mmLib.Structure.AlphaHelix

Package mmLib :: Module Structure :: Class AlphaHelix

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Class 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)
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
Inherited from type
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T

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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