BioSimSpace._SireWrappers.Molecules

class BioSimSpace._SireWrappers.Molecules(molecules)

An immutable container class for storing molecules.

__init__(molecules)

Constructor.

Parameters

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

Methods

__add__(other)

Addition operator.

__delattr__

Implement delattr(self, name).

__dir__

Default dir() implementation.

__eq__(other)

Equals to operator.

__format__

Default object formatter.

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(key)

Get a molecule from the container.

__gt__

Return self>value.

__hash__()

Hash operator.

__init__(molecules)

Constructor.

__init_subclass__

This method is called when a class is subclassed.

__iter__()

An iterator for the object.

__le__

Return self<=value.

__len__()

Return the size of the container.

__lt__

Return self<value.

__ne__(other)

Not equals to operator.

__new__

Create and return a new object.

__next__()

An iterator for the object.

__reduce__

Helper for pickle.

__reduce_ex__

Helper for pickle.

__repr__()

Return a string showing how to instantiate the object.

__setattr__

Implement setattr(self, name, value).

__setitem__(key, value)

Set a molecule in the container.

__sizeof__

Size of object in memory, in bytes.

__str__()

Return a human readable string representation of the object.

__subclasshook__

Abstract classes can override this to customize issubclass().

_getAABox([property_map])

Get the axis-aligned bounding box for the molecular system.

_getSireObject()

Return the underlying Sire object.

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.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)

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

system – 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” }