Source code for MDAnalysis.core.universe

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
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# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
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# 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 object: Universe --- :mod:`MDAnalysis.core.universe`
=========================================================

The :class:`~MDAnalysis.core.universe.Universe` class ties a topology
and a trajectory together. Almost all code in MDAnalysis starts with a
``Universe``.

Normally, a ``Universe`` is created from files::

  import MDAnalysis as mda
  u = mda.Universe("topology.psf", "trajectory.dcd")

In order to construct new simulation system it is also convenient to
construct a ``Universe`` from existing
:class:`~MDAnalysis.core.group.AtomGroup` instances with the
:func:`Merge` function.


Classes
=======

.. autoclass:: Universe
   :members:

Functions
=========

.. autofunction:: Merge

"""
from __future__ import absolute_import
from six.moves import range
import six

import errno
import numpy as np
import logging
import copy
import warnings
import collections

import MDAnalysis
import sys

# When used in an MPI environment with Infiniband, importing MDAnalysis may
# trigger an MPI warning because importing the uuid module triggers a call to
# os.fork(). This happens if MPI_Init() has been called prior to importing
# MDAnalysis. The problem is actually caused by the uuid module and not by
# MDAnalysis itself. Python 3.7 fixes the problem. However, for Python < 3.7,
# the uuid module works perfectly fine with os.fork() disabled during import.
# A clean solution is therefore simply to disable os.fork() prior to importing
# the uuid module and to re-enable it afterwards.
import os

# Windows doesn't have os.fork so can ignore
# the issue for that platform
if sys.version_info >= (3, 7) or os.name == 'nt':
    import uuid
else:
    _os_dot_fork, os.fork = os.fork, None
    import uuid
    os.fork = _os_dot_fork
    del _os_dot_fork

from .. import _ANCHOR_UNIVERSES, _TOPOLOGY_ATTRS, _PARSERS
from ..exceptions import NoDataError
from ..lib import util
from ..lib.log import ProgressBar
from ..lib.util import cached, NamedStream, isstream
from ..lib.mdamath import find_fragments
from . import groups
from ._get_readers import get_reader_for, get_parser_for
from .groups import (ComponentBase, GroupBase,
                     Atom, Residue, Segment,
                     AtomGroup, ResidueGroup, SegmentGroup)
from .topology import Topology
from .topologyattrs import AtomAttr, ResidueAttr, SegmentAttr
from .topologyobjects import TopologyObject

logger = logging.getLogger("MDAnalysis.core.universe")



def _check_file_like(topology):
    if isstream(topology):
        if hasattr(topology, 'name'):
            _name = topology.name
        else:
            _name = None
        return NamedStream(topology, _name)
    return topology

def _topology_from_file_like(topology_file, topology_format=None,
                             **kwargs):
    parser = get_parser_for(topology_file, format=topology_format)

    try:
        with parser(topology_file) as p:
            topology = p.parse(**kwargs)
    except (IOError, OSError) as err:
        # There are 2 kinds of errors that might be raised here:
        # one because the file isn't present
        # or the permissions are bad, second when the parser fails
        if (err.errno is not None and
            errno.errorcode[err.errno] in ['ENOENT', 'EACCES']):
            # Runs if the error is propagated due to no permission / file not found
            six.reraise(*sys.exc_info())
        else:
            # Runs when the parser fails
            raise IOError("Failed to load from the topology file {0}"
                            " with parser {1}.\n"
                            "Error: {2}".format(topology_file, parser, err))
    except (ValueError, NotImplementedError) as err:
        raise ValueError(
            "Failed to construct topology from file {0}"
            " with parser {1}.\n"
            "Error: {2}".format(topology_file, parser, err))
    return topology

# py3 TODO
#def _resolve_formats(*coordinates, format=None, topology_format=None):
def _resolve_formats(*coordinates, **kwargs):
    format = kwargs.get('format', None)
    topology_format = kwargs.get('topology_format', None)
    if not coordinates:
        if format is None:
            format = topology_format
        elif topology_format is None:
            topology_format = format
    return format, topology_format

# py3 TODO
#def _resolve_coordinates(filename, *coordinates, format=None,
#                         all_coordinates=False):
def _resolve_coordinates(*args, **kwargs):
    filename = args[0]
    coordinates = args[1:]
    format = kwargs.get('format', None)
    all_coordinates = kwargs.get('all_coordinates', False)

    if all_coordinates or not coordinates and filename is not None:
        try:
            get_reader_for(filename, format=format)
        except ValueError:
            warnings.warn('No coordinate reader found for {}. Skipping '
                            'this file.'.format(filename))
        else:
            coordinates = (filename,) + coordinates
    return coordinates

def _generate_from_topology(universe):
    # generate Universe version of each class
    # AG, RG, SG, A, R, S
    universe._class_bases, universe._classes = groups.make_classes()

    # Put Group level stuff from topology into class
    for attr in universe._topology.attrs:
        universe._process_attr(attr)

    # Generate atoms, residues and segments.
    # These are the first such groups generated for this universe, so
    #  there are no cached merged classes yet. Otherwise those could be
    #  used directly to get a (very) small speedup. (Only really pays off
    #  the readability loss if instantiating millions of AtomGroups at
    #  once.)
    universe.atoms = AtomGroup(np.arange(universe._topology.n_atoms), universe)

    universe.residues = ResidueGroup(
            np.arange(universe._topology.n_residues), universe)

    universe.segments = SegmentGroup(
            np.arange(universe._topology.n_segments), universe)


