| Method Summary |
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__init__(self,
model_id,
**args)
|
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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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__deepcopy__(self,
memo)
|
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__ge__(self,
other)
|
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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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__gt__(self,
other)
|
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__iter__(self)
Iterates the Chain objects in the Model. |
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__le__(self,
other)
|
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__len__(self)
Returns the number of stored Chain objects. |
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__lt__(self,
other)
|
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__str__(self)
|
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add_alpha_helix(self,
alpha_helix)
Adds a AlphaHelix object to the Model. |
| |
add_atom(self,
atom,
delay_sort)
|
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add_beta_sheet(self,
beta_sheet)
Adds a BetaSheet object to the Model. |
| |
add_chain(self,
chain,
delay_sort)
Adds a Chain to the Model. |
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add_fragment(self,
fragment,
delay_sort)
Adds a Fragment instance |
| |
add_site(self,
site)
Adds a Site (of interest) object to the Model. |
| |
count_all_atoms(self)
Counts all Atom objects including all atoms in multiple
conformations. |
| |
count_amino_acids(self)
|
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count_atoms(self)
Counts all Atom objects in according to the Structure defaults. |
| |
count_bonds(self)
Counts all Bond objects. |
| |
count_chains(self)
Counts all Chain objects. |
| |
count_fragments(self)
Counts all Fragment objects. |
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count_non_standard_residues(self)
|
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count_nucleic_acids(self)
|
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count_standard_residues(self)
|
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count_waters(self)
|
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get_chain(self,
chain_id)
Returns the Chain object matching the chain_id charactor. |
| |
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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get_structure(self)
Returns the parent Structure. |
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has_amino_acids(self)
|
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has_non_standard_residues(self)
|
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has_nucleic_acids(self)
|
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has_standard_residues(self)
|
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has_waters(self)
|
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index(self,
chain)
Returns the numeric index of the Chain object in the Model. |
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iter_all_atoms(self)
Iterates over all Atom objects including all atoms in multiple
conformations. |
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iter_alpha_helicies(self)
Iterates over all AlphaHelix objects in the Model. |
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iter_amino_acids(self)
|
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iter_atoms(self)
Iterates over all Atom objects according to the Structure
defaults. |
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iter_beta_sheets(self)
Iterate over all child BetaSheet objects in the Model. |
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iter_bonds(self)
Iterates over all Bond objects. |
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iter_chains(self)
Iterates over all Chain objects in alphabetical order according to
their chain_id. |
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iter_fragments(self)
Iterates over all Fragment objects. |
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iter_non_standard_residues(self)
|
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iter_nucleic_acids(self)
|
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iter_sites(self)
Iterate over all active/important sites defined in the Structure. |
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iter_standard_residues(self)
|
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iter_waters(self)
|
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remove_alpha_helix(self,
alpha_helix)
Removes a AlphaHelix object from the Model. |
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remove_atom(self,
atom)
Removes a Atom object. |
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remove_beta_sheet(self,
beta_sheet)
Removes a BetaSheet object from the Model. |
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remove_chain(self,
chain)
Removes the Chain from the Model. |
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remove_fragment(self,
fragment)
Removes a Fragment object. |
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remove_site(self,
site)
Removes a Site (of interest) object from the Model. |
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set_model_id(self,
model_id)
Sets the model_id of all contained objects. |
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sort(self)
Sorts all Chains in the Model by their chain_id. |
| Inherited from object |
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__delattr__(...)
x.__delattr__('name') <==> del x.name |
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__getattribute__(...)
x.__getattribute__('name') <==> x.name |
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__hash__(x)
x.__hash__() <==> hash(x) |
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__new__(T,
S,
...)
T.__new__(S, ...) -> a new object with type S, a subtype of T |
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__reduce__(...)
helper for pickle |
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__reduce_ex__(...)
helper for pickle |
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__repr__(x)
x.__repr__() <==> repr(x) |
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__setattr__(...)
x.__setattr__('name', value) <==> x.name = value |