Jmol floating residue glitch12/21/2023 ![]() import ( _ANCHOR_UNIVERSES, _CONVERTERS, _TOPOLOGY_ATTRS, _TOPOLOGY_TRANSPLANTS, _TOPOLOGY_ATTRNAMES ) from. This can be used to verify that two objects are of the same level, or to access a particular class:: u = mda.Universe() ag = u.atoms at = u.atoms ag.level = at.level # Returns True ag.level.singular # Returns Atom class at.ural # Returns AtomGroup class """ from _future_ import absolute_import, division from six.moves import zip from six import raise_from, string_types from collections import namedtuple import numpy as np import functools import itertools import numbers import os import warnings from. autoclass:: Segment :members: :inherited-members: Levels - Each of the above classes has a *level* attribute. autoclass:: Residue :members: :inherited-members. autoclass:: Atom :members: :inherited-members. autoclass:: UpdatingAtomGroup :members: Chemical units. autoclass:: SegmentGroup :members: :inherited-members. autoclass:: ResidueGroup :members: :inherited-members. autoclass:: AtomGroup :members: :inherited-members. For convenience, chemically meaningful groups of :class:`Atoms` such as a :class:`Residue` or a :class:`Segment` (typically a whole molecule or all of the solvent) also exist as containers, as well as groups of these units (:class:`ResidueGroup`, :class:`SegmentGroup`). :class:`AtomGroup` instances can be easily created (e.g., from an :meth:`lect_atoms` selection or simply by slicing). The :class:`AtomGroup` is probably the most important object in MDAnalysis because virtually everything can be accessed through it. Groups of :class:`atoms` are handled as :class:`AtomGroup` instances. 32 (2011), 2319-2327, doi:10.1002/jcc.21787 # """\ = Core objects: Containers - :mod:`` = The :class:`~` instance contains all the particles in the system (which MDAnalysis calls :class:`Atom`). # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. Rostrup editors, Proceedings of the 15th # Python in Science Conference, pages 102-109, Austin, TX, 2016. # MDAnalysis: A Python package for the rapid analysis of molecular dynamics # simulations. # -*- Mode: python tab-width: 4 indent-tabs-mode:nil coding:utf-8 -*- # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 # MDAnalysis - # 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.
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