7.7. 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
7.7.1. 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