[docs]class Universe(object): """The MDAnalysis Universe contains all the information describing the system. The system always requires a *topology* file --- in the simplest case just a list of atoms. This can be a CHARMM/NAMD PSF file or a simple coordinate file with atom informations such as XYZ, PDB, Gromacs GRO, or CHARMM CRD. See :ref:`Supported topology formats` for what kind of topologies can be read. A trajectory provides coordinates; the coordinates have to be ordered in the same way as the list of atoms in the topology. A trajectory can be a single frame such as a PDB, CRD, or GRO file, or it can be a MD trajectory (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format). See :ref:`Supported coordinate formats` for what can be read as a "trajectory". As a special case, when the topology is a file that contains atom information *and* coordinates (such as XYZ, PDB, GRO or CRD, see :ref:`Supported coordinate formats`) then the coordinates are immediately loaded from the "topology" file unless a trajectory is supplied. Examples for setting up a universe:: u = Universe(topology, trajectory) # read system from file(s) u = Universe(pdbfile) # read atoms and coordinates from PDB or GRO u = Universe(topology, [traj1, traj2, ...]) # read from a list of trajectories u = Universe(topology, traj1, traj2, ...) # read from multiple trajectories Load new data into a universe (replaces old trajectory and does *not* append):: u.load_new(trajectory) # read from a new trajectory file Select atoms, with syntax similar to CHARMM (see :class:`~Universe.select_atoms` for details):: u.select_atoms(...) Parameters ---------- topology: str, stream, `~MDAnalysis.core.topology.Topology`, `np.ndarray`, None A CHARMM/XPLOR PSF topology file, PDB file or Gromacs GRO file; used to define the list of atoms. If the file includes bond information, partial charges, atom masses, ... then these data will be available to MDAnalysis. Alternatively, an existing :class:`MDAnalysis.core.topology.Topology` instance may be given, numpy coordinates, or None for an empty universe. coordinates: str, stream, list of str, list of stream (optional) Coordinates can be provided as files of a single frame (eg a PDB, CRD, or GRO file); a list of single frames; or a trajectory file (in CHARMM/NAMD/LAMMPS DCD, Gromacs XTC/TRR, or generic XYZ format). The coordinates must be ordered in the same way as the list of atoms in the topology. See :ref:`Supported coordinate formats` for what can be read as coordinates. Alternatively, streams can be given. topology_format: str, ``None``, default ``None`` Provide the file format of the topology file; ``None`` guesses it from the file extension. Can also pass a subclass of :class:`MDAnalysis.topology.base.TopologyReaderBase` to define a custom reader to be used on the topology file. format: str, ``None``, default ``None`` Provide the file format of the coordinate or trajectory file; ``None`` guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the "chained" reader has to guess the file format for each individual list member. Can also pass a subclass of :class:`MDAnalysis.coordinates.base.ProtoReader` to define a custom reader to be used on the trajectory file. all_coordinates: bool, default ``False`` If set to ``True`` specifies that if more than one filename is passed they are all to be used, if possible, as coordinate files (employing a :class:`MDAnalysis.coordinates.chain.ChainReader`). The default behavior is to take the first file as a topology and the remaining as coordinates. The first argument will always always be used to infer a topology regardless of *all_coordinates*. guess_bonds: bool, default ``False`` Once Universe has been loaded, attempt to guess the connectivity between atoms. This will populate the .bonds, .angles, and .dihedrals attributes of the Universe. vdwradii: dict, ``None``, default ``None`` For use with *guess_bonds*. Supply a dict giving a vdwradii for each atom type which are used in guessing bonds. is_anchor: bool, default ``True`` When unpickling instances of :class:`MDAnalysis.core.groups.AtomGroup` existing Universes are searched for one where to anchor those atoms. Set to ``False`` to prevent this Universe from being considered. anchor_name: str, ``None``, default ``None`` Setting to other than ``None`` will cause :class:`MDAnalysis.core.groups.AtomGroup` instances pickled from the Universe to only unpickle if a compatible Universe with matching *anchor_name* is found. Even if *anchor_name* is set *is_anchor* will still be honored when unpickling. transformations: function or list, ``None``, default ``None`` Provide a list of transformations that you wish to apply to the trajectory upon reading. Transformations can be found in :mod:`MDAnalysis.transformations`, or can be user-created. in_memory: bool, default ``False`` After reading in the trajectory, transfer it to an in-memory representations, which allow for manipulation of coordinates. in_memory_step: int, default 1 Only read every nth frame into in-memory representation. continuous: bool, default ``False`` The `continuous` option is used by the :mod:`ChainReader<MDAnalysis.coordinates.chain>`, which contains the functionality to treat independent trajectory files as a single virtual trajectory. Attributes ---------- trajectory currently loaded trajectory reader; dimensions current system dimensions (simulation unit cell, if set in the trajectory) atoms, residues, segments master Groups for each topology level bonds, angles, dihedrals master