Source code for MDAnalysis.coordinates.base

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# MDAnalysis --- https://www.mdanalysis.org
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# (see the file AUTHORS for the full list of names)
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# Please cite your use of MDAnalysis in published work:
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# 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
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#


"""\
Base classes --- :mod:`MDAnalysis.coordinates.base`
===================================================

Derive, FrameIterator, Reader and Writer classes from the classes
in this module. The derived classes must follow the :ref:`Trajectory API`.


.. _FrameIterators:

FrameIterators
--------------

FrameIterators are "sliced trajectories" (a trajectory is a
:ref:`Reader <Readers>`) that can be iterated over. They are typically
created by slicing a trajectory or by fancy-indexing of a trajectory
with an array of frame numbers or a boolean mask of all frames.

Iterator classes used by the by the :class:`ProtoReader`:

.. autoclass:: FrameIteratorBase

.. autoclass:: FrameIteratorSliced

.. autoclass:: FrameIteratorAll

.. autoclass:: FrameIteratorIndices


.. _ReadersBase:

Readers
-------

Readers know how to take trajectory data in a given format and present it in a
common API to the user in MDAnalysis. There are two types of readers:

1. Readers for *multi frame trajectories*, i.e., file formats that typically
   contain many frames. These readers are typically derived from
   :class:`ReaderBase`.

2. Readers for *single frame formats*: These file formats only contain a single
   coordinate set. These readers are derived from
   :class:`SingleFrameReaderBase`.

The underlying low-level readers handle closing of files in different
ways. Typically, the MDAnalysis readers try to ensure that files are always
closed when a reader instance is garbage collected, which relies on
implementing a :meth:`~ReaderBase.__del__` method. However, in some cases, this
is not necessary (for instance, for the single frame formats) and then such a
method can lead to undesirable side effects (such as memory leaks). In this
case, :class:`ProtoReader` should be used.


.. autoclass:: ReaderBase
   :members:
   :inherited-members:

.. autoclass:: SingleFrameReaderBase
   :members:
   :inherited-members:

.. autoclass:: ProtoReader
   :members:



.. _WritersBase:

Writers
-------

Writers know how to write information in a :class:`Timestep` to a trajectory
file.

.. autoclass:: WriterBase
   :members:
   :inherited-members:


Converters
----------

Converters output information to other libraries.

.. autoclass:: ConverterBase
   :members:
   :inherited-members:


Helper classes
--------------

The following classes contain basic functionality that all readers and
writers share.

.. autoclass:: IOBase
   :members:

"""
import abc
import numpy as np
import numbers
import warnings
from typing import Any, Union, Optional, List, Dict

from .timestep import Timestep
from . import core
from .. import (
    _READERS, _READER_HINTS,
    _SINGLEFRAME_WRITERS,
    _MULTIFRAME_WRITERS,
    _CONVERTERS
)
from .. import units
from ..auxiliary.base import AuxReader
from ..auxiliary.core import auxreader
from ..auxiliary.core import get_auxreader_for
from ..auxiliary import _AUXREADERS
from ..lib.util import asiterable, Namespace, store_init_arguments
from ..lib.util import NamedStream


