BioSimSpace._SireWrappers.Molecules¶

class BioSimSpace._SireWrappers.Molecules(molecules)¶

An immutable container class for storing molecules.

__init__(molecules)¶

Constructor.

Parameters: molecules (Sire.Mol.MoleculeGroup, Sire.System.System, System [Molecule]) – A Sire Molecues object, a Sire or BioSimSpace System object, or a list of BioSimSpace Molecule objects.

Methods

`__init__`(molecules)	Constructor.
`charge`([property_map, is_lambda1])	Return the total molecular charge.
`copy`()	Return a copy of this object.
`getAxisAlignedBoundingBox`([property_map])	Get the axis-aligned bounding box enclosing the object.
`getMolecule`(index)	Return the molecule at the given index.
`nMolecules`()	Return the number of molecules in the system.
`search`(query)	Search the molecules for atoms and residues.
`toSystem`()	Convert to a System object.
`translate`(vector[, property_map])	Translate each molecule in the container.

charge(property_map={}, is_lambda1=False)¶

Return the total molecular 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 a molecule is merged.

Returns

charge – The molecular 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: object – A copy of the object.
Return type: Atom, Residue, Molecule, Molecules, System

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.

getMolecule(index)¶

Return the molecule at the given index.

Parameters: index (int) – The index of the molecule.
Returns: molecule – The requested molecule.
Return type: Molecule

nMolecules()¶

Return the number of molecules in the system.

Returns: num_molecules – The number of molecules in the system.
Return type: int

search(query)¶

Search the molecules for atoms and residues. Search results will be reduced to their minimal representation, i.e. a residue containing a single atom will be returned as a atom.

Parameters: query (str) – The search query.
Returns: results – A list of objects matching the search query.
Return type: [Atom, Residue, …]

Examples

Search for all residues named ALA.

>>> result = molecules.search("resname ALA")

Search for all oxygen or hydrogen atoms.

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

Search for atom index 23.

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

toSystem()¶

Convert to a System object.

Returns: system
Return type: System

translate(vector, property_map={})¶

Translate each molecule in the container.

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” }