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.
save(filebase)	Stream a wrapped Sire object to file.
smiles()	Return the SMILES string representation of this object.
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:

object – 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

save(filebase)

Stream a wrapped Sire object to file.

Parameters:

• sire_object (System) – A wrapped Sire object.

• filebase (str) – The base name of the binary output file.

smiles()

Return the SMILES string representation of this object.

Returns:

smiles – The SMILES string representation of the object(s).

Return type:

str, [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” }