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.
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class
Bio.PDB.Entity.
Entity
(id)¶ Bases:
object
Basic container object for PDB heirachy.
Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup.
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__init__
(self, id)¶ Initialize the class.
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__len__
(self)¶ Return the number of children.
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__getitem__
(self, id)¶ Return the child with given id.
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__delitem__
(self, id)¶ Remove a child.
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__contains__
(self, id)¶ Check if there is a child element with the given id.
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__iter__
(self)¶ Iterate over children.
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__eq__
(self, other)¶ Test for equality. This compares full_id including the IDs of all parents.
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__ne__
(self, other)¶ Test for inequality.
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__gt__
(self, other)¶ Test greater than.
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__ge__
(self, other)¶ Test greater or equal.
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__lt__
(self, other)¶ Test less than.
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__le__
(self, other)¶ Test less or equal.
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__hash__
(self)¶ Hash method to allow uniqueness (set).
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property
id
¶ Return identifier.
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get_level
(self)¶ Return level in hierarchy.
A - atom R - residue C - chain M - model S - structure
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set_parent
(self, entity)¶ Set the parent Entity object.
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detach_parent
(self)¶ Detach the parent.
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detach_child
(self, id)¶ Remove a child.
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add
(self, entity)¶ Add a child to the Entity.
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insert
(self, pos, entity)¶ Add a child to the Entity at a specified position.
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get_iterator
(self)¶ Return iterator over children.
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get_list
(self)¶ Return a copy of the list of children.
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has_id
(self, id)¶ Check if a child with given id exists.
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get_parent
(self)¶ Return the parent Entity object.
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get_id
(self)¶ Return the id.
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get_full_id
(self)¶ 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”.
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transform
(self, rot, tran)¶ Apply rotation and translation to the atomic coordinates.
- Parameters
rot (3x3 Numeric array) – A right multiplying rotation matrix
tran (size 3 Numeric 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)
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copy
(self)¶ Copy entity recursively.
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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.
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__init__
(self, id)¶ Initialize the class.
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__getattr__
(self, method)¶ Forward the method call to the selected child.
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__getitem__
(self, id)¶ Return the child with the given id.
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__setitem__
(self, id, child)¶ Add a child, associated with a certain id.
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__contains__
(self, id)¶ Check if the child has the given id.
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__iter__
(self)¶ Return the number of children.
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__len__
(self)¶ Return the number of children.
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__sub__
(self, other)¶ Subtraction with another object.
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__gt__
(self, other)¶ Return if child is greater than other.
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__ge__
(self, other)¶ Return if child is greater or equal than other.
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__lt__
(self, other)¶ Return if child is less than other.
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__le__
(self, other)¶ Return if child is less or equal than other.
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copy
(self)¶ Copy disorderd entity recursively.
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get_id
(self)¶ Return the id.
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disordered_has_id
(self, id)¶ Check if there is an object present associated with this id.
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detach_parent
(self)¶ Detach the parent.
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get_parent
(self)¶ Return parent.
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set_parent
(self, parent)¶ Set the parent for the object and its children.
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disordered_select
(self, id)¶ Select the object with given id as the currently active object.
Uncaught method calls are forwarded to the selected child object.
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disordered_add
(self, child)¶ Add disordered entry.
This is implemented by DisorderedAtom and DisorderedResidue.
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is_disordered
(self)¶ Return 2, indicating that this Entity is a collection of Entities.
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disordered_get_id_list
(self)¶ Return a list of id’s.
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disordered_get
(self, id=None)¶ Get the child object associated with id.
If id is None, the currently selected child is returned.
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disordered_get_list
(self)¶ Return list of children.
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