Bio.PDB.Entity.Entity

Class Entity

object --+ | Entity

Basic container object. Structure, Model, Chain and Residue are subclasses of Entity. It deals with storage and lookup.

Instance Methods

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__contains__(self, id)
True if there is a child element with the given id.

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__delitem__(self, id)
Remove a child.

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__getitem__(self, id)
Return the child with given id.

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__init__(self, id)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

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__iter__(self)
Iterate over children.

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__len__(self)
Return the number of children.

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add(self, entity)
Add a child to the Entity.

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copy(self)

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detach_child(self, id)
Remove a child.

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detach_parent(self)
Detach the parent.

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get_full_id(self)
Return the full id.

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get_id(self)
Return the id.

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get_iterator(self)
Return iterator over children.

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get_level(self)
Return level in hierarchy.

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get_list(self)
Return a copy of the list of children.

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get_parent(self)
Return the parent Entity object.

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has_id(self, id)
True if a child with given id exists.

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insert(self, pos, entity)
Add a child to the Entity at a specified position.

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set_parent(self, entity)
Set the parent Entity object.

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transform(self, rot, tran)
Apply rotation and translation to the atomic coordinates.

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Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

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Inherited from object: __class__

init(self, id)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

get_full_id(self)

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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) beacuse it has a blank hetero field, that its sequence
identifier is 10 and its insertion code "A".

get_level(self)

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Return level in hierarchy.

A - atom
R - residue
C - chain
M - model
S - structure

transform(self, rot, tran)

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Apply rotation and translation to the atomic coordinates.

Example:
        >>> rotation=rotmat(pi, Vector(1,0,0))
        >>> translation=array((0,0,1), 'f')
        >>> entity.transform(rotation, translation)

@param rot: A right multiplying rotation matrix
@type rot: 3x3 Numeric array

@param tran: the translation vector
@type tran: size 3 Numeric array

Class Entity

__init__(self, id) (Constructor)

get_full_id(self)

get_level(self)

transform(self, rot, tran)

init(self, id)
(Constructor)