalcharge -1`` to select all oxygens with a
negative 1 formal charge.
**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
isolayer *inner radius* *outer radius* *selection*
Similar to sphlayer, but will find layer around all reference
layer, creating an iso-surface.
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.core.universe.Universe` are
consecutively numbered, and the index runs from 1 up to the
total number of atoms.
index *index-range*
selects all atoms within a range of (0-based) inclusive indices,
e.g. ``index 0`` selects the first atom in the universe;
``index 5:10`` selects atoms 6 through 11 inclusive. All atoms
in the :class:`~MDAnalysis.core.universe.Universe` are
consecutively numbered, and the index runs from 0 up to the
total number of atoms - 1.
**Preexisting selections**
group `group-name`
selects the atoms in the :class:`AtomGroup` passed to the
function as a keyword 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:`~MDAnalysis.core.universe.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.
.. versionchanged:: 0.13.0 Added *bonded* selection.
.. versionchanged:: 0.16.0 Resid selection now takes icodes into account
where present.
.. versionchanged:: 0.16.0 Updating selections now possible by setting
the `updating` argument.
.. versionchanged:: 0.17.0 Added *moltype* and *molnum* selections.
.. versionchanged:: 0.19.0
Added strict type checking for passed groups.
Added periodic kwarg (default True)
.. versionchanged:: 0.19.2
Empty sel string now returns an empty Atom group.
.. versionchanged:: 1.0.0
The ``fullgroup`` selection has now been removed in favor of the
equivalent ``global group`` selection.
Removed flags affecting default behaviour for periodic selections;
periodic are now on by default (as with default flags)
.. versionchanged:: 2.0.0
Added the *smarts* selection. Added `atol` and `rtol` keywords
to select float values. Added the ``sort`` keyword. Added
`rdkit_kwargs` to pass parameters to the RDKitConverter.
.. versionchanged:: 2.2.0
Added `smarts_kwargs` to pass parameters to the RDKit
GetSubstructMatch for *smarts* selection.
"""
if not sel:
warnings.warn("Empty string to select atoms, empty group returned.",
UserWarning)
return self[[]]
sel_strs = (sel,) + othersel
for group, thing in selgroups.items():
if not isinstance(thing, AtomGroup):
raise TypeError("Passed groups must be AtomGroups. "
"You provided {} for group '{}'".format(
thing.__class__.__name__, group))
selections = tuple((selection.Parser.parse(s, selgroups,
periodic=periodic,
atol=atol, rtol=rtol,
sorted=sorted,
rdkit_kwargs=rdkit_kwargs,
smarts_kwargs=smarts_kwargs)
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 :class:`AtomGroup` into a :class:`list` of
:class:`AtomGroups<AtomGroup>` 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:
errmsg = (f'This universe does not have {level} information. Maybe'
f' it is not provided in the topology format in use.')
raise AttributeError(errmsg) from None
except KeyError:
errmsg = (f"level = '{level}' not supported, must be one of "
f"{accessors.keys()}")
raise ValueError(errmsg) from None
return [self[levelindices == index] for index in
unique_int_1d(levelindices)]
[docs] def guess_bonds(self, vdwradii=None, fudge_factor=0.55, lower_bound=0.1):
"""Guess bonds, angles, and dihedrals between the atoms in this
:class:`AtomGroup` and add them to the underlying
:attr:`~AtomGroup.universe`.
Parameters
----------
vdwradii : dict, optional
Dict relating atom types: vdw radii
fudge_factor : float, optional
The factor by which atoms must overlap each other to be considered
a bond. Larger values will increase the number of bonds found. [0.55]
lower_bound : float, optional
The minimum bond length. All bonds found shorter than this length
will be ignored. This is useful for parsing PDB with altloc records
where atoms with altloc A and B may be very close together and
there should be no chemical bond between them. [0.1]
See Also
--------
:func:`MDAnalysis.topology.guessers.guess_bonds`
:func:`MDAnalysis.topology.guessers.guess_angles`
:func:`MDAnalysis.topology.guessers.guess_dihedrals`
.. versionadded:: 0.10.0
.. versionchanged:: 0.20.2
Now applies periodic boundary conditions when guessing bonds.
