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, Sire.Mol.SelectorMol, 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.
smiles()	Return the SMILES string representation of this object.
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")

smiles()

Return the SMILES string representation of this object.

Returns:

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

Return type:

str, [str]

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” }