[docs]class FrameIteratorBase(object): """ Base iterable over the frames of a trajectory. A frame iterable has a length that can be accessed with the :func:`len` function, and can be indexed similarly to a full trajectory. When indexed, indices are resolved relative to the iterable and not relative to the trajectory. .. versionadded:: 0.19.0 """ def __init__(self, trajectory): self._trajectory = trajectory def __len__(self): raise NotImplementedError() @staticmethod def _avoid_bool_list(frames): if isinstance(frames, list) and frames and isinstance(frames[0], bool): return np.array(frames, dtype=bool) return frames @property def trajectory(self): return self._trajectory
[docs]class FrameIteratorSliced(FrameIteratorBase): """ Iterable over the frames of a trajectory on the basis of a slice. Parameters ---------- trajectory: ProtoReader The trajectory over which to iterate. frames: slice A slice to select the frames of interest. See Also -------- FrameIteratorBase .. versionadded:: 0.19.0 """ def __init__(self, trajectory, frames): # It would be easier to store directly a range object, as it would # store its parameters in a single place, calculate its length, and # take care of most the indexing. Though, doing so is not compatible # with python 2 where xrange (or range with six) is only an iterator. super(FrameIteratorSliced, self).__init__(trajectory) self._start, self._stop, self._step = trajectory.check_slice_indices( frames.start, frames.stop, frames.step, ) def __len__(self): return range_length(self.start, self.stop, self.step) def __iter__(self): for i in range(self.start, self.stop, self.step): yield self.trajectory[i] self.trajectory.rewind() def __getitem__(self, frame): if isinstance(frame, numbers.Integral): length = len(self) if not -length < frame < length: raise IndexError('Index {} is out of range of the range of length {}.' .format(frame, length)) if frame < 0: frame = len(self) + frame frame = self.start + frame * self.step return self.trajectory._read_frame_with_aux(frame) elif isinstance(frame, slice): step = (frame.step or 1) * self.step if frame.start is None: if frame.step is None or frame.step > 0: start = self.start else: start = self.start + (len(self) - 1) * self.step else: start = self.start + (frame.start or 0) * self.step if frame.stop is None: if frame.step is None or frame.step > 0: last = start + (range_length(start, self.stop, step) - 1) * step else: last = self.start stop = last + np.sign(step) else: stop = self.start + (frame.stop or 0) * self.step new_slice = slice(start, stop, step) frame_iterator = FrameIteratorSliced(self.trajectory, new_slice) # The __init__ of FrameIteratorSliced does some conversion between # the way indices are handled in slices and the way they are # handled by range. We need to overwrite this conversion as we # already use the logic for range. frame_iterator._start = start frame_iterator._stop = stop frame_iterator._step = step return frame_iterator else: # Indexing with a lists of bools does not behave the same in all # version of numpy. frame = self._avoid_bool_list(frame) frames = np.array(list(range(self.start, self.stop, self.step)))[frame] return FrameIteratorIndices(self.trajectory, frames) @property def start(self): return self._start @property def stop(self): return self._stop @property def step(self): return self._step
[docs]class FrameIteratorAll(FrameIteratorBase): """ Iterable over all the frames of a trajectory. Parameters ---------- trajectory: ProtoReader The trajectory over which to iterate. See Also -------- FrameIteratorBase .. versionadded:: 0.19.0 """ def __init__(self, trajectory): super(FrameIteratorAll, self).__init__(trajectory) def __len__(self): return self.trajectory.n_frames def __iter__(self): return iter(self.trajectory) def __getitem__(self, frame): return self.trajectory[frame]
[docs]class FrameIteratorIndices(FrameIteratorBase): """ Iterable over the frames of a trajectory listed in a sequence of indices. Parameters ---------- trajectory: ProtoReader The trajectory over which to iterate. frames: sequence A sequence of indices. See Also -------- FrameIteratorBase """ def __init__(self, trajectory, frames): super(FrameIteratorIndices, self).__init__(trajectory) self._frames = [] for frame in frames: if not isinstance(frame, numbers.Integral): raise TypeError("Frames indices must be integers.") frame = trajectory._apply_limits(frame) self._frames.append(frame) self._frames = tuple(self._frames) def __len__(self): return len(self.frames) def __iter__(self): for frame in self.frames: yield self.trajectory._read_frame_with_aux(frame) self.trajectory.rewind() def __getitem__(self, frame): if isinstance(frame, numbers.Integral): frame = self.frames[frame] return self.trajectory._read_frame_with_aux(frame) else: frame = self._avoid_bool_list(frame) frames = np.array(self.frames)[frame] return FrameIteratorIndices(self.trajectory, frames) @property def frames(self): return self._frames
[docs]class IOBase(object): """Base class bundling common functionality for trajectory I/O. .. versionchanged:: 0.8 Added context manager protocol. """ #: dict with units of of *time* and *length* (and *velocity*, *force*, #: ... for formats that support it) units = {'time': None, 'length': None, 'velocity': None}
[docs] def convert_pos_from_native(self, x, inplace=True): """Conversion of coordinate array x from native units to base units. Parameters ---------- x : array_like Positions to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input `x` is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionchanged:: 0.7.5 Keyword `inplace` can be set to ``False`` so that a modified copy is returned *unless* no conversion takes place, in which case the reference to the unmodified `x` is returned. """ f = units.get_conversion_factor('length', self.units['length'], 'Angstrom') if f == 1.: return x if not inplace: return f * x x *= f return x
[docs] def convert_velocities_from_native(self, v, inplace=True): """Conversion of velocities array *v* from native to base units Parameters ---------- v : array_like Velocities to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input *v* is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionadded:: 0.7.5 """ f = units.get_conversion_factor( 'speed', self.units['velocity'], 'Angstrom/ps') if f == 1.: return v if not inplace: return f * v v *= f return v
