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

object --+    
         |    
   Segment --+
             |
            Chain


Chain objects conatain a ordered list of Fragment objects.
Method Summary
  __init__(self, model_id, chain_id, **args)
  __deepcopy__(self, memo)
Implements the copy module deepcopy() protocol.
  __str__(self)
  add_fragment(self, fragment, delay_sort)
Adds a Fragment instance to the Chain.
  construct_segment(self)
Constructs a new Segment object so that it has a valid .chain reference.
  construct_sequence_list(self)
Constructs and returns a list with the 3-letter residue codes for the polymer sequence.
  get_fragment_sequence_index(self, seq_index)
  iter_sequence(self)
Iterates over all 3-letter residue codes for the polymer sequence.
  remove_fragment(self, fragment)
Remove the Fragment from the Chain.
  remove_sequence(self)
Removes the current sequence mapping.
  set_chain_id(self, chain_id)
Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.
  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.
    Inherited from Segment
  __contains__(self, fragment_idx)
Checks for Fragment objects, or the fragment_id string.
  __ge__(self, other)
Greator than or equal to operator based on chain_id.
  __getitem__(self, fragment_idx)
Retrieve a Fragment within the Segment.
  __gt__(self, other)
Greator than operator based on chain_id.
  __iter__(self)
Iterate all Fragments contained in the Segment.
  __le__(self, other)
Less than or equal operator based on chain_id.
  __len__(self)
Return the number of Fragments in the Segment.
  __lt__(self, other)
Less than operator based on the chain_id.
  add_atom(self, atom, delay_sort)
Adds a Atom.
  construct_sub_segment(self, start_frag_id, stop_frag_id)
Construct and return a sub-Segment between start_frag_id and stop_frag_id.
  count_all_atoms(self)
  count_amino_acids(self)
  count_atoms(self)
  count_fragments(self)
Return the number of Fragment objects.
  count_non_standard_residues(self)
  count_nucleic_acids(self)
  count_standard_residues(self)
  count_waters(self)
  get_chain(self)
Returns the Chain object this Segment is part of.
  get_equivalent_atom(self, atom)
Returns the atom with the same fragment_id and name as the argument atom, or None if it is not found.
  get_fragment(self, fragment_id)
Returns the PDB fragment uniquely identified by its fragment_id.
  get_model(self)
Returns the parent Model object.
  get_structure(self)
Returns the parent Structure object.
  has_amino_acids(self)
  has_non_standard_residues(self)
  has_nucleic_acids(self)
  has_standard_residues(self)
  has_waters(self)
  index(self, fragment)
Return the 0-based index of the Framgent in the segment list.
  is_homolog(self, segment2)
Returns True if there are no dissagreements in the sequences of this segment and segment2.
  iter_all_atoms(self)
Performs a in-order iteration of all atoms in the Segment, including alternate conformations.
  iter_amino_acids(self)
  iter_atoms(self)
Iterates over all Atom objects within the Segment using the default conformation set in the parent Structure.
  iter_bonds(self)
Iterates over all Bond objects attached to Atom objects within the Segment.
  iter_fragments(self, frag_id_begin, frag_id_end)
Iterates over all Fragment objects.
  iter_non_standard_residues(self)
  iter_nucleic_acids(self)
  iter_standard_residues(self)
  iter_waters(self)
  remove_atom(self, atom)
Removes a Atom object.
  set_model_id(self, model_id)
Sets the model_id of all contained objects.
  sort(self)
Sort the Fragments in the Segment into proper order.
    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

__deepcopy__(self, memo)

Implements the copy module deepcopy() protocol.
Overrides:
mmLib.Structure.Segment.__deepcopy__

add_fragment(self, fragment, delay_sort=False)

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:
mmLib.Structure.Segment.add_fragment

construct_segment(self)

Constructs a new Segment object so that it has a valid .chain reference.
Overrides:
mmLib.Structure.Segment.construct_segment

construct_sequence_list(self)

Constructs and returns a list with the 3-letter residue codes for the polymer sequence.

iter_sequence(self)

Iterates over all 3-letter residue codes for the polymer sequence.

remove_fragment(self, fragment)

Remove the Fragment from the Chain.
Overrides:
mmLib.Structure.Segment.remove_fragment

remove_sequence(self)

Removes the current sequence mapping.

set_chain_id(self, chain_id)

Sets a new ID for the Chain, updating the chain_id for all objects in the Structure hierarchy.
Overrides:
mmLib.Structure.Segment.set_chain_id

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. Setting the sequence attempts to map the sequence codes to Fragment objects.

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