Package schrodinger :: Module structure :: Class _Chain

Class _Chain

object --+
         |
        _Chain

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

Important methods include extractStructure and getAtomList. 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.

_getAtomIterator(self)

_getChainResidueIterator(self)

_getChainName(self)

_setChainName(self, newname)

_getChainBF(self)

getAtomList(self)
Return a list of atom indices in this chain.

extractStructure(self, copy_props=False)
Return a new Structure containing only this chain.

__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 object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties

[hide private]

atom
Returns an atom iterator for all atoms in the chain

residue
Returns residue iterator for all residues in the chain

name
Chain name

temperature_factor
Chain B (temperature) factor

Inherited from object: __class__

Method Details

[hide private]

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

Initialize the Chain object.

Overrides: object.__init__

extractStructure(self, copy_props=False)

Return a new Structure containing only this chain. Structure properties, including the title, are inherited only if copy_props is set to True.

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]

atom

Returns an atom iterator for all atoms in the chain

Get Method:: _getAtomIterator(self)

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)

temperature_factor

Chain B (temperature) factor

Get Method:: _getChainBF(self)

Class _Chain

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

extractStructure(self, copy_props=False)

__str__(self) (Informal representation operator)

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

atom

residue

name

temperature_factor

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

str(self)
(Informal representation operator)