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.Molecule, Molecule, [Molecule]) – A Sire or BioSimSpace System object, a Sire or BioSimSpace Molecule object, or a list of BioSimSpace molecule objects.

Methods

__init__(system) Constructor.
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 system.
fileFormat([property_map]) Return the file formats associated with the system.
getBox([property_map]) Get the size of the periodic simulation box.
getMolWithResName(resname) Return the molecule containing the given residue.
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.
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.
addMolecules(molecules)

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

Parameters:molecules (Molecule, [Molecule]) – A Molecule, or list of Molecule objects.
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 if the molecule is merged.
Returns:

charge – The molecular charge.

Return type:

Charge

copy()

Return a copy of this system.

Returns:system – A copy of the system.
Return type:System
fileFormat(property_map={})

Return the file formats associated with the system.

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:format – The file formats associated with the system.
Return type:str
getBox(property_map={})

Get the size of the periodic simulation box.

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_size – The size of the box in each dimension.
Return type:[Length]
getMolWithResName(resname)

Return the molecule containing the given residue.

Parameters:resname (str) – The name of a residue unique to the molecule.
Returns:molecule – The matching molecule.
Return type:Molecule
getMolecules(group='all')

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

Parameters:group (str) – The name of the molecule group.
Returns:molecules – The list of molecules in the group.
Return type:[Molecule]
getPerturbableMolecules()

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

Returns:molecules – A list of perturbable molecules.
Return type:[Molecule]
getWaterMolecules()

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

Returns:molecules – A list of water molecule objects.
Return type:[Molecule]
nAtoms()

Return the number of atoms in the system.

Returns:num_atoms – The number of atoms in the system.
Return type:int
nChains()

Return the number of chains in the system.

Returns:num_chains – The number of chains in the system.
Return type:int
nMolecules()

Return the number of molecules in the system.

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

Return the number of perturbable molecules in the system.

Returns:num_perturbable – The number of perturbable molecules in the system.
Return type:int
nResidues()

Return the number of residues in the system.

Returns:num_residues – The number of residues in the system.
Return type:int
nWaterMolecules()

Return the number of water molecules in the system.

Returns:num_waters – The number of water molecules in the system.
Return type:int
removeMolecules(molecules)

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

Parameters:molecules (Molecule, [Molecule]) – A Molecule, or list of Molecule objects.
removeWaterMolecules()

Remove all of the water molecules from the system.

setBox(size, property_map={})

Set the size of the periodic simulation box.

Parameters:
  • size ([Length]) – The size of the box in each dimension.
  • 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” }
translate(vector, property_map={})

Translate the system.

Parameters:
  • vector ([Length]) – The translation vector.
  • 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” }
updateMolecules(molecules)

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

Parameters:molecules (Molecule, [Molecule]) – A Molecule, or list of Molecule objects.