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Package csb :: Package bio :: Package structure :: Class ResidueAtomsTable
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Class ResidueAtomsTable

source code

              object --+            
                       |            
    core.AbstractIndexer --+        
                           |        
core.BaseDictionaryContainer --+    
                               |    
        core.DictionaryContainer --+
                                   |
                                  ResidueAtomsTable

Represents a collection of atoms. Provides dictionary-like access, where PDB atom names are used for lookup.

Instance Methods
 
__init__(self, residue, atoms=None)
x.__init__(...) initializes x; see help(type(x)) for signature		 source code
 
__repr__(self)
repr(x)		 source code
 
append(self, atom)
Append a new Atom to the catalog.		 source code
 
update(self, atom_name, atom)
Update the atom with the specified name.		 source code

Inherited from core.BaseDictionaryContainer: __bool__, __contains__, __getitem__, __iter__, __len__, __nonzero__, keys

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

Inherited from core.BaseDictionaryContainer: length

Inherited from object: __class__

Method Details

__init__(self, residue, atoms=None)
(Constructor)

source code 

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:
  • items - an initialization dictionary
  • restrict - a list of keys allowed for this dictionary
Overrides: object.__init__
(inherited documentation)

__repr__(self)
(Representation operator)

source code 

repr(x)

Overrides: object.__repr__
(inherited documentation)

append(self, atom)

source code 

Append a new Atom to the catalog.

If the atom has an alternate position, a disordered proxy will be created instead and the atom will be appended to the DisorderedAtom's list of children. If a disordered atom with that name already exists, the atom will be appended to its children only. If an atom with the same name exists, but it was erroneously not marked as disordered, that terrible condition will be fixed too.

Parameters:
  • atom (Atom) - the new atom to append
Raises:
  • DuplicateAtomIDError - if an atom with the same sequence number and insertion code already exists in that residue
Overrides: core.DictionaryContainer.append

update(self, atom_name, atom)

source code 

Update the atom with the specified name.

Parameters:
  • atom_name (str) - update key
  • atom (Atom) - new value for this key
Raises:
  • ValueError - if atom has a different name than atom_name

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