.. versionchanged:: 2.5.0
Corrected misleading docs, and now allows passing of `fudge_factor`
and `lower_bound` arguments.
"""
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,
box=self.dimensions,
fudge_factor=fudge_factor,
lower_bound=lower_bound,
)
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 :class:`AtomGroup` represented as a
:class:`MDAnalysis.core.topologyobjects.Bond` object
Raises
------
ValueError
If the :class:`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 :class:`AtomGroup` represented as an
:class:`MDAnalysis.core.topologyobjects.Angle` object
Raises
------
ValueError
If the :class:`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 :class:`AtomGroup` represented as a
:class:`~MDAnalysis.core.topologyobjects.Dihedral` object
Raises
------
ValueError
If the :class:`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 :class:`AtomGroup` represented as an
:class:`MDAnalysis.core.topologyobjects.ImproperDihedral` object
Raises
------
ValueError
If the :class:`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)
@property
def ureybradley(self):
"""This :class:`AtomGroup` represented as an
:class:`MDAnalysis.core.topologyobjects.UreyBradley` object
Raises
------
ValueError
If the :class:`AtomGroup` is not length 2
.. versionadded:: 1.0.0
"""
if len(self) != 2:
raise ValueError(
"urey bradley only makes sense for a group with exactly 2 atoms")
return topologyobjects.UreyBradley(self.ix, self.universe)
@property
def cmap(self):
"""This :class:`AtomGroup` represented as an
:class:`MDAnalysis.core.topologyobjects.CMap` object
Raises
------
ValueError
If the :class:`AtomGroup` is not length 5
.. versionadded:: 1.0.0
"""
if len(self) != 5:
raise ValueError(
"cmap only makes sense for a group with exactly 5 atoms")
return topologyobjects.CMap(self.ix, self.universe)
convert_to = Accessor("convert_to", ConverterWrapper)
[docs] def write(self, filename=None, file_format=None,
filenamefmt="{trjname}_{frame}", frames=None, **kwargs):
"""Write `AtomGroup` to a file.
The output can either be a coordinate file or a selection, depending on
the format.
Examples
--------
>>> ag = u.atoms
>>> ag.write('selection.ndx') # Write a gromacs index file
>>> ag.write('coordinates.pdb') # Write the current frame as PDB
>>> # Write the trajectory in XTC format
>>> ag.write('trajectory.xtc', frames='all')
>>> # Write every other frame of the trajectory in PBD format
>>> ag.write('trajectory.pdb', frames=u.trajectory[::2])
Parameters
----------
filename : str, optional
``None``: create TRJNAME_FRAME.FORMAT from filenamefmt [``None``]
file_format : str, optional
The name or extension of a coordinate, trajectory, or selection
file format such as PDB, CRD, GRO, VMD (tcl), PyMol (pml), Gromacs
(ndx) CHARMM (str) or Jmol (spt); case-insensitive [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 is ``"conect"``.
frames: array-like or slice or FrameIteratorBase or str, optional
An ensemble of frames to write. The ensemble can be an list or
array of frame indices, a mask of booleans, an instance of
:class:`slice`, or the value returned when a trajectory is indexed.
By default, `frames` is set to ``None`` and only the current frame
is written. If `frames` is set to "all", then all the frame from
trajectory are written.
.. versionchanged:: 0.9.0 Merged with write_selection. This method can
now write both selections out.
.. versionchanged:: 0.19.0
Can write multiframe trajectories with the 'frames' argument.