[docs] def convert_forces_from_native(self, force, inplace=True): """Conversion of forces array *force* from native to base units Parameters ---------- force : array_like Forces to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input *force* is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionadded:: 0.7.7 """ f = units.get_conversion_factor( 'force', self.units['force'], 'kJ/(mol*Angstrom)') if f == 1.: return force if not inplace: return f * force force *= f return force
[docs] def convert_time_from_native(self, t, inplace=True): """Convert time *t* from native units to base units. Parameters ---------- t : array_like Time values to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input `t` is modified in place and also returned (although note that scalar values `t` are passed by value in Python and hence an in-place modification has no effect on the caller.) In-place operations improve performance because allocating new arrays is avoided. .. versionchanged:: 0.7.5 Keyword `inplace` can be set to ``False`` so that a modified copy is returned *unless* no conversion takes place, in which case the reference to the unmodified `x` is returned. """ f = units.get_conversion_factor( 'time', self.units['time'], 'ps') if f == 1.: return t if not inplace: return f * t t *= f return t
[docs] def convert_pos_to_native(self, x, inplace=True): """Conversion of coordinate array `x` from base units to native units. Parameters ---------- x : array_like Positions to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input `x` is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionchanged:: 0.7.5 Keyword `inplace` can be set to ``False`` so that a modified copy is returned *unless* no conversion takes place, in which case the reference to the unmodified `x` is returned. """ f = units.get_conversion_factor( 'length', 'Angstrom', self.units['length']) if f == 1.: return x if not inplace: return f * x x *= f return x
[docs] def convert_velocities_to_native(self, v, inplace=True): """Conversion of coordinate array `v` from base to native units Parameters ---------- v : array_like Velocities to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input `v` is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionadded:: 0.7.5 """ f = units.get_conversion_factor( 'speed', 'Angstrom/ps', self.units['velocity']) if f == 1.: return v if not inplace: return f * v v *= f return v
[docs] def convert_forces_to_native(self, force, inplace=True): """Conversion of force array *force* from base to native units. Parameters ---------- force : array_like Forces to transform inplace : bool (optional) Whether to modify the array inplace, overwriting previous data Note ---- By default, the input `force` is modified in place and also returned. In-place operations improve performance because allocating new arrays is avoided. .. versionadded:: 0.7.7 """ f = units.get_conversion_factor( 'force', 'kJ/(mol*Angstrom)', self.units['force']) if f == 1.: return force if not inplace: return f * force force *= f return force
[docs] def convert_time_to_native(self, t, inplace=True): """Convert time *t* from base units to native units. Parameters ---------- t : array_like Time values to transform inplace : bool, optional Whether to modify the array inplace, overwriting previous data Note ---- By default, the input *t* is modified in place and also returned. (Also note that scalar values *t* are passed by value in Python and hence an in-place modification has no effect on the caller.) .. versionchanged:: 0.7.5 Keyword *inplace* can be set to ``False`` so that a modified copy is returned *unless* no conversion takes place, in which case the reference to the unmodified *x* is returned. """ f = units.get_conversion_factor( 'time', 'ps', self.units['time']) if f == 1.: return t if not inplace: return f * t t *= f return t
[docs] def close(self): """Close the trajectory file.""" pass # pylint: disable=unnecessary-pass
def __enter__(self): return self def __exit__(self, exc_type, exc_val, exc_tb): # see http://docs.python.org/2/library/stdtypes.html#typecontextmanager self.close() return False # do not suppress exceptions
class _Readermeta(abc.ABCMeta): """Automatic Reader registration metaclass .. versionchanged:: 1.0.0 Added _format_hint functionality """ # Auto register upon class creation def __init__(cls, name, bases, classdict): type.__init__(type, name, bases, classdict) # pylint: disable=non-parent-init-called try: fmt = asiterable(classdict['format']) except KeyError: pass else: for fmt_name in fmt: fmt_name = fmt_name.upper() _READERS[fmt_name] = cls if '_format_hint' in classdict: # isn't bound yet, so access __func__ _READER_HINTS[fmt_name] = classdict['_format_hint'].__func__
[docs]class ProtoReader(IOBase, metaclass=_Readermeta): """Base class for Readers, without a :meth:`__del__` method. Extends :class:`IOBase` with most attributes and methods of a generic Reader, with the exception of a :meth:`__del__` method. It should be used as base for Readers that do not need :meth:`__del__`, especially since having even an empty :meth:`__del__` might lead to memory leaks. See the :ref:`Trajectory API` definition in :mod:`MDAnalysis.coordinates.__init__` for the required attributes and methods. See Also -------- :class:`ReaderBase` .. versionchanged:: 0.11.0 Frames now 0-based instead of 1-based .. versionchanged:: 2.0.0 Now supports (un)pickle. Upon unpickling, the current timestep is retained by reconstrunction. """ #: The appropriate Timestep class, e.g. #: :class:`MDAnalysis.coordinates.xdrfile.XTC.Timestep` for XTC. _Timestep = Timestep _transformations: list _auxs: dict _filename: Any n_frames: int def __init__(self): # initialise list to store added auxiliary readers in # subclasses should now call super self._auxs = {} self._transformations=[] def __len__(self) -> int: return self.n_frames
[docs] @classmethod def parse_n_atoms(cls, filename, **kwargs): """Read the coordinate file and deduce the number of atoms Returns ------- n_atoms : int the number of atoms in the coordinate file Raises ------ NotImplementedError when the number of atoms can't be deduced """ raise NotImplementedError("{} cannot deduce the number of atoms" "".format(cls.__name__))
[docs] def next(self) -> Timestep: """Forward one step to next frame.""" try: ts = self._read_next_timestep() except (EOFError, IOError): self.rewind() raise StopIteration from None else: for auxname, reader in self._auxs.items(): ts = self._auxs[auxname].update_ts(ts) ts = self._apply_transformations(ts) return ts
def __next__(self) -> Timestep: """Forward one step to next frame when using the `next` builtin.""" return self.next()
[docs] def rewind(self) -> Timestep: """Position at beginning of trajectory""" self._reopen() self.next()
@property def dt(self) -> float: """Time between two trajectory frames in picoseconds.""" return self.ts.dt @property def totaltime(self) -> float: """Total length of the trajectory The time is calculated as ``(n_frames - 1) * dt``, i.e., we assume that the first frame no time as elapsed. Thus, a trajectory with two frames will be considered to have a length of a single time step `dt` and a "trajectory" with a single frame will be reported as length 0. """ return (self.n_frames - 1) * self.dt @property def frame(self) -> int: """Frame number of the current time step. This is a simple short cut to :attr:`Timestep.frame`. """ return self.ts.frame @property def time(self): """Time of the current frame in MDAnalysis time units (typically ps). This is either read straight from the Timestep, or calculated as time = :attr:`Timestep.frame` * :attr:`Timestep.dt` """ return self.ts.time @property def trajectory(self): # Makes a reader effectively commpatible with a FrameIteratorBase return self
[docs] def Writer(self, filename, **kwargs): """A trajectory writer with the same properties as this trajectory.""" raise NotImplementedError( "Sorry, there is no Writer for this format in MDAnalysis. " "Please file an enhancement request at " "https://github.com/MDAnalysis/mdanalysis/issues")
[docs] def OtherWriter(self, filename, **kwargs): """Returns a writer appropriate for *filename*. Sets the default keywords *start*, *step* and *dt* (if available). *n_atoms* is always set from :attr:`Reader.n_atoms`. See Also -------- :meth:`Reader.Writer` and :func:`MDAnalysis.Writer` """ kwargs['n_atoms'] = self.n_atoms # essential kwargs.setdefault('start', self.frame) try: kwargs.setdefault('dt', self.dt) except KeyError: pass return core.writer(filename, **kwargs)
@abc.abstractmethod def _read_next_timestep(self, ts=None): # Example from DCDReader: # if ts is None: # ts = self.ts # ts.frame = self._read_next_frame(etc) # return ts ... def __iter__(self): """ Iterate over trajectory frames. """ self._reopen() return self @abc.abstractmethod def _reopen(self): """Should position Reader to just before first frame Calling next after this should return the first frame """ pass # pylint: disable=unnecessary-pass def _apply_limits(self, frame): if frame < 0: frame += len(self) if frame < 0 or frame >= len(self): raise IndexError("Index {} exceeds length of trajectory ({})." "".format(frame, len(self))) return frame def __getitem__(self, frame): """Return the Timestep corresponding to *frame*. If `frame` is a integer then the corresponding frame is returned. Negative numbers are counted from the end. If frame is a :class:`slice` then an iterator is returned that allows iteration over that part of the trajectory. Note ---- *frame* is a 0-based frame index. """ if isinstance(frame, numbers.Integral): frame = self._apply_limits(frame) return self._read_frame_with_aux(frame) elif isinstance(frame, (list, np.ndarray)): if len(frame) != 0 and isinstance(frame[0], (bool, np.bool_)): # Avoid having list of bools frame = np.asarray(frame, dtype=bool) # Convert bool array to int array frame = np.arange(len(self))[frame] return FrameIteratorIndices(self, frame) elif isinstance(frame, slice): start, stop, step = self.check_slice_indices( frame.start, frame.stop, frame.step) if start == 0 and stop == len(self) and step == 1: return FrameIteratorAll(self) else: return FrameIteratorSliced(self, frame) else: raise TypeError("Trajectories must be an indexed using an integer," " slice or list of indices") def _read_frame(self, frame): """Move to *frame* and fill timestep with data.""" raise TypeError("{0} does not support direct frame indexing." "".format(self.__class__.__name__)) # Example implementation in the DCDReader: # self._jump_to_frame(frame) # ts = self.ts # ts.frame = self._read_next_frame(ts._x, ts._y, ts._z, # ts.dimensions, 1) # return ts def _read_frame_with_aux(self, frame): """Move to *frame*, updating ts with trajectory, transformations and auxiliary data.""" ts = self._read_frame(frame) # pylint: disable=assignment-from-no-return for aux in self.aux_list: ts = self._auxs[aux].update_ts(ts) ts = self._apply_transformations(ts) return ts def _sliced_iter(self, start, stop, step): """Generator for slicing a trajectory. *start* *stop* and *step* are 3 integers describing the slice. Error checking is not done past this point. A :exc:`NotImplementedError` is raised if random access to frames is not implemented. """ # override with an appropriate implementation e.g. using self[i] might # be much slower than skipping steps in a next() loop try: for i in range(start, stop, step): yield self._read_frame_with_aux(i) self.rewind() except TypeError: # if _read_frame not implemented errmsg = f"{self.__class__.__name__} does not support slicing." raise TypeError(errmsg) from None
[docs] def check_slice_indices(self, start, stop, step): """Check frame indices are valid and clip to fit trajectory. The usage follows standard Python conventions for :func:`range` but see the warning below. Parameters ---------- start : int or None Starting frame index (inclusive). ``None`` corresponds to the default of 0, i.e., the initial frame. stop : int or None Last frame index (exclusive). ``None`` corresponds to the default of n_frames, i.e., it includes the last frame of the trajectory. step : int or None step size of the slice, ``None`` corresponds to the default of 1, i.e, include every frame in the range `start`, `stop`. Returns ------- start, stop, step : tuple (int, int, int) Integers representing the slice Warning ------- The returned values `start`, `stop` and `step` give the expected result when passed in :func:`range` but gives unexpected behavior when passed in a :class:`slice` when ``stop=None`` and ``step=-1`` This can be a problem for downstream processing of the output from this method. For example, slicing of trajectories is implemented by passing the values returned by :meth:`check_slice_indices` to :func:`range` :: range(start, stop, step) and using them as the indices to randomly seek to. On the other hand, in :class:`MDAnalysis.analysis.base.AnalysisBase` the values returned by :meth:`check_slice_indices` are used to splice the trajectory by creating a :class:`slice` instance :: slice(start, stop, step) This creates a discrepancy because these two lines are not equivalent:: range(10, -1, -1) # [10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0] range(10)[slice(10, -1, -1)] # [] """ slice_dict = {'start': start, 'stop': stop, 'step': step} for varname, var in slice_dict.items(): if isinstance(var, numbers.Integral): slice_dict[varname] = int(var) elif (var is None): pass else: raise TypeError("{0} is not an integer".format(varname)) start = slice_dict['start'] stop = slice_dict['stop'] step = slice_dict['step'] if step == 0: raise ValueError("Step size is zero") nframes = len(self) step = step or 1 if start is None: start = 0 if step > 0 else nframes - 1 elif start < 0: start += nframes if start < 0: start = 0 if step < 0 and start >= nframes: start = nframes - 1 if stop is None: stop = nframes if step > 0 else -1 elif stop < 0: stop += nframes if step > 0 and stop > nframes: stop = nframes return start, stop, step
def __repr__(self): return ("<{cls} {fname} with {nframes} frames of {natoms} atoms>" "".format( cls=self.__class__.__name__, fname=self.filename, nframes=self.n_frames, natoms=self.n_atoms ))
[docs] def timeseries(self, asel: Optional['AtomGroup']=None, start: Optional[int]=None, stop: Optional[int]=None, step: Optional[int]=None, order: Optional[str]='fac') -> np.ndarray: """Return a subset of coordinate data for an AtomGroup Parameters ---------- asel : AtomGroup (optional) The :class:`~MDAnalysis.core.groups.AtomGroup` to read the coordinates from. Defaults to ``None``, in which case the full set of coordinate data is returned. start : int (optional) Begin reading the trajectory at frame index `start` (where 0 is the index of the first frame in the trajectory); the default ``None`` starts at the beginning. stop : int (optional) End reading the trajectory at frame index `stop`-1, i.e, `stop` is excluded. The trajectory is read to the end with the default ``None``. step : int (optional) Step size for reading; the default ``None`` is equivalent to 1 and means to read every frame. order : str (optional) the order/shape of the return data array, corresponding to (a)tom, (f)rame, (c)oordinates all six combinations of 'a', 'f', 'c' are allowed ie "fac" - return array where the shape is (frame, number of atoms, coordinates) See Also -------- :class:`MDAnalysis.coordinates.memory` .. versionadded:: 2.4.0 """ start, stop, step = self.check_slice_indices(start, stop, step) nframes = len(range(start, stop, step)) if asel is not None: if len(asel) == 0: raise ValueError( "Timeseries requires at least one atom to analyze") atom_numbers = asel.indices natoms = len(atom_numbers) else: natoms = self.n_atoms atom_numbers = np.arange(natoms) # allocate output array in 'fac' order coordinates = np.empty((nframes, natoms, 3), dtype=np.float32) for i, ts in enumerate(self[start:stop:step]): coordinates[i, :] = ts.positions[atom_numbers] # switch axes around default_order = 'fac' if order != default_order: try: newidx = [default_order.index(i) for i in order] except ValueError: raise ValueError(f"Unrecognized order key in {order}, " "must be permutation of 'fac'") try: coordinates = np.moveaxis(coordinates, newidx, [0, 1, 2]) except ValueError: errmsg = ("Repeated or missing keys passed to argument " f"`order`: {order}, each key must be used once") raise ValueError(errmsg) return coordinates
# TODO: Change order of aux_spec and auxdata for 3.0 release, cf. Issue #3811
[docs] def add_auxiliary(self, aux_spec: Union[str, Dict[str, str]] = None, auxdata: Union[str, AuxReader] = None, format: str = None, **kwargs) -> None: """Add auxiliary data to be read alongside trajectory. Auxiliary data may be any data timeseries from the trajectory additional to that read in by the trajectory reader. *auxdata* can be an :class:`~MDAnalysis.auxiliary.base.AuxReader` instance, or the data itself as e.g. a filename; in the latter case an appropriate :class:`~MDAnalysis.auxiliary.base.AuxReader` is guessed from the data/file format. An appropriate `format` may also be directly provided as a key word argument. On adding, the AuxReader is initially matched to the current timestep of the trajectory, and will be updated when the trajectory timestep changes (through a call to :meth:`next()` or jumping timesteps with ``trajectory[i]``). The representative value(s) of the auxiliary data for each timestep (as calculated by the :class:`~MDAnalysis.auxiliary.base.AuxReader`) are stored in the current timestep in the ``ts.aux`` namespace under *aux_spec*; e.g. to add additional pull force data stored in pull-force.xvg:: u = MDAnalysis.Universe(PDB, XTC) u.trajectory.add_auxiliary('pull', 'pull-force.xvg') The representative value for the current timestep may then be accessed as ``u.trajectory.ts.aux.pull`` or ``u.trajectory.ts.aux['pull']``. The following applies to energy readers like the :class:`~MDAnalysis.auxiliary.EDR.EDRReader`. All data that is present in the (energy) file can be added by omitting `aux_spec` like so:: u.trajectory.add_auxiliary(auxdata="ener.edr") *aux_spec* is expected to be a dictionary that maps the desired attribute name in the ``ts.aux`` namespace to the precise data to be added as identified by a :attr:`data_selector`:: term_dict = {"temp": "Temperature", "epot": "Potential"} u.trajectory.add_auxiliary(term_dict, "ener.edr") Adding this data can be useful, for example, to filter trajectory frames based on non-coordinate data like the potential energy of each time step. Trajectory slicing allows working on a subset of frames:: selected_frames = np.array([ts.frame for ts in u.trajectory if ts.aux.epot < some_threshold]) subset = u.trajectory[selected_frames] See Also -------- :meth:`remove_auxiliary` Note ---- Auxiliary data is assumed to be time-ordered, with no duplicates. See the :ref:`Auxiliary API`. """ if auxdata is None: raise ValueError("No input `auxdata` specified, but it needs " "to be provided.") if type(auxdata) not in list(_AUXREADERS.values()): # i.e. if auxdata is a file, not an instance of an AuxReader reader_type = get_auxreader_for(auxdata) auxreader = reader_type(auxdata) else: auxreader = auxdata auxreader.attach_auxiliary(self, aux_spec, format, **kwargs)
[docs] def remove_auxiliary(self, auxname): """Clear data and close the :class:`~MDAnalysis.auxiliary.base.AuxReader` for the auxiliary *auxname*. See Also -------- :meth:`add_auxiliary` """ aux = self._check_for_aux(auxname) aux.close() del aux delattr(self.ts.aux, auxname)
@property def aux_list(self): """ Lists the names of added auxiliary data. """ return self._auxs.keys() def _check_for_aux(self, auxname): """ Check for the existance of an auxiliary *auxname*. If present, return the AuxReader; if not, raise ValueError """ if auxname in self.aux_list: return self._auxs[auxname] else: raise ValueError("No auxiliary named {name}".format(name=auxname))
[docs] def next_as_aux(self, auxname): """ Move to the next timestep for which there is at least one step from the auxiliary *auxname* within the cutoff specified in *auxname*. This allows progression through the trajectory without encountering ``NaN`` representative values (unless these are specifically part of the auxiliary data). If the auxiliary cutoff is not set, where auxiliary steps are less frequent (``auxiliary.dt > trajectory.dt``), this allows progression at the auxiliary pace (rounded to nearest timestep); while if the auxiliary steps are more frequent, this will work the same as calling :meth:`next()`. See the :ref:`Auxiliary API`. See Also -------- :meth:`iter_as_aux` """ aux = self._check_for_aux(auxname) ts = self.ts # catch up auxiliary if it starts earlier than trajectory while aux.step_to_frame(aux.step + 1, ts) is None: next(aux) # find the next frame that'll have a representative value next_frame = aux.next_nonempty_frame(ts) if next_frame is None: # no more frames with corresponding auxiliary values; stop iteration raise StopIteration # some readers set self._frame to -1, rather than self.frame, on # _reopen; catch here or doesn't read first frame while self.frame != next_frame or getattr(self, '_frame', 0) == -1: # iterate trajectory until frame is reached ts = self.next() return ts
[docs] def iter_as_aux(self, auxname): """Iterate through timesteps for which there is at least one assigned step from the auxiliary *auxname* within the cutoff specified in *auxname*. See Also -------- :meth:`next_as_aux` :meth:`iter_auxiliary` """ aux = self._check_for_aux(auxname) self._reopen() aux._restart() while True: try: yield self.next_as_aux(auxname) except StopIteration: return
[docs] def iter_auxiliary(self, auxname, start=None, stop=None, step=None, selected=None): """ Iterate through the auxiliary *auxname* independently of the trajectory. Will iterate over the specified steps of the auxiliary (defaults to all steps). Allows to access all values in an auxiliary, including those out of the time range of the trajectory, without having to also iterate through the trajectory. After interation, the auxiliary will be repositioned at the current step. Parameters ---------- auxname : str Name of the auxiliary to iterate over. (start, stop, step) : optional Options for iterating over a slice of the auxiliary. selected : lst | ndarray, optional List of steps to iterate over. Yields ------ :class:`~MDAnalysis.auxiliary.base.AuxStep` object See Also -------- :meth:`iter_as_aux` """ aux = self._check_for_aux(auxname) if selected is not None: selection = selected else: selection = slice(start, stop, step) for i in aux[selection]: yield i aux.read_ts(self.ts)
[docs] def get_aux_attribute(self, auxname, attrname): """Get the value of *attrname* from the auxiliary *auxname* Parameters ---------- auxname : str Name of the auxiliary to get value for attrname : str Name of gettable attribute in the auxiliary reader See Also -------- :meth:`set_aux_attribute` """ aux = self._check_for_aux(auxname) return getattr(aux, attrname)
[docs] def set_aux_attribute(self, auxname, attrname, new): """ Set the value of *attrname* in the auxiliary *auxname*. Parameters ---------- auxname : str Name of the auxiliary to alter attrname : str Name of settable attribute in the auxiliary reader new New value to try set *attrname* to See Also -------- :meth:`get_aux_attribute` :meth:`rename_aux` - to change the *auxname* attribute """ aux = self._check_for_aux(auxname) if attrname == 'auxname': self.rename_aux(auxname, new) else: setattr(aux, attrname, new)
[docs] def rename_aux(self, auxname, new): """ Change the name of the auxiliary *auxname* to *new*. Provided there is not already an auxiliary named *new*, the auxiliary name will be changed in ts.aux namespace, the trajectory's list of added auxiliaries, and in the auxiliary reader itself. Parameters ---------- auxname : str Name of the auxiliary to rename new : str New name to try set Raises ------ ValueError If the name *new* is already in use by an existing auxiliary. """ aux = self._check_for_aux(auxname) if new in self.aux_list: raise ValueError("Auxiliary data with name {name} already " "exists".format(name=new)) aux.auxname = new self._auxs[new] = self._auxs.pop(auxname) setattr(self.ts.aux, new, self.ts.aux[auxname]) delattr(self.ts.aux, auxname)
[docs] def get_aux_descriptions(self, auxnames=None): """Get descriptions to allow reloading the specified auxiliaries. If no auxnames are provided, defaults to the full list of added auxiliaries. Passing the resultant description to ``add_auxiliary()`` will allow recreation of the auxiliary. e.g., to duplicate all auxiliaries into a second trajectory:: descriptions = trajectory_1.get_aux_descriptions() for aux in descriptions: trajectory_2.add_auxiliary(**aux) Returns ------- list List of dictionaries of the args/kwargs describing each auxiliary. See Also -------- :meth:`MDAnalysis.auxiliary.base.AuxReader.get_description` """ if not auxnames: auxnames = self.aux_list descriptions = [self._auxs[aux].get_description() for aux in auxnames] return descriptions
@property def transformations(self): """ Returns the list of transformations""" return self._transformations @transformations.setter def transformations(self, transformations): if not self._transformations: self._transformations = transformations else: raise ValueError("Transformations are already set")
[docs] def add_transformations(self, *transformations): """Add all transformations to be applied to the trajectory. This function take as list of transformations as an argument. These transformations are functions that will be called by the Reader and given a :class:`Timestep` object as argument, which will be transformed and returned to the Reader. The transformations can be part of the :mod:`~MDAnalysis.transformations` module, or created by the user, and are stored as a list `transformations`. This list can only be modified once, and further calls of this function will raise an exception. .. code-block:: python u = MDAnalysis.Universe(topology, coordinates) workflow = [some_transform, another_transform, this_transform] u.trajectory.add_transformations(*workflow) The transformations are applied in the order given in the list `transformations`, i.e., the first transformation is the first or innermost one to be applied to the :class:`Timestep`. The example above would be equivalent to .. code-block:: python for ts in u.trajectory: ts = this_transform(another_transform(some_transform(ts))) Parameters ---------- transform_list : list list of all the transformations that will be applied to the coordinates in the order given in the list See Also -------- :mod:`MDAnalysis.transformations` """ try: self.transformations = transformations except ValueError: errmsg = ("Can't add transformations again. Please create a new " "Universe object") raise ValueError(errmsg) from None else: self.ts = self._apply_transformations(self.ts)
# call reader here to apply the newly added transformation on the # current loaded frame? def _apply_transformations(self, ts): """Applies all the transformations given by the user """ for transform in self.transformations: ts = transform(ts) return ts def __setstate__(self, state): self.__dict__ = state self[self.ts.frame]
[docs]class ReaderBase(ProtoReader): """Base class for trajectory readers that extends :class:`ProtoReader` with a :meth:`__del__` method. New Readers should subclass :class:`ReaderBase` and properly implement a :meth:`close` method, to ensure proper release of resources (mainly file handles). Readers that are inherently safe in this regard should subclass :class:`ProtoReader` instead. See the :ref:`Trajectory API` definition in for the required attributes and methods. See Also -------- :class:`ProtoReader` .. versionchanged:: 0.11.0 Most of the base Reader class definitions were offloaded to :class:`ProtoReader` so as to allow the subclassing of ReaderBases without a :meth:`__del__` method. Created init method to create common functionality, all ReaderBase subclasses must now :func:`super` through this class. Added attribute :attr:`_ts_kwargs`, which is created in init. Provides kwargs to be passed to :class:`Timestep` .. versionchanged:: 1.0 Removed deprecated flags functionality, use convert_units kwarg instead """ @store_init_arguments def __init__(self, filename, convert_units=True, **kwargs): super(ReaderBase, self).__init__() if isinstance(filename, NamedStream): self.filename = filename else: self.filename = str(filename) self.convert_units = convert_units ts_kwargs = {} for att in ('dt', 'time_offset'): try: val = kwargs[att] except KeyError: pass else: ts_kwargs[att] = val self._ts_kwargs = ts_kwargs
[docs] def copy(self): """Return independent copy of this Reader. New Reader will have its own file handle and can seek/iterate independently of the original. Will also copy the current state of the Timestep held in the original Reader. .. versionchanged:: 2.2.0 Arguments used to construct the reader are correctly captured and passed to the creation of the new class. Previously the only ``n_atoms`` was passed to class copies, leading to a class created with default parameters which may differ from the original class. """ new = self.__class__(**self._kwargs) if self.transformations: new.add_transformations(*self.transformations) # seek the new reader to the same frame we started with new[self.ts.frame] # then copy over the current Timestep in case it has # been modified since initial load new.ts = self.ts.copy() for auxname, auxread in self._auxs.items(): new.add_auxiliary(auxname, auxread.copy()) return new
def __del__(self): for aux in self.aux_list: self._auxs[aux].close() self.close()
class _Writermeta(type): # Auto register this format upon class creation def __init__(cls, name, bases, classdict): type.__init__(type, name, bases, classdict) try: # grab the string which describes this format # could be either 'PDB' or ['PDB', 'ENT'] for multiple formats fmt = asiterable(classdict['format']) except KeyError: # not required however pass else: # does the Writer support single and multiframe writing? single = classdict.get('singleframe', True) multi = classdict.get('multiframe', False) if single: for f in fmt: f = f.upper() _SINGLEFRAME_WRITERS[f] = cls if multi: for f in fmt: f = f.upper() _MULTIFRAME_WRITERS[f] = cls
[docs]class WriterBase(IOBase, metaclass=_Writermeta): """Base class for trajectory writers. See :ref:`Trajectory API` definition in for the required attributes and methods. .. versionchanged:: 2.0.0 Deprecated :func:`write_next_timestep` has now been removed, please use :func:`write` instead. """
[docs] def convert_dimensions_to_unitcell(self, ts, inplace=True): """Read dimensions from timestep *ts* and return appropriate unitcell. The default is to return ``[A,B,C,alpha,beta,gamma]``; if this is not appropriate then this method has to be overriden. """ # override if the native trajectory format does NOT use # [A,B,C,alpha,beta,gamma] if ts.dimensions is None: lengths, angles = np.zeros(3), np.zeros(3) else: lengths, angles = ts.dimensions[:3], ts.dimensions[3:] if not inplace: lengths = lengths.copy() lengths = self.convert_pos_to_native(lengths) return np.concatenate([lengths, angles])
[docs] def write(self, obj): """Write current timestep, using the supplied `obj`. Parameters ---------- obj : :class:`~MDAnalysis.core.groups.AtomGroup` or :class:`~MDAnalysis.core.universe.Universe` write coordinate information associate with `obj` Note ---- The size of the `obj` must be the same as the number of atoms provided when setting up the trajectory. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument to write has now been removed. Use AtomGroup or Universe as an input instead. """ return self._write_next_frame(obj)
