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

Known Subclasses:

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
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

__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:

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

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