"""
# TODO: Add a 'verbose' option alongside 'frames'.
# 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 frames is None or frames == 'all':
trj_frames = trj[::]
elif isinstance(frames, numbers.Integral):
# We accept everything that indexes a trajectory and returns a
# subset of it. Though, numbers return a Timestep instead.
raise TypeError('The "frames" argument cannot be a number.')
else:
try:
test_trajectory = frames.trajectory
except AttributeError:
trj_frames = trj[frames]
else:
if test_trajectory is not trj:
raise ValueError(
'The trajectory of {} provided to the frames keyword '
'attribute is different from the trajectory of the '
'AtomGroup.'.format(frames)
)
trj_frames = frames
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 if file_format is not None else 'PDB',
keep=True)
# Some writer behave differently when they are given a "multiframe"
# argument. It is the case of the PDB writer tht writes models when
# "multiframe" is True.
# We want to honor what the user provided with the argument if
# provided explicitly. If not, then we need to figure out if we write
# multiple frames or not.
multiframe = kwargs.pop('multiframe', None)
if len(trj_frames) > 1 and multiframe == False:
raise ValueError(
'Cannot explicitely set "multiframe" to False and request '
'more than 1 frame with the "frames" keyword argument.'
)
elif multiframe is None:
if frames is None:
# By default we only write the current frame.
multiframe = False
else:
multiframe = len(trj_frames) > 1
# 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:
writer = get_writer_for(
filename, format=file_format, multiframe=multiframe)
except (ValueError, TypeError):
pass
else:
with writer(filename, n_atoms=self.n_atoms, **kwargs) as w:
if frames is None:
w.write(self.atoms)
else:
current_frame = trj.ts.frame
try:
for _ in trj_frames:
w.write(self.atoms)
finally:
trj[current_frame]
return
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 if file_format is not None else 'PDB')
except (TypeError, NotImplementedError):
pass
else:
with writer(filename, n_atoms=self.n_atoms, **kwargs) as w:
w.write(self.atoms)
return
raise ValueError("No writer found for format: {}".format(filename))
[docs] def sort(self, key='ix', keyfunc=None):
"""
Returns a sorted ``AtomGroup`` using a specified attribute as the key.
Parameters
----------
key: str, optional
The name of the ``AtomGroup`` attribute to sort by (e.g. ``ids``,
``ix``. default= ``ix`` ).
keyfunc: callable, optional
A function to convert multidimensional arrays to a single
dimension. This 1D array will be used as the sort key and
is required when sorting with an ``AtomGroup`` attribute
key which has multiple dimensions. Note: this argument
is ignored when the attribute is one dimensional.
Returns
----------
:class:`AtomGroup`
Sorted ``AtomGroup``.
Example
----------
.. code-block:: python
>>> import MDAnalysis as mda
>>> from MDAnalysisTests.datafiles import PDB_small
>>> u = mda.Universe(PDB_small)
>>> ag = u.atoms[[3, 2, 1, 0]]
>>> ag.ix
array([3 2 1 0])
>>> ag = ag.sort()
>>> ag.ix
array([0 1 2 3])
>>> ag.positions
array([[-11.921, 26.307, 10.41 ],
[-11.447, 26.741, 9.595],
[-12.44 , 27.042, 10.926],
[-12.632, 25.619, 10.046]], dtype=float32)
>>> ag = ag.sort("positions", lambda x: x[:, 1])
>>> ag.positions
array([[-12.632, 25.619, 10.046],
[-11.921, 26.307, 10.41 ],
[-11.447, 26.741, 9.595],
[-12.44 , 27.042, 10.926]], dtype=float32)
Note
----------
This uses a stable sort as implemented by
`numpy.argsort(kind='stable')`.
.. versionadded:: 2.0.0
"""
idx = getattr(self.atoms, key)
if len(idx) != len(self.atoms):
raise ValueError("The array returned by the attribute '{}' "
"must have the same length as the number of "
"atoms in the input AtomGroup".format(key))
if idx.ndim == 1:
order = np.argsort(idx, kind='stable')
elif idx.ndim > 1:
if keyfunc is None:
raise NameError("The {} attribute returns a multidimensional "
"array. In order to sort it, a function "
"returning a 1D array (to be used as the sort "
"key) must be passed to the keyfunc argument"
.format(key))
sortkeys = keyfunc(idx)
if sortkeys.ndim != 1:
raise ValueError("The function assigned to the argument "
"'keyfunc':{} doesn't return a 1D array."