ConnectivityGroups for each connectivity type .. versionchanged:: 1.0.0 Universe() now raises an error. Use Universe(None) or :func:`Universe.empty()` instead. Removed instant selectors. """ # Py3 TODO # def __init__(self, topology=None, *coordinates, all_coordinates=False, # format=None, topology_format=None, transformations=None, # guess_bonds=False, vdwradii=None, anchor_name=None, # is_anchor=True, in_memory=False, in_memory_step=1, # **kwargs): def __init__(self, *args, **kwargs): topology = args[0] if args else None coordinates = args[1:] all_coordinates = kwargs.pop('all_coordinates', False) format = kwargs.pop('format', None) topology_format = kwargs.pop('topology_format', None) transformations = kwargs.pop('transformations', None) guess_bonds = kwargs.pop('guess_bonds', False) vdwradii = kwargs.pop('vdwradii', None) anchor_name = kwargs.pop('anchor_name', None) is_anchor = kwargs.pop('is_anchor', True) in_memory = kwargs.pop('in_memory', False) in_memory_step = kwargs.pop('in_memory_step', 1) self._trajectory = None # managed attribute holding Reader self._cache = {} self._anchor_name = anchor_name self.is_anchor = is_anchor self.atoms = None self.residues = None self.segments = None self.filename = None self._kwargs = { 'transformations': transformations, 'guess_bonds': guess_bonds, 'vdwradii': vdwradii, 'anchor_name': anchor_name, 'is_anchor': is_anchor, 'in_memory': in_memory, 'in_memory_step': in_memory_step, 'format': format, 'topology_format': topology_format, 'all_coordinates': all_coordinates } self._kwargs.update(kwargs) format, topology_format = _resolve_formats(*coordinates, format=format, topology_format=topology_format) if not isinstance(topology, Topology) and not topology is None: self.filename = _check_file_like(topology) topology = _topology_from_file_like(self.filename, topology_format=topology_format, **kwargs) if topology is not None: self._topology = topology else: # point to Universe.empty instead of making empty universe raise TypeError('Topology argument required to make Universe. ' 'Try Universe.empty(n_atoms, ...) to construct ' 'your own Universe.') _generate_from_topology(self) # make real atoms, res, segments coordinates = _resolve_coordinates(self.filename, *coordinates, format=format, all_coordinates=all_coordinates) if coordinates: self.load_new(coordinates, format=format, in_memory=in_memory, in_memory_step=in_memory_step, **kwargs) if transformations: if callable(transformations): transformations = [transformations] self._trajectory.add_transformations(*transformations) if guess_bonds: self.atoms.guess_bonds(vdwradii=vdwradii)
[docs] def copy(self): """Return an independent copy of this Universe""" new = self.__class__(self._topology.copy()) new.trajectory = self.trajectory.copy() return new
[docs] @classmethod def empty(cls, n_atoms, n_residues=1, n_segments=1, atom_resindex=None, residue_segindex=None, trajectory=False, velocities=False, forces=False): """Create a blank Universe Useful for building a Universe without requiring existing files, for example for system building. If `trajectory` is set to True, a :class:`MDAnalysis.coordinates.memory.MemoryReader` will be attached to the Universe. Parameters ---------- n_atoms: int number of Atoms in the Universe n_residues: int, default 1 number of Residues in the Universe, defaults to 1 n_segments: int, default 1 number of Segments in the Universe, defaults to 1 atom_resindex: array like, optional mapping of atoms to residues, e.g. with 6 atoms, `atom_resindex=[0, 0, 1, 1, 2, 2]` would put 2 atoms into each of 3 residues. residue_segindex: array like, optional mapping of residues to segments trajectory: bool, optional if True, attaches a :class:`MDAnalysis.coordinates.memory.MemoryReader` allowing coordinates to be set and written. Default is False velocities: bool, optional include velocities in the :class:`MDAnalysis.coordinates.memory.MemoryReader` forces: bool, optional include forces in the :class:`MDAnalysis.coordinates.memory.MemoryReader` Returns ------- MDAnalysis.Universe object Examples -------- For example to create a new Universe with 6 atoms in 2 residues, with positions for the atoms and a mass attribute: >>> u = mda.Universe.empty(6, 2, atom_resindex=np.array([0, 0, 0, 1, 1, 1]), trajectory=True, ) >>> u.add_TopologyAttr('masses') .. versionadded:: 0.17.0 .. versionchanged:: 0.19.0 The attached Reader when trajectory=True is now a MemoryReader .. versionchanged:: 0.21.0 Universes can now be created with 0 atoms """ if not n_atoms: n_residues = 0 n_segments = 0 if atom_resindex is None: warnings.warn( 'Residues specified but no atom_resindex given. ' 'All atoms will be placed in first Residue.', UserWarning) if residue_segindex is None: warnings.warn( 'Segments specified but no segment_resindex given. ' 'All residues will be placed in first Segment', UserWarning) top = Topology(n_atoms, n_residues, n_segments, atom_resindex=atom_resindex, residue_segindex=residue_segindex, ) u = cls(top) if trajectory: coords = np.zeros((1, n_atoms, 3), dtype=np.float32) dims = np.zeros(6, dtype=np.float32) vels = np.zeros_like(coords) if velocities else None forces = np.zeros_like(coords) if forces else None # grab and attach a MemoryReader u.trajectory = get_reader_for(coords)( coords, order='fac', n_atoms=n_atoms, dimensions=dims, velocities=vels, forces=forces) return u
@property def universe(self): # for Writer.write(universe), see Issue 49 # Encapsulation in an accessor prevents the Universe from # having to keep a reference to itself, # which might be undesirable if it has a __del__ method. # It is also cleaner than a weakref. return self
