BioSimSpace._SireWrappers.System

class BioSimSpace._SireWrappers.System(system)

A container class for storing molecular systems.

__init__(system)

Constructor.

Parameters

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

Methods

__add__(other)

Addition operator.

__delattr__(name, /)

Implement delattr(self, name).

__dir__()

Default dir() implementation.

__eq__(other)

Equals to operator.

__format__(format_spec, /)

Default object formatter.

__ge__(value, /)

Return self>=value.

__getattribute__(name, /)

Return getattr(self, name).

__getitem__(key)

Get a molecule from the system.

__gt__(value, /)

Return self>value.

__hash__()

Hash operator.

__init__(system)

Constructor.

__init_subclass__

This method is called when a class is subclassed.

__iter__()

An iterator for the object.

__le__(value, /)

Return self<=value.

__len__()

Return the number of molecules in the system.

__lt__(value, /)

Return self<value.

__ne__(other)

Not equals to operator.

__new__(**kwargs)

Create and return a new object.

__next__()

An iterator for the object.

__reduce__()

Helper for pickle.

__reduce_ex__(protocol, /)

Helper for pickle.

__repr__()

Return a string showing how to instantiate the object.

__setattr__(name, value, /)

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.

__sub__(other)

Subtraction operator.

__subclasshook__

Abstract classes can override this to customize issubclass().

_createSireSystem(molecules)

Create a Sire system from a Molecules object or a list of Molecule objects.

_getAABox([property_map])

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

_getSireObject()

Return the underlying Sire object.

_renumberMolecules(molecules[, is_rebuild])

Helper function to renumber the molecules to be consistent with the system.

_reset_mappings()

Internal function to reset index mapping dictionaries.

_updateCoordinates(system[, property_map0, …])

Update the coordinates of atoms in the system.

addMolecules(molecules)

Add a molecule, or list of molecules to the system.

charge([property_map, is_lambda1])

Return the total molecular charge.

copy()

Return a copy of this object.

fileFormat([property_map])

Return the file formats associated with the system.

getAxisAlignedBoundingBox([property_map])

Get the axis-aligned bounding box enclosing the object.

getBox([property_map])

Get the size of the periodic simulation box.

getIndex(item)

Convert indices of atoms and residues to their absolute values in this system.

getMolecule(index)

Return the molecule at the given index.

getMolecules([group])

Return a list containing all of the molecules in the specified group.

getPerturbableMolecules()

Return a list containing all of the perturbable molecules in the system.

getWaterMolecules()

Return a list containing all of the water molecules in the system.

nAtoms()

Return the number of atoms in the system.

nChains()

Return the number of chains in the system.

nMolecules()

Return the number of molecules in the system.

nPerturbableMolecules()

Return the number of perturbable molecules in the system.

nResidues()

Return the number of residues in the system.

nWaterMolecules()

Return the number of water molecules in the system.

removeMolecules(molecules)

Remove a molecule, or list of molecules from the system.

removeWaterMolecules()

Remove all of the water molecules from the system.

search(query)

Search the system for atoms, residues, and molecules.

setBox(size[, property_map])

Set the size of the periodic simulation box.

translate(vector[, property_map])

Translate the system.

updateMolecules(molecules)

Update a molecule, or list of molecules in the system.

Attributes

__dict__

__doc__

__module__

__weakref__

list of weak references to the object (if defined)