Bio.PDB.Entity module
Base class for Residue, Chain, Model and Structure classes.
It is a simple container class, with list and dictionary like properties.
- class Bio.PDB.Entity.Entity(id)
Bases:
Generic
[_Parent
,_Child
]Basic container object for PDB hierarchy.
Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup.
- level: str
- __init__(id)
Initialize the class.
- parent: _Parent | None
- child_list: list[_Child]
- child_dict: dict[Any, _Child]
- __len__()
Return the number of children.
- __getitem__(id)
Return the child with given id.
- __delitem__(id)
Remove a child.
- __contains__(id)
Check if there is a child element with the given id.
- __iter__()
Iterate over children.
- __eq__(other)
Test for equality. This compares full_id including the IDs of all parents.
- __ne__(other)
Test for inequality.
- __gt__(other)
Test greater than.
- __ge__(other)
Test greater or equal.
- __lt__(other)
Test less than.
- __le__(other)
Test less or equal.
- __hash__()
Hash method to allow uniqueness (set).
- property id
Return identifier.
- strictly_equals(other: _Self, compare_coordinates: bool = False) bool
Compare this entity to the other entity for equality.
Recursively compare the children of this entity to the other entity’s children. Compare most properties including names and IDs.
- Parameters:
other (Entity) – The entity to compare this entity with
compare_coordinates (bool) – Whether to compare atomic coordinates
- Returns:
Whether the two entities are strictly equal
- Return type:
bool
- get_level()
Return level in hierarchy.
A - atom R - residue C - chain M - model S - structure
- set_parent(entity: _Parent)
Set the parent Entity object.
- detach_parent()
Detach the parent.
- detach_child(id)
Remove a child.
- add(entity: _Child)
Add a child to the Entity.
- insert(pos: int, entity: _Child)
Add a child to the Entity at a specified position.
- get_iterator()
Return iterator over children.
- get_list()
Return a copy of the list of children.
- has_id(id)
Check if a child with given id exists.
- get_parent()
Return the parent Entity object.
- get_id()
Return the id.
- get_full_id()
Return the full id.
The full id is a tuple containing all id’s starting from the top object (Structure) down to the current object. A full id for a Residue object e.g. is something like:
(“1abc”, 0, “A”, (” “, 10, “A”))
This corresponds to:
Structure with id “1abc” Model with id 0 Chain with id “A” Residue with id (” “, 10, “A”)
The Residue id indicates that the residue is not a hetero-residue (or a water) because it has a blank hetero field, that its sequence identifier is 10 and its insertion code “A”.
- transform(rot, tran)
Apply rotation and translation to the atomic coordinates.
- Parameters:
rot (3x3 NumPy array) – A right multiplying rotation matrix
tran (size 3 NumPy array) – the translation vector
Examples
This is an incomplete but illustrative example:
from numpy import pi, array from Bio.PDB.vectors import Vector, rotmat rotation = rotmat(pi, Vector(1, 0, 0)) translation = array((0, 0, 1), 'f') entity.transform(rotation, translation)
- center_of_mass(geometric=False)
Return the center of mass of the Entity as a numpy array.
If geometric is True, returns the center of geometry instead.
- copy()
Copy entity recursively.
- __annotations__ = {'child_dict': dict[typing.Any, ~_Child], 'child_list': list[~_Child], 'level': <class 'str'>, 'parent': typing.Optional[~_Parent]}
- __orig_bases__ = (typing.Generic[~_Parent, ~_Child],)
- __parameters__ = (~_Parent, ~_Child)
- class Bio.PDB.Entity.DisorderedEntityWrapper(id)
Bases:
object
Wrapper class to group equivalent Entities.
This class is a simple wrapper class that groups a number of equivalent Entities and forwards all method calls to one of them (the currently selected object). DisorderedResidue and DisorderedAtom are subclasses of this class.
E.g.: A DisorderedAtom object contains a number of Atom objects, where each Atom object represents a specific position of a disordered atom in the structure.
- __init__(id)
Initialize the class.
- __getattr__(method)
Forward the method call to the selected child.
- __getitem__(id)
Return the child with the given id.
- __setitem__(id, child)
Add a child, associated with a certain id.
- __contains__(id)
Check if the child has the given id.
- __iter__()
Return the number of children.
- __len__()
Return the number of children.
- __sub__(other)
Subtraction with another object.
- __gt__(other)
Return if child is greater than other.
- __ge__(other)
Return if child is greater or equal than other.
- __lt__(other)
Return if child is less than other.
- __le__(other)
Return if child is less or equal than other.
- copy()
Copy disorderd entity recursively.
- get_id()
Return the id.
- strictly_equals(other: DisorderedEntityWrapper, compare_coordinates: bool = False) bool
Compare this entity to the other entity using a strict definition of equality.
Recursively compare the children of this entity to the other entity’s children. Compare most properties including the selected child, names, and IDs.
- Parameters:
other (DisorderedEntityWrapper) – The entity to compare this entity with
compare_coordinates (bool) – Whether to compare atomic coordinates
- Returns:
Whether the two entities are strictly equal
- Return type:
bool
- disordered_has_id(id)
Check if there is an object present associated with this id.
- detach_parent()
Detach the parent.
- get_parent()
Return parent.
- set_parent(parent)
Set the parent for the object and its children.
- disordered_select(id)
Select the object with given id as the currently active object.
Uncaught method calls are forwarded to the selected child object.
- disordered_add(child)
Add disordered entry.
This is implemented by DisorderedAtom and DisorderedResidue.
- disordered_remove(child)
Remove disordered entry.
This is implemented by DisorderedAtom and DisorderedResidue.
- is_disordered()
Return 2, indicating that this Entity is a collection of Entities.
- disordered_get_id_list()
Return a list of id’s.
- disordered_get(id=None)
Get the child object associated with id.
If id is None, the currently selected child is returned.
- disordered_get_list()
Return list of children.