[docs] def load_new(self, filename, format=None, in_memory=False, in_memory_step=1, **kwargs): """Load coordinates from `filename`. The file format of `filename` is autodetected from the file name suffix or can be explicitly set with the `format` keyword. A sequence of files can be read as a single virtual trajectory by providing a list of filenames. Parameters ---------- filename: str or list the coordinate file (single frame or trajectory) *or* a list of filenames, which are read one after another. format: str or list or object (optional) provide the file format of the coordinate or trajectory file; ``None`` guesses it from the file extension. Note that this keyword has no effect if a list of file names is supplied because the "chained" reader has to guess the file format for each individual list member [``None``]. Can also pass a subclass of :class:`MDAnalysis.coordinates.base.ProtoReader` to define a custom reader to be used on the trajectory file. in_memory: bool (optional) Directly load trajectory into memory with the :class:`~MDAnalysis.coordinates.memory.MemoryReader` .. versionadded:: 0.16.0 **kwargs: dict Other kwargs are passed to the trajectory reader (only for advanced use) Returns ------- universe: Universe Raises ------ TypeError if trajectory format can not be determined or no appropriate trajectory reader found .. versionchanged:: 0.8 If a list or sequence that is provided for `filename` only contains a single entry then it is treated as single coordinate file. This has the consequence that it is not read by the :class:`~MDAnalysis.coordinates.chain.ChainReader` but directly by its specialized file format reader, which typically has more features than the :class:`~MDAnalysis.coordinates.chain.ChainReader`. .. versionchanged:: 0.17.0 Now returns a :class:`Universe` instead of the tuple of file/array and detected file type. """ # filename==None happens when only a topology is provided if filename is None: return self if len(util.asiterable(filename)) == 1: # make sure a single filename is not handed to the ChainReader filename = util.asiterable(filename)[0] logger.debug("Universe.load_new(): loading {0}...".format(filename)) try: reader = get_reader_for(filename, format=format) except ValueError as err: raise TypeError( "Cannot find an appropriate coordinate reader for file '{0}'.\n" " {1}".format(filename, err)) # supply number of atoms for readers that cannot do it for themselves kwargs['n_atoms'] = self.atoms.n_atoms self.trajectory = reader(filename, format=format, **kwargs) if self.trajectory.n_atoms != len(self.atoms): raise ValueError("The topology and {form} trajectory files don't" " have the same number of atoms!\n" "Topology number of atoms {top_n_atoms}\n" "Trajectory: {fname} Number of atoms {trj_n_atoms}".format( form=self.trajectory.format, top_n_atoms=len(self.atoms), fname=filename, trj_n_atoms=self.trajectory.n_atoms)) if in_memory: self.transfer_to_memory(step=in_memory_step) return self
[docs] def transfer_to_memory(self, start=None, stop=None, step=None, verbose=False): """Transfer the trajectory to in memory representation. Replaces the current trajectory reader object with one of type :class:`MDAnalysis.coordinates.memory.MemoryReader` to support in-place editing of coordinates. Parameters ---------- start: int, optional start reading from the nth frame. stop: int, optional read upto and excluding the nth frame. step: int, optional Read in every nth frame. [1] verbose: bool, optional Will print the progress of loading trajectory to memory, if set to True. Default value is False. .. versionadded:: 0.16.0 """ from ..coordinates.memory import MemoryReader if not isinstance(self.trajectory, MemoryReader): n_frames = len(range( *self.trajectory.check_slice_indices(start, stop, step) )) n_atoms = len(self.atoms) coordinates = np.zeros((n_frames, n_atoms, 3), dtype=np.float32) ts = self.trajectory.ts has_vels = ts.has_velocities has_fors = ts.has_forces has_dims = ts.dimensions is not None velocities = np.zeros_like(coordinates) if has_vels else None forces = np.zeros_like(coordinates) if has_fors else None dimensions = (np.zeros((n_frames, 6), dtype=np.float32) if has_dims else None) for i, ts in enumerate(ProgressBar(self.trajectory[start:stop:step], verbose=verbose, desc="Loading frames")): np.copyto(coordinates[i], ts.positions) if has_vels: np.copyto(velocities[i], ts.velocities) if has_fors: np.copyto(forces[i], ts.forces) if has_dims: np.copyto(dimensions[i], ts.dimensions) # Overwrite trajectory in universe with an MemoryReader # object, to provide fast access and allow coordinates # to be manipulated if step is None: step = 1 self.trajectory = MemoryReader( coordinates, dimensions=dimensions, dt=self.trajectory.ts.dt * step, filename=self.trajectory.filename, velocities=velocities, forces=forces, )
# python 2 doesn't allow an efficient splitting of kwargs in function # argument signatures. # In python3-only we'd be able to explicitly define this function with # something like (sel, *othersels, updating=False, **selgroups)
[docs] def select_atoms(self, *args, **kwargs): """Select atoms. See Also -------- :meth:`MDAnalysis.core.groups.AtomGroup.select_atoms` """ return self.atoms.select_atoms(*args, **kwargs)
