Package schrodinger :: Module structure :: Class _Chain

Class _Chain

     object --+    
              |    
_AtomCollection --+
                  |
                 _Chain

A class used to return chain information when iterating over chains in a Structure object.

Important methods include extractStructure and getAtomIndices. The atom attribute can be used to iterate over all atoms in the molecule, and the number of atoms can be determined via len(molecule.atom).

The residue iterator allows for iteration over residues of the chain, returning _Residue instances.

Instance Methods

[hide private]

__init__(self, st, chain, atoms)
Initialize the Chain object.

_getChainResidueIterator(self)

_getChainName(self)

_setChainName(self, newname)

__str__(self)
Return a string representation - consistent with other structure.py code.

applyStyle(self, atoms=3, bonds=3)
Applies the given display styles to the atoms and bonds of the chain.

Inherited from _AtomCollection: __eq__, __hash__, __len__, extractStructure, getAtomIndices, getAtomList

Inherited from object: __delattr__, __format__, __getattribute__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties

[hide private]

residue
Returns residue iterator for all residues in the chain

name
Chain name

Inherited from _AtomCollection: atom, structure, temperature_factor

Inherited from object: __class__

Method Details

[hide private]

init(self, st, chain, atoms)
(Constructor)

Initialize the Chain object.

Overrides: object.__init__

str(self)
(Informal representation operator)

Return a string representation - consistent with other structure.py code.

Overrides: object.__str__

applyStyle(self, atoms=3, bonds=3)

Applies the given display styles to the atoms and bonds of the chain.

Parameters:

atoms (int) - display style for atoms given by structure module constants ATOM_NOSTYLE, ATOM_CIRCLE, ATOM_CPK, ATOM_BALLNSTICK. Default is ATOM_BALLNSTICK.
atoms (int) - display style for bonds given by structure module constants BOND_NOSTYLE, BOND_WIRE, BOND_TUBE, BOND_BALLNSTICK. Default is BOND_BALLNSTICK.
bonds (int)

Property Details

[hide private]

residue

Returns residue iterator for all residues in the chain

Get Method:: _getChainResidueIterator(self)

name

Chain name

Get Method:: _getChainName(self)
Set Method:: _setChainName(self, newname)

Class _Chain

__init__(self, st, chain, atoms) (Constructor)

__str__(self) (Informal representation operator)

applyStyle(self, atoms=3, bonds=3)

residue

name

init(self, st, chain, atoms)
(Constructor)

str(self)
(Informal representation operator)