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

__init__(residue)	Constructor.
charge([property_map, is_lambda1])	Return the charge.
coordinates([property_map])	Return the coordinates of the atoms in the residue.
copy()	Return a copy of this object.
getAtoms()	Return a list containing all of the atoms in the residue.
getAxisAlignedBoundingBox([property_map])	Get the axis-aligned bounding box enclosing the object.
index()	Return the index of the residue.
moleculeNumber()	Return the number of the molecule to which this residue belongs.
nAtoms()	Return the number of atoms in the residue.
name()	Return the name of the residue.
save(filebase)	Stream a wrapped Sire object to file.
search(query[, property_map])	Search the residue for atoms and residues.
smiles()	Return the SMILES string representation of this object.
toMolecule()	Convert a single Residue 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 atoms in the residue.

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 atoms in the residue.

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

getAtoms()

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

Returns:

atoms – The list of atoms in the residue.

Return type:

[Atoms]

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

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.

search(query, property_map={})

Search the residue for atoms and residues.

Parameters:

• query (str) – The search query.

• 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:

results – A list of objects matching the search query.

Return type:

[Atom]

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")

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 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” }