Package Scientific :: Package IO :: Module PDB :: Class Chain

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Class Chain

Known Subclasses:: DummyChain, NucleotideChain, PeptideChain

Chain of PDB residues

This is an abstract base class. Instances can be created using one of the subclasses (PeptideChain, NucleotideChain).

Chain objects respond to len() and return their residues by indexing with integers.

Instance Methods

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AminoAcidResidue or NucleotideResidue __getitem__(self, index)
Returns the residue corresponding to the index

PeptideChain or NucleotideChain __getslice__(self, i1, i2)
Returns the subchain from i1 to i2

__init__(self, residues=None, chain_id=None, segment_id=None)

int __len__(self)
Returns the number of residues in the chain

addResidue(self, residue)
Add a residue at the end of the chain

deleteHydrogens(self)
Remove all hydrogen atoms in the chain

removeResidues(self, first, last)
Remove residues in a given index range.

list of str sequence(self)
Returns the list of residue names

writeToFile(self, file)
Write the chain to a file

Method Details

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getitem(self, index)
(Indexing operator)

Parameters:

index (int) - an index into the chain

Returns: AminoAcidResidue or NucleotideResidue: the residue corresponding to the index

Raises:

IndexError - if index exceeds the chain length

getslice(self, i1, i2)
(Slicling operator)

Parameters:

i1 (int) - in index into the chain
i2 - in index into the chain @type i12 int

Returns: PeptideChain or NucleotideChain: the subchain from i1 to i2

init(self, residues=None, chain_id=None, segment_id=None)
(Constructor)

Parameters:

residues (list or NoneType) - a list of residue objects, or None meaning that the chain is initially empty
chain_id (str or NoneType) - a one-letter chain identifier or None
segment_id (str or NoneType) - a multi-character segment identifier or None

len(self)
(Length operator)

Returns: int: the number of residues in the chain

addResidue(self, residue)

Add a residue at the end of the chain

Parameters:

residue (AminoAcidResidue or NucleotideResidue) - the residue to be added

deleteHydrogens(self)

Remove all hydrogen atoms in the chain

removeResidues(self, first, last)

Remove residues in a given index range.

Parameters:

first (int) - the index of the first residue to be removed
last (int or NoneType) - the index of the first residue to be kept, or None meaning remove everything to the end of the chain.

sequence(self)

Returns: list of str: the list of residue names

writeToFile(self, file)

Write the chain to a file

Parameters:

file (PDBFile or str) - a PDBFile object or a file name