The Structure object is the parent container object for the entire
macromolecular data structure. It contains a list of the Chain objects in
the structure hierarchy, and contains these additional data objects:
cifdb(mmLib.mmCIFDB) A mmCIF database with additional structure
data.
unit_cell(mmLib.UnitCell) Unit cell/Spacegroup for the structure.
default_alt_loc(string) The default alternate location identifier used
when iterating or retreiving Atom objects in the structure.
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__init__(self,
**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 Structure. |
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__contains__(self,
model_chain_idx)
Returns True if item is a Model in the Structure, or a Chain or
chain_id in the default Model. |
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index(self,
model_chain)
If item is a Model, returns the index of the Model in the Structure,
or if the item is a Chain, returns the index of the Chain in the
default Model. |
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sort(self)
Sorts all Models and Chains in the Structure according to standard
model_id, chain_id, and fragment_id sorting rules. |
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get_model(self,
model_id)
Return the Model object with the argument model_id, or None if not
found. |
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get_default_model(self)
Returns the default Model object. |
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set_model(self,
model_id)
DEP: Use set_default_model() Sets the default Model for the Structure
to model_id. |
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iter_models(self)
Iterates over all Model objects. |
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count_models(self)
Counts all Model objects in the Structure. |
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remove_chain(self,
chain)
Removes a Chain object. |
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get_chain(self,
chain_id)
Returns the Chain object matching the chain_id character. |
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count_chains(self)
Counts all Chain objects in the default Model. |
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iter_chains(self)
Iterates over all Chain objects in the default Model, in alphabetical
order according to their chain_id. |
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iter_all_chains(self)
Iterates over all Chain objects in all Model objects. |
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add_fragment(self,
fragment,
delay_sort=True)
Adds a Fragment object. |
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remove_fragment(self,
fragment)
Removes a Fragment object. |
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count_fragments(self)
Counts all Fragment objects in the default Model. |
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has_amino_acids(self)
Returns True if there are AminoAcidResidue objects in the default
Model of the Structure. |
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count_amino_acids(self)
Counts all AminoAcidResidue objects in the default Model. |
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iter_amino_acids(self)
Same as iter_fragments() but only iterates over Fragments of the
subclass AminoAcidResidue. |
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iter_all_amino_acids(self)
Iterates over all AminoAcidResidue objects in all Models. |
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has_nucleic_acids(self)
Returns True if the Structure contains NucleicAcidResiudes in the
default Model. |
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count_nucleic_acids(self)
Counts all NucleicAcidResidue objects in the default Model. |
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iter_nucleic_acids(self)
Same as iter_fragments() but only iterates over Fragments of the
subclass NucleicAcidResidue. |
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iter_all_nucleic_acids(self)
Iterates over all NucleicAcidResidue objects in all Models. |
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has_standard_residues(self)
Returns True if the Structure contains amino or nucleic acids in the
default Model. |
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count_standard_residues(self)
Counts the number of standard residues in the default Model. |
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iter_standard_residues(self)
Iterates over standard residues in the default Model. |
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has_non_standard_residues(self)
Returns True if there are non-standard residues in the default Model. |
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count_non_standard_residues(self)
Counts all non-standard residues in the default Model. |
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has_waters(self)
Returns True if there are waters in the default Model. |
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count_waters(self)
Counts all waters in the default Model. |
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iter_waters(self)
Iterate over all waters in the default Model. |
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iter_atoms(self)
Iterates over all Atom objects in the default Model, using the
default alt_loc. |
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count_atoms(self)
Counts all Atom objects in the default Model using the default
alt_loc. |
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count_all_atoms(self)
Counts all atoms in the default Model using the default alt_loc. |
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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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count_bonds(self)
Counts all Bond objects using the default Model and default alt_loc. |
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alt_loc_list(self)
Return the unique list of Atom alternate location IDs found in the
Structure. |
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add_alpha_helix(self,
alpha_helix)
Adds an AlphaHelix to the default Model object. |
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iter_alpha_helicies(self)
Iterates over all child AlphaHelix objects in the default Model. |
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add_beta_sheet(self,
beta_sheet)
Adds a BetaSheet to the default Model object. |
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iter_beta_sheets(self)
Iterate over all beta sheets in the Structure. |
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add_site(self,
site)
Adds a Site object to the default Model. |
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iter_sites(self)
Iterate over all active/important sites defined in the Structure. |
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get_default_alt_loc(self)
Returns the default alt_loc string. |
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set_default_alt_loc(self,
alt_loc)
Sets the default alt_loc for the Stucture. |
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add_bonds_from_library(self)
Builds bonds for all Fragments in the Structure from bond tables for
monomers retrieved from the Library implementation of the Structure. |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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