def __del__(self): self.close() def __repr__(self): try: return "< {0!s} {1!r} for {2:d} atoms >".format(self.__class__.__name__, self.filename, self.n_atoms) except (TypeError, AttributeError): # no trajectory loaded yet or a Writer that does not need e.g. # self.n_atoms return "< {0!s} {1!r} >".format(self.__class__.__name__, self.filename)
[docs] def has_valid_coordinates(self, criteria, x): """Returns ``True`` if all values are within limit values of their formats. Due to rounding, the test is asymmetric (and *min* is supposed to be negative): min < x <= max Parameters ---------- criteria : dict dictionary containing the *max* and *min* values in native units x : numpy.ndarray ``(x, y, z)`` coordinates of atoms selected to be written out Returns ------- bool """ x = np.ravel(x) return np.all(criteria["min"] < x) and np.all(x <= criteria["max"])
[docs]class SingleFrameReaderBase(ProtoReader): """Base class for Readers that only have one frame. To use this base class, define the method :meth:`_read_first_frame` to read from file `self.filename`. This should populate the attribute `self.ts` with a :class:`Timestep` object. .. versionadded:: 0.10.0 .. versionchanged:: 0.11.0 Added attribute "_ts_kwargs" for subclasses Keywords "dt" and "time_offset" read into _ts_kwargs .. versionchanged:: 2.2.0 Calling `__iter__` now rewinds the reader before yielding a :class:`Timestep` object (fixing behavior that was not well defined previously). """ _err = "{0} only contains a single frame" @store_init_arguments def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs): super(SingleFrameReaderBase, self).__init__() self.filename = filename self.convert_units = convert_units self.n_frames = 1 self.n_atom = n_atoms ts_kwargs = {} for att in ('dt', 'time_offset'): try: val = kwargs[att] except KeyError: pass else: ts_kwargs[att] = val self._ts_kwargs = ts_kwargs self._read_first_frame()
[docs] def copy(self): """Return independent copy of this Reader. New Reader will have its own file handle and can seek/iterate independently of the original. Will also copy the current state of the Timestep held in the original Reader. .. versionchanged:: 2.2.0 Arguments used to construct the reader are correctly captured and passed to the creation of the new class. Previously the only ``n_atoms`` was passed to class copies, leading to a class created with default parameters which may differ from the original class. """ new = self.__class__(**self._kwargs) new.ts = self.ts.copy() for auxname, auxread in self._auxs.items(): new.add_auxiliary(auxname, auxread.copy()) # since the transformations have already been applied to the frame # simply copy the property new.transformations = self.transformations return new
def _read_first_frame(self): # pragma: no cover # Override this in subclasses to create and fill a Timestep pass
[docs] def rewind(self): self._read_first_frame() for auxname, auxread in self._auxs.items(): self.ts = auxread.update_ts(self.ts) super(SingleFrameReaderBase, self)._apply_transformations(self.ts)
def _reopen(self): pass
[docs] def next(self): raise StopIteration(self._err.format(self.__class__.__name__))
def _read_next_timestep(self, ts=None): raise NotImplementedError(self._err.format(self.__class__.__name__)) def __iter__(self): self.rewind() yield self.ts return def _read_frame(self, frame): if frame != 0: raise IndexError(self._err.format(self.__class__.__name__)) return self.ts
[docs] def close(self): # all single frame readers should use context managers to access # self.filename. Explicitly setting it to the null action in case # the IOBase.close method is ever changed from that. pass
[docs] def add_transformations(self, *transformations): """ Add all transformations to be applied to the trajectory. This function take as list of transformations as an argument. These transformations are functions that will be called by the Reader and given a :class:`Timestep` object as argument, which will be transformed and returned to the Reader. The transformations can be part of the :mod:`~MDAnalysis.transformations` module, or created by the user, and are stored as a list `transformations`. This list can only be modified once, and further calls of this function will raise an exception. .. code-block:: python u = MDAnalysis.Universe(topology, coordinates) workflow = [some_transform, another_transform, this_transform] u.trajectory.add_transformations(*workflow) Parameters ---------- transform_list : list list of all the transformations that will be applied to the coordinates See Also -------- :mod:`MDAnalysis.transformations` """ #Overrides :meth:`~MDAnalysis.coordinates.base.ProtoReader.add_transformations` #to avoid unintended behaviour where the coordinates of each frame are transformed #multiple times when iterating over the trajectory. #In this method, the trajectory is modified all at once and once only. super(SingleFrameReaderBase, self).add_transformations(*transformations) for transform in self.transformations: self.ts = transform(self.ts)
def _apply_transformations(self, ts): """ Applies the transformations to the timestep.""" # Overrides :meth:`~MDAnalysis.coordinates.base.ProtoReader.add_transformations` # to avoid applying the same transformations multiple times on each frame return ts
def range_length(start, stop, step): if (step > 0 and start < stop): # We go from a lesser number to a larger one. return int(1 + (stop - 1 - start) // step) elif (step < 0 and start > stop): # We count backward from a larger number to a lesser one. return int(1 + (start - 1 - stop) // (-step)) else: # The range is empty. return 0 class _Convertermeta(type): # Auto register upon class creation def __init__(cls, name, bases, classdict): type.__init__(type, name, bases, classdict) try: fmt = asiterable(classdict['lib']) except KeyError: pass else: for f in fmt: f = f.upper() _CONVERTERS[f] = cls
[docs]class ConverterBase(IOBase, metaclass=_Convertermeta): """Base class for converting to other libraries. See Also -------- :mod:`MDAnalysis.converters` """ def __repr__(self): return "<{cls}>".format(cls=self.__class__.__name__) def convert(self, obj): raise NotImplementedError