Package mmLib :: Module Structure :: Class AlphaHelix
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Class AlphaHelix

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object --+
         |
        AlphaHelix

Class containing information on a protein alpha helix.

Instance Methods [hide private]
 
__init__(self, helix_id='', helix_class='1', helix_length=0, chain_id1='', frag_id1='', res_name1='', chain_id2='', frag_id2='', res_name2='', details='', **args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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__str__(self)
str(x)
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add_segment(self, segment)
Adds the Segment object this AlphaHelix spans.
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construct_segment(self)
Constructs the child Segment object from the Chain object found in the parent Structure object by the AlphaHelix chain_id/fragment_id information.
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get_chain(self)
Returns the parent Chain object.
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get_model(self)
Returns the parent Model object.
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get_structure(self)
Returns the parent Structure object.
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get_segment(self)
Return the child Segment object this AlphaHelix spans in the parent Model.
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iter_fragments(self)
Iterates all Fragment objects in the AlphaHelix.
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iter_atoms(self)
Iterates all Atom objects in the AlphaHelix.
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iter_all_atoms(self)
Iterates all Atom objects in all AlphaHelix, plus any in non-default alt_loc conformations.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, helix_id='', helix_class='1', helix_length=0, chain_id1='', frag_id1='', res_name1='', chain_id2='', frag_id2='', res_name2='', details='', **args)
(Constructor)

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

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

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str(x)

Overrides: object.__str__
(inherited documentation)

add_segment(self, segment)

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Adds the Segment object this AlphaHelix spans. If the AlphaHelix already has a Segment, then it is replaced. The Segment objects added to AlphaHelix objects must have the attribute segment.chain referencing the source Chain object the Segment was sliced from.

construct_segment(self)

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Constructs the child Segment object from the Chain object found in the parent Structure object by the AlphaHelix chain_id/fragment_id information. Returns True if the Segment was created, or False if it was not. The Segment is not created when the fragment range fragment_id1:fragment_id2 cannot be found in the parent Chain object.

get_chain(self)

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Returns the parent Chain object. If the AlphaHelix does not have a Segment child the raised AttributeError.