8.7. AtomGroup accessors — MDAnalysis.core.accessors

This module provides classes for accessing and converting AtomGroup objects. It is used for the convert_to() method to make it usable in two different ways: ag.convert_to("PACKAGE") or ag.convert_to.package()

Example

>>> class SpeechWrapper:
...     def __init__(self, person):
...         self.person = person
...     def __call__(self, *args):
...         print(self.person.name, "says", *args)
...     def whoami(self):
...         print("I am %s" % self.person.name)
...
>>> class Person:
...     def __init__(self, name):
...         self.name = name
...     say = Accessor("say", SpeechWrapper)
...
>>> bob = Person("Bob")
>>> bob.say("hello")
Bob says hello
>>> bob.say.whoami()
I am Bob

8.7.1. Classes

class MDAnalysis.core.accessors.Accessor(name, accessor)[source]

Used to pass data between two classes

Parameters:

  • name (str) – Name of the property in the parent class

  • accessor (class) – A class that needs access to its parent’s instance

Example

If you want the property to be named “convert_to” in the AtomGroup class, use:

>>> class AtomGroup:
>>>     # ...
>>>     convert_to = Accessor("convert_to", ConverterWrapper)

And when calling ag.convert_to.rdkit(), the “rdkit” method of the ConverterWrapper will be able to have access to “ag”

Added in version 2.0.0.

class MDAnalysis.core.accessors.ConverterWrapper(ag)[source]

Convert AtomGroup to a structure from another Python package.

The converters are accessible to any AtomGroup through the convert_to property. ag.convert_to will return this ConverterWrapper, which can be called directly with the name of the destination package as a string (similarly to the old API), or through custom methods named after the package (in lowercase) that are automatically constructed thanks to metaclass magic.

Example

The code below converts a Universe to a parmed.structure.Structure

>>> import MDAnalysis as mda
>>> from MDAnalysis.tests.datafiles import GRO
>>> u = mda.Universe(GRO)
>>> parmed_structure = u.atoms.convert_to('PARMED')
>>> parmed_structure
<Structure 47681 atoms; 11302 residues; 0 bonds; PBC (triclinic); NOT parametrized>

You can also directly use u.atoms.convert_to.parmed()

Parameters:

  • package (str) – The name of the package to convert to, e.g. "PARMED"

  • *args – Positional arguments passed to the converter

  • **kwargs – Keyword arguments passed to the converter

Returns:

An instance of the structure type from another package.

Return type:

output

Raises:

ValueError: – No converter was found for the required package

Added in version 1.0.0.

Changed in version 2.0.0: Moved the convert_to method to its own class. The old API is still available and is now case-insensitive to package names, it also accepts positional and keyword arguments. Each converter function can also be accessed as a method with the name of the package in lowercase, i.e. convert_to.parmed()

Parameters:

ag (AtomGroup) – The AtomGroup to convert