.format(keyfunc))
order = np.argsort(sortkeys, kind='stable')
return self.atoms[order]
[docs]class ResidueGroup(GroupBase):
"""ResidueGroup base class.
This class is used by a :class:`~MDAnalysis.core.universe.Universe` for
generating its Topology-specific :class:`ResidueGroup` class. All the
:class:`~MDAnalysis.core.topologyattrs.TopologyAttr` components are obtained
from :class:`GroupBase`, so this class only includes ad-hoc methods
specific to :class:`ResidueGroups<ResidueGroup>`.
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.
.. versionchanged:: 1.0.0
Removed instant selectors, use select_atoms instead
.. versionchanged:: 2.1.0
Indexing an ResidueGroup with ``None`` raises a ``TypeError``.
"""
def __reduce__(self):
return (_unpickle2, (self.universe, self.ix, ResidueGroup))
@property
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`ResidueGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue` in the
:class:`ResidueGroup`. Duplicates are *not* removed.
"""
u = self.universe
ag = u.atoms[u._topology.tt.residues2atoms_1d(self._ix)]
# If the ResidueGroup is known to be unique, this also holds for the
# atoms therein, since atoms can only belong to one residue at a time.
# On the contrary, if the ResidueGroup is not unique, this does not
# imply non-unique atoms, since residues might be empty.
ag._set_unique_caches_from(self)
return ag
@property
def n_atoms(self):
"""Number of :class:`Atoms<Atom>` present in this :class:`ResidueGroup`,
including duplicate residues (and thus, duplicate atoms).
Equivalent to ``len(self.atoms)``.
"""
return len(self.atoms)
@property
def residues(self):
"""The :class:`ResidueGroup` itself.
See Also
--------
copy : return a true copy of the :class:`ResidueGroup`
.. versionchanged:: 0.19.0
In previous versions, this returned a copy, but now
the :class:`ResidueGroup` itself is returned. This should
not affect any code but only speed up calculations.
"""
return self
@property
def n_residues(self):
"""Number of residues in the :class:`ResidueGroup`.
Equivalent to ``len(self)``.
"""
return len(self)
@property
def segments(self):
"""Get sorted :class:`SegmentGroup` of the unique segments present in
the :class:`ResidueGroup`.
"""
sg = self.universe.segments[unique_int_1d(self.segindices)]
sg._cache['isunique'] = True
sg._cache['issorted'] = True
sg._cache['sorted_unique'] = sg
sg._cache['unsorted_unique'] = sg
return sg
@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:
errmsg = ("Can only set ResidueGroup segments to Segment "
"or SegmentGroup, not {}".format(
', '.join(type(r) for r in new
if not isinstance(r, Segment))))
raise TypeError(errmsg) from None
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 present in the ResidueGroup.
Equivalent to ``len(self.segments)``.
"""
return len(self.segments)
@property
def unique(self):
"""Return a :class:`ResidueGroup` containing sorted and unique
:class:`Residues<Residue>` 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])
>>> rg2.unique is rg2
False
.. versionadded:: 0.16.0
.. versionchanged:: 0.19.0 If the :class:`ResidueGroup` is already
unique, :attr:`ResidueGroup.unique` now returns the group itself
instead of a copy.
.. versionchanged:: 2.0.0
This function now always returns a copy.
"""
group = self.sorted_unique[:]
group._cache['isunique'] = True
group._cache['issorted'] = True
group._cache['sorted_unique'] = group
group._cache['unsorted_unique'] = group
return group
[docs] def asunique(self, sorted=False):
"""Return a :class:`ResidueGroup` containing unique
:class:`Residues<Residue>` only, with optional sorting.
If the :class:`ResidueGroup` is unique, this is the group itself.
Parameters
----------
sorted: bool (optional)
Whether or not the returned ResidueGroup should be sorted
by resindex.
Returns
-------
:class:`ResidueGroup`
Unique ``ResidueGroup``
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.asunique()
>>> rg2
<ResidueGroup with 3 residues>
>>> rg2.ix
array([0, 1, 2])
>>> rg2.asunique() is rg2
True
.. versionadded:: 2.0.0
"""
return self._asunique(sorted=sorted, group=self.universe.residues)
[docs]class SegmentGroup(GroupBase):
""":class:`SegmentGroup` base class.
