Segment objects are a container for Fragment objects, but are
disassociated with the Structure object hierarch. Chain objects are a
subclass of Segment objects which are part of the Structure
hierarchy.
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__init__(self,
model_id=1,
chain_id='
' ,
**args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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__deepcopy__(self,
memo)
Implements copy module protocol for deepcopy() operation. |
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__lt__(self,
other)
Less than operator based on the chain_id. |
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__le__(self,
other)
Less than or equal operator based on chain_id. |
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__gt__(self,
other)
Greator than operator based on chain_id. |
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__ge__(self,
other)
Greator than or equal to operator based on chain_id. |
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__len__(self)
Return the number of Fragments in the Segment. |
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__iter__(self)
Iterate all Fragments contained in the Segment. |
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__contains__(self,
fragment_idx)
Checks for Fragment objects, or the fragment_id string. |
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index(self,
fragment)
Return the 0-based index of the fragment in the segment list. |
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sort(self)
Sort the Fragments in the Segment into proper order. |
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construct_segment(self)
Constructs a new Segment object so that it has a valid .chain
reference. |
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remove_fragment(self,
fragment)
Removes a Fragment object from the Segment. |
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get_fragment(self,
fragment_id)
Returns the PDB fragment uniquely identified by its fragment_id. |
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count_fragments(self)
Return the number of Fragment objects. |
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add_atom(self,
atom,
delay_sort=False)
Adds an Atom. |
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remove_atom(self,
atom)
Removes an Atom object. |
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iter_atoms(self)
Iterates over all Atom objects within the Segment using the default
conformation set in the parent Structure. |
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iter_all_atoms(self)
Performs an in-order iteration of all atoms in the Segment, including
alternate conformations. |
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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. |
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iter_bonds(self)
Iterates over all Bond objects attached to Atom objects within the
Segment. |
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get_chain(self)
Returns the Chain object this Segment is part of. |
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get_model(self)
Returns the parent Model object. |
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get_structure(self)
Returns the parent Structure object. |
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set_model_id(self,
model_id)
Sets the model_id of all contained objects. |
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set_chain_id(self,
chain_id)
Sets the model_id of all contained objects. |
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is_homolog(self,
segment2)
Returns True if there are no disagreements in the sequences of this
segment and segment2. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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