Package Scientific :: Package IO :: Module PDB :: Class Structure

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Class Structure

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

The components of a structure 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.

Nested Classes

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molecule_constructor
Molecule in a PDB file

nucleotide_chain_constructor
Nucleotide chain in a PDB file

peptide_chain_constructor
Peptide chain in a PDB file

Instance Methods

[hide private]

__getitem__(self, item)

__init__(self, filename, model=0, alternate_code='A')
Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'),

__len__(self)

__repr__(self)

_joinChains(self, constructor, chain_list, first, second)

_splitChain(self, constructor, chain_list, number, position)

addMolecule(self, molecule)

deleteHydrogens(self)
Remove all hydrogen atoms

extractData(self, data)

joinNucleotideChains(self, first, second)
Join two nucleotide chains into a single one.

joinPeptideChains(self, first, second)
Join two peptide chains into a single one.

newChain(self, residue, chain_data)

newResidue(self, residue_data)

parseFile(self, file)

renumberAtoms(self)
Renumber all atoms sequentially starting with 1

splitNucleotideChain(self, number, position)
Split a nucleotide chain into two chains

splitPeptideChain(self, number, position)
Split a peptide chain into two chains

writeToFile(self, file)
Write everything to a file

Method Details

[hide private]

getitem(self, item)
(Indexing operator)

init(self, filename, model=0, alternate_code='A')
(Constructor)

Constructor: Structure(|filename|, |model|='0', |alternate_code|='"A"'),

Parameters:

filename (str) - the name of the PDB file. Compressed files and URLs are accepted, as for class PDBFile.
model (int) - the number of the model to read from a multiple-model file. Only one model can be treated at a time.
alternate_code (single-letter str) - the version of the positions to be read from a file with alternate positions.

len(self)
(Length operator)

repr(self)
(Representation operator)

_joinChains(self, constructor, chain_list, first, second)

_splitChain(self, constructor, chain_list, number, position)

addMolecule(self, molecule)

deleteHydrogens(self)

Remove all hydrogen atoms

extractData(self, data)

joinNucleotideChains(self, first, second)

Join two nucleotide chains into a single one. The new chain occupies the position of the first chain, the second one is removed from the nucleotide chain list.

Parameters:

first (int) - the number of the first chain
second (int) - the number of the second chain

joinPeptideChains(self, first, second)

Join two peptide chains into a single one. The new chain occupies the position of the first chain, the second one is removed from the peptide chain list.

Parameters:

first (int) - the number of the first chain
second (int) - the number of the second chain

newChain(self, residue, chain_data)

newResidue(self, residue_data)

parseFile(self, file)

renumberAtoms(self)

Renumber all atoms sequentially starting with 1

splitNucleotideChain(self, number, position)

Split a nucleotide chain into two chains

The two chain fragments remain adjacent in the nucleotide chain list, i.e. the numbers of all following chains increase by one.

Parameters:

number (int) - the number of the nucleotide chain to be split
position (int) - the residue index at which the chain is split.

splitPeptideChain(self, number, position)

Split a peptide chain into two chains

The two chain fragments remain adjacent in the peptide chain list, i.e. the numbers of all following chains increase by one.

Parameters:

number (int) - the number of the peptide chain to be split
position (int) - the residue index at which the chain is split.

writeToFile(self, file)

Write everything to a file

Parameters:

file (PDBFile or str) - a PDB file object or a filename

Class Structure

__getitem__(self, item) (Indexing operator)

__init__(self, filename, model=0, alternate_code='A') (Constructor)

__len__(self) (Length operator)

__repr__(self) (Representation operator)

_joinChains(self, constructor, chain_list, first, second)

_splitChain(self, constructor, chain_list, number, position)

addMolecule(self, molecule)

deleteHydrogens(self)

extractData(self, data)

joinNucleotideChains(self, first, second)

joinPeptideChains(self, first, second)

newChain(self, residue, chain_data)

newResidue(self, residue_data)

parseFile(self, file)

renumberAtoms(self)

splitNucleotideChain(self, number, position)

splitPeptideChain(self, number, position)

writeToFile(self, file)

getitem(self, item)
(Indexing operator)

init(self, filename, model=0, alternate_code='A')
(Constructor)

len(self)
(Length operator)

repr(self)
(Representation operator)