This class is used by a :class:`~MDAnalysis.core.universe.Universe` for
generating its Topology-specific :class:`SegmentGroup` class. All the
:class:`~MDAnalysis.core.topologyattrs.TopologyAttr` components are obtained
from :class:`GroupBase`, so this class only includes ad-hoc methods specific
to :class:`SegmentGroups<SegmentGroup>`.
:class:`SegmentGroups<SegmentGroup>` 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.
.. versionchanged:: 1.0.0
Removed instant selectors, use select_atoms instead
.. versionchanged:: 2.1.0
Indexing an SegmentGroup with ``None`` raises a ``TypeError``.
"""
def __reduce__(self):
return (_unpickle2, (self.universe, self.ix, SegmentGroup))
@property
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`SegmentGroup`.
The :class:`Atoms<Atom>` are ordered locally by :class:`Residue`, which
are further ordered by :class:`Segment` in the :class:`SegmentGroup`.
Duplicates are *not* removed.
"""
u = self.universe
ag = u.atoms[u._topology.tt.segments2atoms_1d(self._ix)]
# If the SegmentGroup is known to be unique, this also holds for the
# residues therein, and thus, also for the atoms in those residues.
# On the contrary, if the SegmentGroup is not unique, this does not
# imply non-unique atoms, since segments or residues might be empty.
ag._set_unique_caches_from(self)
return ag
@property
def n_atoms(self):
"""Number of atoms present in the :class:`SegmentGroup`, including
duplicate segments (and thus, duplicate atoms).
Equivalent to ``len(self.atoms)``.
"""
return len(self.atoms)
@property
def residues(self):
"""A :class:`ResidueGroup` of :class:`Residues<Residue>` present in this
:class:`SegmentGroup`.
The :class:`Residues<Residue>` are ordered locally by
:class:`Segment` in the :class:`SegmentGroup`. Duplicates are *not*
removed.
"""
rg = self.universe.residues[np.concatenate(self.resindices)]
# If the SegmentGroup is known to be unique, this also holds for the
# residues therein. On the contrary, if the SegmentGroup is not unique,
# this does not imply non-unique residues, since segments might be
# empty.
rg._set_unique_caches_from(self)
return rg
@property
def n_residues(self):
"""Number of residues present in this :class:`SegmentGroup`, including
duplicate segments (and thus, residues).
Equivalent to ``len(self.residues)``.
"""
return len(self.residues)
@property
def segments(self):
"""The :class:`SegmentGroup` itself.
See Also
--------
copy : return a true copy of the :class:`SegmentGroup`
.. versionchanged:: 0.19.0
In previous versions, this returned a copy, but now
the :class:`SegmentGroup` itself is returned. This should
not affect any code but only speed up calculations.
"""
return self
@property
def n_segments(self):
"""Number of segments in the :class:`SegmentGroup`.
Equivalent to ``len(self)``.
"""
return len(self)
@property
def unique(self):
"""Return a :class:`SegmentGroup` containing sorted and unique
:class:`Segments<Segment>` 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])
>>> sg2.unique is sg2
False
.. versionadded:: 0.16.0
.. versionchanged:: 0.19.0 If the :class:`SegmentGroup` is already
unique, :attr:`SegmentGroup.unique` now returns the group itself
instead of a copy.
.. versionchanged:: 2.0.0
This function now always returns a copy.
"""
group = self.sorted_unique[:]
group._cache['isunique'] = True
group._cache['issorted'] = True
group._cache['sorted_unique'] = group
group._cache['unsorted_unique'] = group
return group
[docs] def asunique(self, sorted=False):
"""Return a :class:`SegmentGroup` containing unique
:class:`Segments<Segment>` only, with optional sorting.
If the :class:`SegmentGroup` is unique, this is the group itself.
Parameters
----------
sorted: bool (optional)
Whether or not the returned SegmentGroup should be sorted
by segindex.
