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

object --+
         |
        AlphaHelix


Class containing information on a protein alpha helix.
Method Summary
  __init__(self, helix_id, helix_class, helix_length, chain_id1, frag_id1, res_name1, chain_id2, frag_id2, res_name2, details, **args)
  __str__(self)
  add_segment(self, segment)
Adds the Segment object this AlphaHelix spans.
  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.
  get_chain(self)
Returns the parent Chain object.
  get_model(self)
Returns the parent Model object.
  get_segment(self)
Return the child Segment object this AlphaHelix spans in the parent Model.
  get_structure(self)
Returns the parent Structure object.
  iter_all_atoms(self)
Iterates all Atom objects in all AlphaHelix, plus any in non-default alt_loc conformations.
  iter_atoms(self)
Iterates all Atom objects in the AlphaHelix.
  iter_fragments(self)
Iterates all Fragment objects in the AlphaHelix.
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name
  __getattribute__(...)
x.__getattribute__('name') <==> x.name
  __hash__(x)
x.__hash__() <==> hash(x)
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T
  __reduce__(...)
helper for pickle
  __reduce_ex__(...)
helper for pickle
  __repr__(x)
x.__repr__() <==> repr(x)
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value

Method Details

add_segment(self, segment)

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)

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)

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

get_model(self)

Returns the parent Model object.

get_segment(self)

Return the child Segment object this AlphaHelix spans in the parent Model.

get_structure(self)

Returns the parent Structure object.

iter_all_atoms(self)

Iterates all Atom objects in all AlphaHelix, plus any in non-default alt_loc conformations.

iter_atoms(self)

Iterates all Atom objects in the AlphaHelix.

iter_fragments(self)

Iterates all Fragment objects in the AlphaHelix.

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