@property def bonds(self): """Bonds between atoms""" return self.atoms.bonds @property def angles(self): """Angles between atoms""" return self.atoms.angles @property def dihedrals(self): """Dihedral angles between atoms""" return self.atoms.dihedrals @property def impropers(self): """Improper dihedral angles between atoms""" return self.atoms.impropers @property def anchor_name(self): # hash used for anchoring. # Try and use anchor_name, else use (and store) uuid if self._anchor_name is not None: return self._anchor_name else: try: return self._anchor_uuid except AttributeError: # store this so we can later recall it if needed self._anchor_uuid = uuid.uuid4() return self._anchor_uuid @anchor_name.setter def anchor_name(self, name): self.remove_anchor() # clear any old anchor self._anchor_name = str(name) if not name is None else name self.make_anchor() # add anchor again @property def is_anchor(self): """Is this Universe an anchoring for unpickling AtomGroups""" return self.anchor_name in _ANCHOR_UNIVERSES @is_anchor.setter def is_anchor(self, new): if new: self.make_anchor() else: self.remove_anchor()
[docs] def remove_anchor(self): """Remove this Universe from the possible anchor list for unpickling""" _ANCHOR_UNIVERSES.pop(self.anchor_name, None)
def make_anchor(self): _ANCHOR_UNIVERSES[self.anchor_name] = self def __repr__(self): # return "<Universe with {n_atoms} atoms{bonds}>".format( # n_atoms=len(self.atoms), # bonds=" and {0} bonds".format(len(self.bonds)) if self.bonds else "") return "<Universe with {n_atoms} atoms>".format( n_atoms=len(self.atoms)) def __getstate__(self): raise NotImplementedError def __setstate__(self, state): raise NotImplementedError # Properties @property def dimensions(self): """Current dimensions of the unitcell""" return self.coord.dimensions @dimensions.setter def dimensions(self, box): """Set dimensions if the Timestep allows this .. versionadded:: 0.9.0 """ # Add fancy error handling here or use Timestep? self.coord.dimensions = box @property def coord(self): """Reference to current timestep and coordinates of universe. The raw trajectory coordinates are :attr:`Universe.coord.positions`, represented as a :class:`numpy.float32` array. Because :attr:`coord` is a reference to a :class:`~MDAnalysis.coordinates.base.Timestep`, it changes its contents while one is stepping through the trajectory. .. Note:: In order to access the coordinates it is better to use the :meth:`AtomGroup.positions` method; for instance, all coordinates of the Universe as a numpy array: :meth:`Universe.atoms.positions`. """ return self.trajectory.ts @property def kwargs(self): """keyword arguments used to initialize this universe""" return copy.deepcopy(self._kwargs) @property def trajectory(self): """Reference to trajectory reader object containing trajectory data.""" if self._trajectory is not None: return self._trajectory else: raise AttributeError("No trajectory loaded into Universe") @trajectory.setter def trajectory(self, value): del self._trajectory # guarantees that files are closed (?) self._trajectory = value
[docs] def add_TopologyAttr(self, topologyattr, values=None): """Add a new topology attribute to the Universe Adding a TopologyAttribute to the Universe makes it available to all AtomGroups etc throughout the Universe. Parameters ---------- topologyattr: TopologyAttr or string Either a MDAnalysis TopologyAttr object or the name of a possible topology attribute. values: np.ndarray, optional If initiating an attribute from a string, the initial values to use. If not supplied, the new TopologyAttribute will have empty or zero values. Example ------- For example to add bfactors to a Universe: >>> u.add_TopologyAttr('bfactors') >>> u.atoms.bfactors array([ 0., 0., 0., ..., 0., 0., 0.]) .. versionchanged:: 0.17.0 Can now also add TopologyAttrs with a string of the name of the attribute to add (eg 'charges'), can also supply initial values using values keyword. """ if isinstance(topologyattr, six.string_types): try: tcls = _TOPOLOGY_ATTRS[topologyattr] except KeyError: six.raise_from(ValueError( "Unrecognised topology attribute name: '{}'." " Possible values: '{}'\n" "To raise an issue go to: http://issues.mdanalysis.org" "".format( topologyattr, ', '.join(sorted(_TOPOLOGY_ATTRS.keys())))), None) else: topologyattr = tcls.from_blank( n_atoms=self._topology.n_atoms, n_residues=self._topology.n_residues, n_segments=self._topology.n_segments, values=values) self._topology.add_TopologyAttr(topologyattr) self._process_attr(topologyattr)
def _process_attr(self, attr): """Squeeze a topologyattr for its information Grabs: - Group properties (attribute access) - Component properties - Transplant methods """ n_dict = {'atom': self._topology.n_atoms, 'residue': self._topology.n_residues, 'segment': self._topology.n_segments} logger.debug("_process_attr: Adding {0} to topology".format(attr)) if (attr.per_object is not None and len(attr) != n_dict[attr.per_object]): raise ValueError('Length of {attr} does not' ' match number of {obj}s.\n' 'Expect: {n:d} Have: {m:d}'.format( attr=attr.attrname, obj=attr.per_object, n=n_dict[attr.per_object], m=len(attr))) for cls in attr.target_classes: self._class_bases[cls]._add_prop(attr) # TODO: Try and shove this into cls._add_prop # Group transplants for cls in (Atom, Residue, Segment, GroupBase, AtomGroup, ResidueGroup, SegmentGroup): for funcname, meth in attr.transplants[cls]: setattr(self._class_bases[cls], funcname, meth) # Universe transplants for funcname, meth in attr.transplants['Universe']: setattr(self.__class__, funcname, meth)
