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Scientific::IO::PDB::Structure Class Reference

List of all members.


Detailed Description

A high-level representation of the contents of a PDB file

Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'),
where |filename| is the name of the PDB file. Compressed files
and URLs are accepted, as for class PDBFile. The two optional
arguments specify which data should be read in case of a
multiple-model file or in case of a file that contains alternative
positions for some atoms.

The components of a system can be accessed in several ways
('s' is an instance of this class):

- 's.residues' is a list of all PDB residues, in the order in
  which they occurred in the file.

- 's.peptide_chains' is a list of PeptideChain objects, containing
  all peptide chains in the file in their original order.

- 's.nucleotide_chains' is a list of NucleotideChain objects, containing
  all nucleotide chains in the file in their original order.

- 's.molecules' is a list of all PDB residues that are neither
  amino acid residues nor nucleotide residues, in their original
  order.

- 's.objects' is a list of all high-level objects (peptide chains,
  nucleotide chains, and molecules) in their original order.

An iteration over a Structure instance by a for-loop is equivalent
to an iteration over the residue list.

Definition at line 846 of file PDB.py.


Public Member Functions

def __getitem__
def __init__
def __len__
def __repr__
def addMolecule
def deleteHydrogens
def extractData
def joinNucleotideChains
def joinPeptideChains
def newChain
def newResidue
def parseFile
def renumberAtoms
def splitNucleotideChain
def splitPeptideChain
def writeToFile

Public Attributes

 alternate
 filename
 model
 molecules
 nucleotide_chains
 objects
 pdb_code
 peptide_chains
 residues

Static Public Attributes

 molecule_constructor = Molecule
 nucleotide_chain_constructor = NucleotideChain
 peptide_chain_constructor = PeptideChain

Private Member Functions

def _joinChains
def _splitChain

The documentation for this class was generated from the following file:

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