Package mmLib :: Module Structure :: Class Segment
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Type Segment

object --+
         |
        Segment

Known Subclasses:
Chain

Segment objects are a container for Fragment objects, but are disaccociated with the Structure object hierarch. Chain objects are a subclass of Segment objects which are part of the Structure hierarchy.
Method Summary
  __init__(self, model_id, chain_id, **args)
  __contains__(self, fragment_idx)
Checks for Fragment objects, or the fragment_id string.
  __deepcopy__(self, memo)
Implements copy module protocol for deepcopy() operation.
  __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.
  __str__(self)
  add_atom(self, atom, delay_sort)
Adds a Atom.
  add_fragment(self, fragment, delay_sort)
Adds a Fragment instance to the Segment.
  construct_segment(self)
Constructs a new Segment object so that it has a valid .chain reference.
  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.
  remove_fragment(self, fragment)
Removes a Fragment object from the Segment.
  set_chain_id(self, chain_id)
Sets the model_id of all contained objects.
  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

__contains__(self, fragment_idx)
(In operator)

Checks for Fragment objects, or the fragment_id string.

__deepcopy__(self, memo)

Implements copy module protocol for deepcopy() operation.

__ge__(self, other)
(Greater-than-or-equals operator)

Greator than or equal to operator based on chain_id.

__getitem__(self, fragment_idx)
(Indexing operator)

Retrieve a Fragment within the Segment. This can take a integer index of the Fragment's position within the segment, the fragment_id string of the Fragment to retrieve, or a slice of the Segment to return a new Segment object containing the sliced subset of Fragments. If the slice values are fragment_id strings, then the Segment which is returned includes those Fragments. If the slice values are integers, then normal list slicing rules apply.

__gt__(self, other)
(Greater-than operator)

Greator than operator based on chain_id.

__iter__(self)

Iterate all Fragments contained in the Segment.

__le__(self, other)
(Less-than-or-equals operator)

Less than or equal operator based on chain_id.

__len__(self)
(Length operator)

Return the number of Fragments in the Segment.

__lt__(self, other)
(Less-than operator)

Less than operator based on the chain_id.

add_atom(self, atom, delay_sort=False)

Adds a Atom.

add_fragment(self, fragment, delay_sort=False)

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

construct_segment(self)

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

construct_sub_segment(self, start_frag_id, stop_frag_id)

Construct and return a sub-Segment between start_frag_id and stop_frag_id. If start_frag_id is None, then the slice is taken from the beginning of this Segment, and if stop_frag_id is None it is taken to the end of this Segment.

count_fragments(self)

Return the number of Fragment objects.

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.

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_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=None, frag_id_end=None)

Iterates over all Fragment objects. The iteration is performed in order according to the Fragment's position within the Segment object.

remove_atom(self, atom)

Removes a Atom object.

remove_fragment(self, fragment)

Removes a Fragment object from the Segment.

set_chain_id(self, chain_id)

Sets the model_id of all contained objects.

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.

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