[docs] def add_Residue(self, segment=None, **attrs): """Add a new Residue to this Universe New Residues will not contain any Atoms, but can be assigned to Atoms as per usual. If the Universe contains multiple segments, this must be specified as a keyword. Parameters ---------- segment: MDAnalysis.Segment If there are multiple segments, then the Segment that the new Residue will belong in must be specified. attrs: dict For each Residue attribute, the value for the new Residue must be specified Returns ------- A reference to the new Residue Raises ------ NoDataError If any information was missing. This happens before any changes have been made, ie the change is rolled back. Example ------- Adding a new GLY residue, then placing atoms within it: >>> newres = u.add_Residue(segment=u.segments[0], resid=42, resname='GLY') >>> u.atoms[[1, 2, 3]].residues = newres >>> u.select_atoms('resname GLY and resid 42') <AtomGroup with 3 atoms> """ if len(self.segments) == 1: # if only one segment, use this segment = self.segments[0] if segment is None: raise NoDataError("") # pass this information to the topology residx = self._topology.add_Residue(segment, **attrs) # resize my residues self.residues = ResidueGroup(np.arange(self._topology.n_residues), self) # return the new residue return self.residues[residx]
[docs] def add_Segment(self, **attrs): """Add a new Segment to this Universe Parameters ---------- attrs: dict For each Segment attribute as a key, give the value in the new Segment Returns ------- A reference to the new Segment Raises ------ NoDataError If any attributes were not specified as a keyword. """ # pass this information to the topology segidx = self._topology.add_Segment(**attrs) # resize my segments self.segments = SegmentGroup(np.arange(self._topology.n_segments), self) # return the new segment return self.segments[segidx]
def _add_topology_objects(self, object_type, values, types=None, guessed=False, order=None): """Add new TopologyObjects to this Universe Parameters ---------- object_type : {'bonds', 'angles', 'dihedrals', 'impropers'} The type of TopologyObject to add. values : TopologyGroup or iterable of tuples, AtomGroups, or TopologyObjects An iterable of: tuples of atom indices, or AtomGroups, or TopologyObjects. If every value is a TopologyObject, all keywords are ignored. If AtomGroups or TopologyObjects are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` order : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 0.21.0 """ if all(isinstance(x, TopologyObject) for x in values): try: types = [t.type for t in values] except AttributeError: types = None guessed = [t.is_guessed for t in values] order = [t.order for t in values] indices = [] for x in values: if isinstance(x, (AtomGroup, TopologyObject)): if x.universe is not self: err_msg = 'Cannot add {} from different Universes.' raise ValueError(err_msg.format(object_type)) indices.append(x.indices) else: indices.append(x) all_indices = set([i for obj in indices for i in obj]) nonexistent = all_indices - set(self.atoms.indices) if nonexistent: istr = ', '.join(map(str, nonexistent)) err_msg = 'Cannot add {} for nonexistent atom indices: {}' raise ValueError(err_msg.format(object_type, istr)) try: attr = getattr(self._topology, object_type) except AttributeError: self.add_TopologyAttr(object_type, []) attr = getattr(self._topology, object_type) attr._add_bonds(indices, types=types, guessed=guessed, order=order)
[docs] def add_bonds(self, values, types=None, guessed=False, order=None): """Add new Bonds to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms, or Bonds. If every value is a Bond, all keywords are ignored. If AtomGroups, Bonds, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` order : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` Example ------- Adding TIP4P water bonds with a list of AtomGroups:: import MDAnalysis as mda from MDAnalysis.tests.datafiles import GRO u = mda.Universe(GRO) sol = u.select_atoms('resname SOL') ow_hw1 = sol.select_atoms('name OW or name HW1').split('residue') ow_hw2 = sol.select_atoms('name OW or name HW2').split('residue') ow_mw = sol.select_atoms('name OW or name MW').split('residue') u.add_bonds(ow_hw1 + ow_hw2 + ow_mw) You can only add bonds from the same Universe. If you would like to add AtomGroups, Bonds, or a TopologyGroup from a different Universe, convert them to indices first. :: from MDAnalysis.tests.datafiles import PSF u2 = mda.Universe(PSF) # assuming you have already added bonds to u u2.add_bonds(u.bonds.to_indices()) .. versionadded:: 0.21.0 """ self._add_topology_objects('bonds', values, types=types, guessed=guessed, order=order) self._cache.pop('fragments', None)
[docs] def add_angles(self, values, types=None, guessed=False): """Add new Angles to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms, or Angles. If every value is a Angle, all keywords are ignored. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 0.21.0 """ self._add_topology_objects('angles', values, types=types, guessed=guessed)
[docs] def add_dihedrals(self, values, types=None, guessed=False): """Add new Dihedrals to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Dihedrals. If every value is a Dihedral, all keywords are ignored. If AtomGroups, Dihedrals, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 0.21.0 """ self._add_topology_objects('dihedrals', values, types=types, guessed=guessed)
