MDAnalysis 2.8.0__cp313-cp313-win_amd64.whl

MDAnalysis/__init__.py

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+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# 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 Lesser GNU Public Licence, v2.1 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+"""
+:mod:`MDAnalysis` --- analysis of molecular simulations in python
+=================================================================
+
+MDAnalysis (https://www.mdanalysis.org) is a python toolkit to analyze
+molecular dynamics trajectories generated by CHARMM, NAMD, Amber,
+Gromacs, or LAMMPS.
+
+It allows one to read molecular dynamics trajectories and access the
+atomic coordinates through numpy arrays. This provides a flexible and
+relatively fast framework for complex analysis tasks. In addition,
+CHARMM-style atom selection commands are implemented. Trajectories can
+also be manipulated (for instance, fit to a reference structure) and
+written out. Time-critical code is written in C for speed.
+
+Help is also available through GitHub Discussions at
+https://github.com/MDAnalysis/mdanalysis/discussions
+
+Please report bugs and feature requests through the issue tracker at
+https://github.com/MDAnalysis/mdanalysis/issues
+
+Citation
+--------
+
+When using MDAnalysis in published work, please cite
+
+    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 98-105, Austin, TX, 2016. SciPy, 
+    doi:10.25080/majora-629e541a-00e
+
+    N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and
+    O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics
+    Simulations. J. Comput. Chem. 32 (2011), 2319--2327, doi:`10.1002/jcc.21787`_
+    https://www.mdanalysis.org
+
+For citations of included algorithms and sub-modules please see the references_.
+
+.. _`10.1002/jcc.21787`: http://dx.doi.org/10.1002/jcc.21787
+.. _references: https://docs.mdanalysis.org/documentation_pages/references.html
+
+
+Getting started
+---------------
+
+Import the package::
+
+  >>> import MDAnalysis
+
+(note that not everything in MDAnalysis is imported right away; for
+additional functionality you might have to import sub-modules
+separately, e.g. for RMS fitting ``import MDAnalysis.analysis.align``.)
+
+Build a "universe" from a topology (PSF, PDB) and a trajectory (DCD, XTC/TRR);
+here we are assuming that PSF, DCD, etc contain file names. If you don't have
+trajectories at hand you can play with the ones that come with MDAnalysis for
+testing (see below under `Examples`_)::
+
+  >>> u = MDAnalysis.Universe(PSF, DCD)
+
+Select the C-alpha atoms and store them as a group of atoms::
+
+  >>> ca = u.select_atoms('name CA')
+  >>> len(ca)
+  214
+
+Calculate the centre of mass of the CA and of all atoms::
+
+  >>> ca.center_of_mass()
+  array([ 0.06873595, -0.04605918, -0.24643682])
+  >>> u.atoms.center_of_mass()
+  array([-0.01094035,  0.05727601, -0.12885778])
+
+Calculate the CA end-to-end distance (in angstroem)::
+  >>> import numpy as np
+  >>> coord = ca.positions
+  >>> v = coord[-1] - coord[0]   # last Ca minus first one
+  >>> np.sqrt(np.dot(v, v,))
+  10.938133
+
+Define a function eedist():
+  >>> def eedist(atoms):
+  ...     coord = atoms.positions
+  ...     v = coord[-1] - coord[0]
+  ...     return sqrt(dot(v, v,))
+  ...
+  >>> eedist(ca)
+  10.938133
+
+and analyze all timesteps *ts* of the trajectory::
+  >>> for ts in u.trajectory:
+  ...      print eedist(ca)
+  10.9381
+  10.8459
+  10.4141
+   9.72062
+  ....
+
+See Also
+--------
+:class:`MDAnalysis.core.universe.Universe` for details
+
+
+Examples
+--------
+
+MDAnalysis comes with a number of real trajectories for testing. You
+can also use them to explore the functionality and ensure that
+everything is working properly::
+
+  from MDAnalysis import *
+  from MDAnalysis.tests.datafiles import PSF,DCD, PDB,XTC
+  u_dims_adk = Universe(PSF,DCD)
+  u_eq_adk = Universe(PDB, XTC)
+