Returns
-------
:class:`SegmentGroup`
Unique ``SegmentGroup``
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.asunique()
>>> sg2
<SegmentGroup with 3 segments>
>>> sg2.ix
array([0, 1, 2])
>>> sg2.asunique() is sg2
True
.. versionadded:: 2.0.0
"""
return self._asunique(sorted=sorted, group=self.universe.segments)
@functools.total_ordering
class ComponentBase(_MutableBase):
r"""Base class from which a :class:`~MDAnalysis.core.universe.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 __getattr__(self, attr):
selfcls = type(self).__name__
if attr in _TOPOLOGY_ATTRS:
cls = _TOPOLOGY_ATTRS[attr]
if attr == cls.attrname and attr != cls.singular:
err = ('{selfcls} has no attribute {attr}. '
'Do you mean {singular}?')
raise AttributeError(err.format(selfcls=selfcls, attr=attr,
singular=cls.singular))
else:
err = 'This Universe does not contain {singular} information'
raise NoDataError(err.format(singular=cls.singular))
else:
return super(ComponentBase, self).__getattr__(attr)
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 :class:`Atom`, this is the index of the
:class:`Atom`.
If it is a :class:`Residue`, this is the index of the :class:`Residue`.
If it is a :class:`Segment`, this is the index of the :class:`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):
""":class:`Atom` base class.
This class is used by a :class:`~MDAnalysis.core.universe.Universe` for
generating its Topology-specific :class:`Atom` class. All the
:class:`~MDAnalysis.core.topologyattrs.TopologyAttr` components are obtained
from :class:`ComponentBase`, so this class only includes ad-hoc methods
specific to :class:`Atoms<Atom>`.
"""
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 + '>'
def __reduce__(self):
return (_unpickle2, (self.universe, self.ix, Atom))
def __getattr__(self, attr):
# special-case timestep info
ts = {'velocity': 'velocities', 'force': 'forces'}
if attr in ts:
raise NoDataError('This Timestep has no ' + ts[attr])
elif attr == 'position':
raise NoDataError('This Universe has no coordinates')
return super(Atom, self).__getattr__(attr)
@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
Raises
------
~MDAnalysis.exceptions.NoDataError
If the underlying :class:`~MDAnalysis.coordinates.timestep.Timestep`
does not contain
:attr:`~MDAnalysis.coordinates.timestep.Timestep.positions`.
"""
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
Raises
------
~MDAnalysis.exceptions.NoDataError
If the underlying :class:`~MDAnalysis.coordinates.timestep.Timestep`
does not contain
:attr:`~MDAnalysis.coordinates.timestep.Timestep.velocities`.
"""
ts = self.universe.trajectory.ts
return ts.velocities[self.ix].copy()
@velocity.setter
def velocity(self, values):
ts = self.universe.trajectory.ts
ts.velocities[self.ix, :] = values
@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
Raises
------
~MDAnalysis.exceptions.NoDataError
If the underlying :class:`~MDAnalysis.coordinates.timestep.Timestep`
does not contain
:attr:`~MDAnalysis.coordinates.timestep.Timestep.forces`.
"""
ts = self.universe.trajectory.ts
return ts.forces[self.ix].copy()
@force.setter
def force(self, values):
ts = self.universe.trajectory.ts
ts.forces[self.ix, :] = values
[docs]class Residue(ComponentBase):
""":class:`Residue` base class.
This class is used by a :class:`~MDAnalysis.core.universe.Universe` for
generating its Topology-specific :class:`Residue` class. All the
:class:`~MDAnalysis.core.topologyattrs.TopologyAttr` components are obtained
from :class:`ComponentBase`, so this class only includes ad-hoc methods
specific to :class:`Residues<Residue>`.
"""
def __repr__(self):
me = '<Residue'
if hasattr(self, 'resname'):
me += ' {},'.format(self.resname)
if hasattr(self, 'resid'):
me += ' {}'.format(self.resid)
return me + '>'
def __reduce__(self):
return (_unpickle2, (self.universe, self.ix, Residue))
@property
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`Residue`.
