BioSimSpace._SireWrappers.Atom

class BioSimSpace._SireWrappers.Atom(atom)

A class for storing an atom.

__init__(atom)

Constructor.

Parameters

atom (Sire.Mol.Atom, Atom) – A Sire or BioSimSpace Atom object.

Methods

__init__(atom)

Constructor.

charge([property_map, is_lambda1])

Return the charge.

coordinates([property_map])

Return the coordinates of the atom.

copy()

Return a copy of this object.

element([property_map])

Return the element.

getAxisAlignedBoundingBox([property_map])

Get the axis-aligned bounding box enclosing the object.

index()

Return the index of the atom.

moleculeNumber()

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

name()

Return the name of the atom.

toMolecule()

Convert a single Atom to a Molecule.

translate(vector[, property_map])

Translate the object.

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

coordinates(property_map={})

Return the coordinates of the atom.

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

coordinates – The coordinates of the atom.

Return type

class:Coordinate

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

Atom, Residue, Molecule, Molecules, System

element(property_map={})

Return the element.

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

element – The element.

Return type

str

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 atom.

Returns

index – The index of the atom.

Return type

int

moleculeNumber()

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

Returns

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

Return type

int

name()

Return the name of the atom.

Returns

name – The name of the atom.

Return type

str

toMolecule()

Convert a single Atom 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” }