+The PSF and DCD file are a closed-form-to-open-form transition of
+Adenylate Kinase (from [Beckstein2009]_) and the PDB+XTC file are ten
+frames from a Gromacs simulation of AdK solvated in TIP4P water with
+the OPLS/AA force field.
+
+.. [Beckstein2009] O. Beckstein, E.J. Denning, J.R. Perilla and T.B. Woolf,
+   Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the
+   Ensemble of Open <--> Closed Transitions. J Mol Biol 394 (2009), 160--176,
+   doi:10.1016/j.jmb.2009.09.009
+
+"""
+
+__all__ = ['Universe', 'Writer',
+           'AtomGroup', 'ResidueGroup', 'SegmentGroup']
+
+import logging
+import warnings
+from typing import Dict
+
+
+logger = logging.getLogger("MDAnalysis.__init__")
+
+from .version import __version__
+try:
+    from .authors import __authors__
+except ImportError:
+    logger.info('Could not find authors.py, __authors__ will be empty.')
+    __authors__ = []
+
+# Registry of Readers, Parsers and Writers known to MDAnalysis
+# Metaclass magic fills these as classes are declared.
+_READERS: Dict = {}
+_READER_HINTS: Dict = {}
+_SINGLEFRAME_WRITERS: Dict = {}
+_MULTIFRAME_WRITERS: Dict = {}
+_PARSERS: Dict = {}
+_PARSER_HINTS: Dict = {}
+_SELECTION_WRITERS: Dict = {}
+_CONVERTERS: Dict = {}
+# Registry of TopologyAttributes
+_TOPOLOGY_ATTRS: Dict = {}   # {attrname: cls}
+_TOPOLOGY_TRANSPLANTS: Dict = {}   # {name: [attrname, method, transplant class]}
+_TOPOLOGY_ATTRNAMES: Dict = {}   # {lower case name w/o _ : name}
+_GUESSERS: Dict = {}
+
+# custom exceptions and warnings
+from .exceptions import (
+    SelectionError, NoDataError, ApplicationError, SelectionWarning,
+    MissingDataWarning, ConversionWarning, FileFormatWarning,
+    StreamWarning
+)
+
+from .lib import log
+from .lib.log import start_logging, stop_logging
+
+logging.getLogger("MDAnalysis").addHandler(log.NullHandler())
+del logging
+
+# only MDAnalysis DeprecationWarnings are loud by default
+warnings.filterwarnings(action='once', category=DeprecationWarning,
+                        module='MDAnalysis')
+
+
+from . import units
+
+# Bring some often used objects into the current namespace
+from .core.universe import Universe, Merge
+from .core.groups import AtomGroup, ResidueGroup, SegmentGroup
+from .coordinates.core import writer as Writer
+
+# After Universe import
+from . import converters
+
+from .due import due, Doi, BibTeX
+
+due.cite(Doi("10.25080/majora-629e541a-00e"),
+         description="Molecular simulation analysis library",
+         path="MDAnalysis", cite_module=True)
+due.cite(Doi("10.1002/jcc.21787"),
+         description="Molecular simulation analysis library",
+         path="MDAnalysis", cite_module=True)
+
+del Doi, BibTeX

MDAnalysis/analysis/__init__.py

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+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
+#
+# 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 Lesser GNU Public Licence, v2.1 or any higher version
+#
+# Please cite your use of MDAnalysis in published work:
+#
+# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
+# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
+# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
+# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
+# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
+# doi: 10.25080/majora-629e541a-00e
+#
+# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
+# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
+# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
+#
+
+__all__ = [
+    'align',
+    'backends',
+    'base',
+    'contacts',
+    'density',
+    'distances',
+    'diffusionmap',
+    'dihedrals',
+    'distances',
+    'dielectric',
+    'gnm',
+    'hbonds',
+    'helix_analysis',
+    'hole2',
+    'hydrogenbonds',
+    'leaflet',
+    'lineardensity',
+    'msd',
+    'nuclinfo',
+    'nucleicacids',
+    'polymer',
+    'pca',
+    'psa',
+    'rdf',
+    'results',
+    'rms',
+    'waterdynamics',
+]