"""
ag = self.universe.atoms[self.universe._topology.indices[self][0]]
ag._cache['isunique'] = True
ag._cache['issorted'] = True
ag._cache['sorted_unique'] = ag
ag._cache['unsorted_unique'] = ag
return ag
@property
def segment(self):
"""The :class:`Segment` this :class:`Residue` belongs to.
"""
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):
""":class:`Segment` base class.
This class is used by a :class:`~MDAnalysis.core.universe.Universe` for
generating its Topology-specific :class:`Segment` class. All the
:class:`~MDAnalysis.core.topologyattrs.TopologyAttr` components are obtained
from :class:`ComponentBase`, so this class only includes ad-hoc methods
specific to :class:`Segments<Segment>`.
.. deprecated:: 0.16.2
*Instant selectors* of :class:`Segments<Segment>` will be removed in the
1.0 release.
.. versionchanged:: 1.0.0
Removed instant selectors, use either segment.residues[...] to select
residue by number, or segment.residues[segment.residue.resnames = ...]
to select by resname.
"""
def __repr__(self):
me = '<Segment'
if hasattr(self, 'segid'):
me += ' {}'.format(self.segid)
return me + '>'
def __reduce__(self):
return (_unpickle2, (self.universe, self.ix, Segment))
@property
def atoms(self):
"""An :class:`AtomGroup` of :class:`Atoms<Atom>` present in this
:class:`Segment`.
"""
ag = self.universe.atoms[self.universe._topology.indices[self][0]]
ag._cache['isunique'] = True
ag._cache['issorted'] = True
ag._cache['sorted_unique'] = ag
ag._cache['unsorted_unique'] = ag
return ag
@property
def residues(self):
"""A :class:`ResidueGroup` of :class:`Residues<Residue>` present in this
:class:`Segment`.
"""
rg = self.universe.residues[self.universe._topology.resindices[self][0]]
rg._cache['isunique'] = True
rg._cache['issorted'] = True
rg._cache['sorted_unique'] = rg
rg._cache['unsorted_unique'] = rg
return rg
# 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)
@property
def atoms(self):
"""Get a *static* :class:`AtomGroup` identical to the group of currently
selected :class:`Atoms<Atom>` in the :class:`UpdatingAtomGroup`.
By returning a *static* :class:`AtomGroup` it becomes possible to
compare the contents of the group *between* trajectory frames. See the
Example below.
Note
----
The :attr:`atoms` attribute of an :class:`UpdatingAtomGroup` behaves
differently from :attr:`AtomGroup.atoms`: the latter returns the
:class:`AtomGroup` itself whereas the former returns a
:class:`AtomGroup` and not an :class:`UpdatingAtomGroup` (for this, use
:meth:`UpdatingAtomGroup.copy`).
Example
-------
The static :attr:`atoms` allows comparison of groups of atoms between
frames. For example, track water molecules that move in and out of a
solvation shell of a protein::
u = mda.Universe(TPR, XTC)
water_shell = u.select_atoms("name OW and around 3.5 protein", updating=True)
water_shell_prev = water_shell.atoms
for ts in u.trajectory:
exchanged = water_shell - water_shell_prev
print(ts.time, "waters in shell =", water_shell.n_residues)
print(ts.time, "waters that exchanged = ", exchanged.n_residues)
print(ts.time, "waters that remained bound = ",
water_shell.n_residues - exchanged.n_residues)
water_shell_prev = water_shell.atoms
By remembering the atoms of the current time step in
`water_shell_prev`, it becomes possible to use the :meth:`subtraction
of AtomGroups<AtomGroup.subtract>` to find the water molecules that
changed.
See Also
--------
copy : return a true copy of the :class:`UpdatingAtomGroup`
"""
return self[:]
[docs] def copy(self):
"""Get another :class:`UpdatingAtomGroup` identical to this one.
.. versionadded:: 0.19.0
"""
return UpdatingAtomGroup(self._base_group, self._selections,
self._selection_strings)
# 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 :class:`AtomGroup` arguments have certain
attributes
Example
-------
When used to wrap a function, will check all :class:`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