[docs] def add_impropers(self, values, types=None, guessed=False): """Add new Impropers to this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Impropers. If every value is an Improper, all keywords are ignored. If AtomGroups, Impropers, or a TopologyGroup are passed, they *must* be from the same Universe. types : iterable (optional, default None) None, or an iterable of hashable values with the same length as ``values`` guessed : bool or iterable (optional, default False) bool, or an iterable of hashable values with the same length as ``values`` .. versionadded:: 0.21.0 """ self._add_topology_objects('impropers', values, types=types, guessed=guessed)
def _delete_topology_objects(self, object_type, values): """Delete TopologyObjects from this Universe Parameters ---------- object_type : {'bonds', 'angles', 'dihedrals', 'impropers'} The type of TopologyObject to add. values : iterable of tuples, AtomGroups, or TopologyObjects; or TopologyGroup An iterable of: tuples of atom indices, or AtomGroups, or TopologyObjects. If AtomGroups, TopologyObjects, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 0.21.0 """ indices = [] for x in values: if isinstance(x, (AtomGroup, TopologyObject)): if x.universe is not self: err_msg = 'Cannot delete {} from different Universes.' raise ValueError(err_msg.format(object_type)) indices.append(x.indices) else: indices.append(x) try: attr = getattr(self._topology, object_type) except AttributeError: raise ValueError('There are no {} to delete'.format(object_type)) attr._delete_bonds(indices)
[docs] def delete_bonds(self, values): """Delete Bonds from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Bonds; or TopologyGroup An iterable of: tuples of 2 atom indices, or AtomGroups with 2 atoms, or Bonds. If AtomGroups, Bonds, or a TopologyGroup are passed, they *must* be from the same Universe. Example ------- Deleting bonds from a Universe:: import MDAnalysis as mda from MDAnalysis.tests.datafiles import PSF u = mda.Universe(PSF) # delete first 5 bonds u.delete_bonds(u.bonds[:5]) If you are deleting bonds in the form of AtomGroups, Bonds, or a TopologyGroup, they must come from the same Universe. If you want to delete bonds from another Universe, convert them to indices first. :: from MDAnalysis.tests.datafiles import PDB u2 = mda.Universe(PDB) u.delete_bonds(u2.bonds.to_indices()) .. versionadded:: 0.21.0 """ self._delete_topology_objects('bonds', values) self._cache.pop('fragments', None)
[docs] def delete_angles(self, values): """Delete Angles from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Angles; or TopologyGroup An iterable of: tuples of 3 atom indices, or AtomGroups with 3 atoms, or Angles. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 0.21.0 """ self._delete_topology_objects('angles', values)
[docs] def delete_dihedrals(self, values): """Delete Dihedrals from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Dihedrals; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Dihedrals. If AtomGroups, Dihedrals, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 0.21.0 """ self._delete_topology_objects('dihedrals', values)
[docs] def delete_impropers(self, values): """Delete Impropers from this Universe. Parameters ---------- values : iterable of tuples, AtomGroups, or Impropers; or TopologyGroup An iterable of: tuples of 4 atom indices, or AtomGroups with 4 atoms, or Impropers. If AtomGroups, Angles, or a TopologyGroup are passed, they *must* be from the same Universe. .. versionadded:: 0.21.0 """ self._delete_topology_objects('impropers', values)
# TODO: Maybe put this as a Bond attribute transplant # Problems: Can we transplant onto Universe? # Probably a smarter way to do this too, could generate # these on demand *per atom*. # Wouldn't then need the Universe linkage here # # Alternate idea: Bonds Attribute generates a Fragments # Attribute (ie, 2 for the price of 1) # Fragments then gets its own Class/namespace/jazz. @property @cached('fragments') def _fragdict(self): """ .. versionadded:: 0.9.0 .. versionchanged:: 0.16.0 Fragment atoms are sorted by their index, and framgents are sorted by their first atom index so their order is predictable. .. versionchanged:: 0.19.0 Uses faster C++ implementation .. versionchanged:: 0.20.0 * _fragdict keys are now atom indices instead of Atoms * _fragdict items are now a namedtuple ``fraginfo(ix, fragment)`` storing the fragindex ``ix`` along with the fragment. """ atoms = self.atoms.ix bonds = self.atoms.bonds.to_indices() frag_indices = find_fragments(atoms, bonds) frags = tuple([AtomGroup(np.sort(ix), self) for ix in frag_indices]) fragdict = {} fraginfo = collections.namedtuple('fraginfo', 'ix, fragment') for i, f in enumerate(frags): for a in f: fragdict[a.ix] = fraginfo(i, f) return fragdict
# TODO: what is the point of this function??? def as_Universe(*args, **kwargs): """Return a universe from the input arguments. 1. If the first argument is a universe, just return it:: as_Universe(universe) --> universe 2. Otherwise try to build a universe from the first or the first and second argument:: as_Universe(PDB, **kwargs) --> Universe(PDB, **kwargs) as_Universe(PSF, DCD, **kwargs) --> Universe(PSF, DCD, **kwargs) as_Universe(*args, **kwargs) --> Universe(*args, **kwargs) Returns ------- :class:`~MDAnalysis.core.groups.Universe` """ if len(args) == 0: raise TypeError("as_Universe() takes at least one argument (%d given)" % len(args)) elif len(args) == 1 and isinstance(args[0], Universe): return args[0] return Universe(*args, **kwargs)
[docs]def Merge(*args): """Create a new new :class:`Universe` from one or more :class:`~MDAnalysis.core.groups.AtomGroup` instances. Parameters ---------- *args: :class:`~MDAnalysis.core.groups.AtomGroup` One or more AtomGroups. Returns ------- universe: :class:`Universe` Raises ------ ValueError Too few arguments or an AtomGroup is empty and TypeError Arguments are not :class:`AtomGroup` instances. Notes ----- The resulting :class:`Universe` will only inherit the common topology attributes that all merged universes share. :class:`AtomGroup` instances can come from different Universes, or can come directly from a :meth:`~Universe.select_atoms` call. :class:`Merge` can also be used with a single :class:`AtomGroup` if the user wants to, for example, re-order the atoms in the :class:`Universe`. If multiple :class:`AtomGroup` instances from the same :class:`Universe` are given, the merge will first simply "add" together the :class:`AtomGroup` instances. Merging does not create a full trajectory but only a single structure even if the input consists of one or more trajectories. However, one can use the :class:`~MDAnalysis.coordinates.memory.MemoryReader` to construct a trajectory for the new Universe as described under :ref:`creating-in-memory-trajectory-label`. Example ------- In this example, protein, ligand, and solvent were externally prepared in three different PDB files. They are loaded into separate :class:`Universe` objects (where they could be further manipulated, e.g. renumbered, relabeled, rotated, ...) The :func:`Merge` command is used to combine all of them together:: u1 = Universe("protein.pdb") u2 = Universe("ligand.pdb") u3 = Universe("solvent.pdb") u = Merge(u1.select_atoms("protein"), u2.atoms, u3.atoms) u.atoms.write("system.pdb") The complete system is then written out to a new PDB file. .. versionchanged:: 0.9.0 Raises exceptions instead of assertion errors. .. versionchanged:: 0.16.0 The trajectory is now a :class:`~MDAnalysis.coordinates.memory.MemoryReader`. """ from ..topology.base import squash_by if len(args) == 0: raise ValueError("Need at least one AtomGroup for merging") for a in args: if not isinstance(a, groups.AtomGroup): raise TypeError(repr(a) + " is not an AtomGroup") for a in args: if len(a) == 0: raise ValueError("cannot merge empty AtomGroup") # Create a new topology using the intersection of topology attributes blank_topology_attrs = set(dir(Topology(attrs=[]))) common_attrs = set.intersection(*[set(dir(ag.universe._topology)) for ag in args]) tops = set(['bonds', 'angles', 'dihedrals', 'impropers']) attrs = [] # Create set of attributes which are array-valued and can be simply # concatenated together common_array_attrs = common_attrs - blank_topology_attrs - tops # Build up array-valued topology attributes including only attributes # that all arguments' universes have for attrname in common_array_attrs: for ag in args: attr = getattr(ag, attrname) attr_class = type(getattr(ag.universe._topology, attrname)) if issubclass(attr_class, AtomAttr): pass elif issubclass(attr_class, ResidueAttr): attr = getattr(ag.residues, attrname) elif issubclass(attr_class, SegmentAttr): attr = getattr(ag.segments, attrname) else: raise NotImplementedError("Don't know how to handle" " TopologyAttr not subclassed" " from AtomAttr, ResidueAttr," " or SegmentAttr.") if type(attr) != np.ndarray: raise TypeError('Encountered unexpected topology ' 'attribute of type {}'.format(type(attr))) try: attr_array.extend(attr) except NameError: attr_array = list(attr) attrs.append(attr_class(np.array(attr_array, dtype=attr.dtype))) del attr_array # Build up topology groups including only those that all arguments' # universes have for t in (tops & common_attrs): offset = 0 bondidx = [] types = [] for ag in args: # create a mapping scheme for this atomgroup mapping = {a.index: i for i, a in enumerate(ag, start=offset)} offset += len(ag) tg = getattr(ag, t) bonds_class = type(getattr(ag.universe._topology, t)) # Create a topology group of only bonds that are within this ag # ie we don't want bonds that extend out of the atomgroup tg = tg.atomgroup_intersection(ag, strict=True) # Map them so they refer to our new indices new_idx = [tuple([mapping[x] for x in entry]) for entry in tg.indices] bondidx.extend(new_idx) if hasattr(tg, '_bondtypes'): types.extend(tg._bondtypes) else: types.extend([None]*len(tg)) if any(t is None for t in types): attrs.append(bonds_class(bondidx)) else: types = np.array(types, dtype='|S8') attrs.append(bonds_class(bondidx, types)) # Renumber residue and segment indices n_atoms = sum([len(ag) for ag in args]) residx = [] segidx = [] res_offset = 0 seg_offset = 0 for ag in args: # create a mapping scheme for this atomgroup's parents res_mapping = {r.resindex: i for i, r in enumerate(ag.residues, start=res_offset)} seg_mapping = {r.segindex: i for i, r in enumerate(ag.segments, start=seg_offset)} res_offset += len(ag.residues) seg_offset += len(ag.segments) # Map them so they refer to our new indices residx.extend([res_mapping[x] for x in ag.resindices]) segidx.extend([seg_mapping[x] for x in ag.segindices]) residx = np.array(residx, dtype=np.int32) segidx = np.array(segidx, dtype=np.int32) _, _, [segidx] = squash_by(residx, segidx) n_residues = len(set(residx)) n_segments = len(set(segidx)) top = Topology(n_atoms, n_residues, n_segments, attrs=attrs, atom_resindex=residx, residue_segindex=segidx) # Create and populate a universe try: #Create universe with coordinates if they exists in args coords = np.vstack([a.positions for a in args]) u = Universe(top, coords[None, :, :], format=MDAnalysis.coordinates.memory.MemoryReader) except AttributeError: #Create universe without coordinates if they dont exists in args u = Universe(top) return u