Multiple models support.
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__init__(self,
model_id=1,
**args)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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__len__(self)
Returns the number of stored Chain objects. |
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__getitem__(self,
chain_idx)
Same as get_chain, but raises KeyError if the requested chain_id is
not found. |
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__iter__(self)
Iterates the Chain objects in the Model. |
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__contains__(self,
chain_idx)
Returns True if the argument Chain or chain_id is in the Model. |
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index(self,
chain)
Returns the numeric index of the Chain object in the Model. |
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sort(self)
Sorts all Chains in the Model by their chain_id. |
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add_chain(self,
chain,
delay_sort=False)
Adds a Chain to the Model. |
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remove_chain(self,
chain)
Removes the Chain from the Model. |
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get_chain(self,
chain_id)
Returns the Chain object matching the chain_id character. |
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iter_chains(self)
Iterates over all Chain objects in alphabetical order according to
their chain_id. |
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count_chains(self)
Counts all Chain objects. |
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add_fragment(self,
fragment,
delay_sort=False)
Adds a Fragment instance |
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remove_fragment(self,
fragment)
Removes a Fragment object. |
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count_fragments(self)
Counts all Fragment objects. |
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remove_atom(self,
atom)
Removes an Atom object. |
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iter_atoms(self)
Iterates over all Atom objects according to the Structure defaults. |
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count_atoms(self)
Counts all Atom objects in according to the Structure defaults. |
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iter_all_atoms(self)
Iterates over all Atom objects including all atoms in multiple
conformations. |
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count_all_atoms(self)
Counts all Atom objects including all atoms in multiple
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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add_alpha_helix(self,
alpha_helix)
Adds an AlphaHelix object to the Model. |
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remove_alpha_helix(self,
alpha_helix)
Removes an AlphaHelix object from the Model. |
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iter_alpha_helicies(self)
Iterates over all AlphaHelix objects in the Model. |
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add_beta_sheet(self,
beta_sheet)
Adds a BetaSheet object to the Model. |
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remove_beta_sheet(self,
beta_sheet)
Removes a BetaSheet object from the Model. |
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iter_beta_sheets(self)
Iterate over all child BetaSheet objects in the Model. |
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add_site(self,
site)
Adds a Site (of interest) object to the Model. |
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remove_site(self,
site)
Removes a Site (of interest) object from the Model. |
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iter_sites(self)
Iterate over all active/important sites defined in the Structure. |
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get_structure(self)
Returns the parent Structure. |
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set_model_id(self,
model_id)
Sets the model_id of all contained objects. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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