Package mmLib :: Module Structure :: Class Chain
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Class Chain

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object --+    
         |    
   Segment --+
             |
            Chain

Chain objects contain an ordered list of Fragment objects.

Instance Methods [hide private]
 
__init__(self, model_id=1, chain_id='', **args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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__str__(self)
str(x)
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__deepcopy__(self, memo)
Implements the copy module deepcopy() protocol.
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construct_segment(self)
Constructs a new Segment object so that it has a valid .chain reference.
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set_sequence(self, sequence_list)
The sequence_list is a list of 3-letter residue name codes which define the polymer sequence for the chain.
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remove_sequence(self)
Removes the current sequence mapping.
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iter_sequence(self)
Iterates over all 3-letter residue codes for the polymer sequence.
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construct_sequence_list(self)
Constructs and returns a list with the 3-letter residue codes for the polymer sequence.
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get_fragment_sequence_index(self, seq_index) source code
 
add_fragment(self, fragment, delay_sort=False)
Adds a Fragment instance to the Chain.
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remove_fragment(self, fragment)
Remove the Fragment from the Chain.
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set_chain_id(self, chain_id)
Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.
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Inherited from Segment: __contains__, __ge__, __getitem__, __gt__, __iter__, __le__, __len__, __lt__, add_atom, construct_sub_segment, count_all_atoms, count_amino_acids, count_atoms, count_fragments, count_non_standard_residues, count_nucleic_acids, count_standard_residues, count_waters, get_chain, get_equivalent_atom, get_fragment, get_model, get_structure, has_amino_acids, has_non_standard_residues, has_nucleic_acids, has_standard_residues, has_waters, index, is_homolog, iter_all_atoms, iter_amino_acids, iter_atoms, iter_bonds, iter_fragments, iter_non_standard_residues, iter_nucleic_acids, iter_standard_residues, iter_waters, remove_atom, set_model_id, sort

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, model_id=1, chain_id='', **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)

__deepcopy__(self, memo)

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Implements the copy module deepcopy() protocol.

Overrides: Segment.__deepcopy__

construct_segment(self)

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Constructs a new Segment object so that it has a valid .chain reference.

Overrides: Segment.construct_segment

set_sequence(self, sequence_list)

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The sequence_list is a list of 3-letter residue name codes which define the polymer sequence for the chain. Setting the sequence attempts to map the sequence codes to Fragment objects.

add_fragment(self, fragment, delay_sort=False)

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Adds a Fragment instance to the Chain. If delay_sort is True, then the fragment is not inserted in the proper position within the chain.

Overrides: Segment.add_fragment

remove_fragment(self, fragment)

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Remove the Fragment from the Chain.

Overrides: Segment.remove_fragment

set_chain_id(self, chain_id)

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Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.

Overrides: Segment.set_chain_id