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

Known Subclasses:

Atom group (residue or molecule) in a PDB file

This is an abstract base class. Instances can be created using one of the subclasses (Molecule, AminoAcidResidue, NucleotideResidue).

Group objects permit iteration over atoms with for-loops, as well as extraction of atoms by indexing with the atom name.

Instance Methods
 
__getitem__(self, item)
 
__init__(self, name, atoms=None, number=None)
 
__len__(self)
 
__repr__(self)
 
__str__(self)
 
addAtom(self, atom)
Add an atom to the group
 
changeName(self, name)
Set the PDB residue name
 
deleteAtom(self, atom)
Remove an atom from the group
 
deleteHydrogens(self)
Remove all hydrogen atoms of the group
 
isCompatible(self, residue_data)
 
writeToFile(self, file)
Write the group to a file
Method Details

__getitem__(self, item)
(Indexing operator)

 
Parameters:
  • item (int or str) - an integer index or an atom name

__init__(self, name, atoms=None, number=None)
(Constructor)

 
Parameters:
  • name (str) - the name of the group
  • atoms (list or NoneType) - a list of atoms (or None for no atoms)
  • number (int or NoneType) - the PDB residue number (or None)

addAtom(self, atom)

 

Add an atom to the group

Parameters:
  • atom (Atom) - the atom

changeName(self, name)

 

Set the PDB residue name

Parameters:
  • name (str) - the new name

deleteAtom(self, atom)

 

Remove an atom from the group

Parameters:
  • atom (Atom) - the atom to be removed
Raises:
  • KeyError - if the atom is not part of the group

writeToFile(self, file)

 

Write the group to a file

Parameters:
  • file (PDBFile or str) - a PDBFile object or a file name

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