# BioSimSpace._SireWrappers.Residue¶

class BioSimSpace._SireWrappers.Residue(residue)

A class for storing a residue.

__init__(residue)

Constructor.

Parameters

residue (Sire.Mol.Residue, Residue) – A Sire or BioSimSpace Residue object.

Methods

 __delattr__ Implement delattr(self, name). __dir__ Default dir() implementation. __eq__(other) Equals to operator. __format__ Default object formatter. __ge__ Return self>=value. __getattribute__ Return getattr(self, name). __getitem__(key) Get an atom from the residue. __gt__ Return self>value. __hash__() Hash operator. __init__(residue) Constructor. __init_subclass__ This method is called when a class is subclassed. __iter__() An iterator for the object. __le__ Return self<=value. __len__() Return the number of atoms in the residue. __lt__ Return self

Attributes

 __dict__ __doc__ __module__ __weakref__ list of weak references to the object (if defined)
charge(property_map={}, is_lambda1=False)

Return the charge.

Parameters
• property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

• is_lambda1 (bool) – Whether to use the charge at lambda = 1 if the object is peturbable.

Returns

charge – The charge.

Return type

Charge

copy()

Return a copy of this object. The return type is same as the object on which copy is called.

Returns

system – A copy of the object.

Return type
getAtoms()

Return a list containing all of the atoms in the residue.

Returns

atoms – The list of atoms in the residue.

Return type
getAxisAlignedBoundingBox(property_map={})

Get the axis-aligned bounding box enclosing the object.

Parameters

property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

Returns

• box_min ([Length]) – The minimum coordinates of the axis-aligned bounding box in each dimension.

• box_max ([Length]) – The minimum coordinates of the axis-aligned bounding box in each dimension.

index()

Return the index of the residue.

Returns

index – The index of the residue.

Return type

int

moleculeNumber()

Return the number of the molecule to which this residue belongs.

Returns

number – The number of the molecule to which the residue belongs.

Return type

int

nAtoms()

Return the number of atoms in the residue.

Returns

num_atoms – The number of atoms in the system.

Return type

int

name()

Return the name of the residue.

Returns

name – The name of the residue.

Return type

str

search(query)

Search the residue for atoms and residues.

Parameters

query (str) – The search query.

Returns

results – A list of objects matching the search query.

Return type

Examples

Search for all oxygen or hydrogen atoms.

>>> result = residue.search("element oxygen or element hydrogen")


Search for atom index 23.

>>> result = residue.search("atomidx 23")

toMolecule()

Convert a single Residue to a Molecule.

Returns

system

Return type

Molecule

translate(vector, property_map={})

Translate the object.

Parameters
• vector ([Length]) – The translation vector in Angstroms.

• property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }