Package csb :: Package bio :: Package structure :: Class Structure |
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# Class Structure

source code

                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)