Package csb :: Package bio :: Package structure :: Class Structure

Class Structure

            object --+        
                     |        
core.AbstractContainer --+    
                         |    
  core.AbstractNIContainer --+
                             |
                object --+   |
                         |   |
            AbstractEntity --+
                             |
                            Structure

Represents a single model of a PDB 3-Dimensional molecular structure. Provides access to the Chain objects, contained in the model:

>>> structure['A']
<Chain A: Protein>
>>> structure.chains['A']
<Chain A: Protein>
>>> structure.items
<iterator of Chain-s>

Nested Classes
Inherited from `core.AbstractContainer`: `__metaclass__`

Instance Methods

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

source code

__repr__(self)
repr(x)

source code

str

to_fasta(self)
Dump the structure in FASTA format.

source code

to_pdb(self, output_file=None)
Dump the whole structure in PDB format.

source code

Inherited from core.AbstractNIContainer: __getitem__

Inherited from core.AbstractContainer: __bool__, __iter__, __len__, __nonzero__

Inherited from AbstractEntity: components, get_coordinates, transform

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

Static Methods

Structure

from_chain(chain)
A Structure factory, which instantiates and returns a new Structure with chain as deep cpoy of chain

source code

Class Variables
	__abstractmethods__ = `frozenset([])`

Properties
str	accession Accession number
StructureChainsTable	chains Access chains by their chain identifiers
Chain or None	first_chain The first Chain in the structure (if available)
iterator of AbstractEntity	items Iterator over all immediate children of the entity
int	model_id Model ID
	resolution Resolution in Angstroms
Inherited from `object`: `__class__`

Method Details

init(self, accession)
(Constructor)

source code

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

Parameters:

accession (str) - accession number of the structure

Overrides: object.__init__

(inherited documentation)

repr(self)
(Representation operator)

source code

repr(x)

Overrides: object.__repr__: (inherited documentation)

from_chain(chain)
Static Method

source code

A Structure factory, which instantiates and returns a new Structure with chain as deep cpoy of chain

Parameters:

chain (Chain) - the chain which will comprise the new structure

Returns: Structure

to_fasta(self)

source code

Dump the structure in FASTA format.

Returns: str: FASTA-formatted string with all chains in the structure

Deprecated: this method will be removed soon. Use csb.bio.sequence.ChainSequence.create instead

to_pdb(self, output_file=None)

source code

Dump the whole structure in PDB format.

Parameters:

output_file (str or stream) - output file name or open stream

Property Details

accession

Accession number

Get Method:: unreachable.accession(self) - Accession number
Set Method:: unreachable.accession(self, accession)
Type:: str

chains

Access chains by their chain identifiers

Get Method:: unreachable.chains(self) - Access chains by their chain identifiers
Type:: StructureChainsTable

first_chain

The first Chain in the structure (if available)

Get Method:: unreachable.first_chain(self) - The first Chain in the structure (if available)
Type:: Chain or None

items

Iterator over all immediate children of the entity

Get Method:: unreachable.items(self)
Type:: iterator of AbstractEntity

model_id

Model ID

Get Method:: unreachable.model_id(self) - Model ID
Set Method:: unreachable.model_id(self, value)
Type:: int

resolution

Resolution in Angstroms

Get Method:: unreachable.resolution(self) - Resolution in Angstroms
Set Method:: unreachable.resolution(self, value)

Class Structure

__init__(self, accession) (Constructor)

__repr__(self) (Representation operator)

from_chain(chain) Static Method

to_fasta(self)

to_pdb(self, output_file=None)

accession

chains

first_chain

items

model_id

resolution

init(self, accession)
(Constructor)

repr(self)
(Representation operator)

from_chain(chain)
Static Method