BioSimSpace._SireWrappers.Molecule

class BioSimSpace._SireWrappers.Molecule(molecule)

A container class for storing a molecule.

__init__(molecule)

Constructor.

Parameters

molecule (Sire.Mol.Molecule, Molecule Molecule) – A Sire or BioSimSpace Molecule object.

Methods

__init__(molecule)

Constructor.

charge([property_map, is_lambda1])

Return the total molecular charge.

copy()

Create a copy of this molecule.

isMerged()

Whether this molecule has been merged with another.

isWater()

Whether this is a water molecule.

molecule0()

Return the component of the merged molecule at lambda = 0.

molecule1()

Return the component of the merged molecule at lambda = 1.

nAtoms()

Return the number of atoms in the molecule.

nChains()

Return the number of chains in the molecule.

nResidues()

Return the number of residues in the molecule.

toSystem()

Convert a single Molecule to a System.

translate(vector[, property_map])

Translate the molecule.

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()

Create a copy of this molecule.

moleculeMolecule

A copy of the molecule.

isMerged()

Whether this molecule has been merged with another.

Returns

is_merged – Whether the molecule has been merged.

Return type

bool

isWater()

Whether this is a water molecule.

Returns

is_water – Whether this is a water molecule.

Return type

bool

molecule0()

Return the component of the merged molecule at lambda = 0.

Returns

molecule – The component of the merged molecule at lambda = 0. Returns None if this isn’t a merged molecule.

Return type

Molecule

molecule1()

Return the component of the merged molecule at lambda = 1.

Returns

molecule – The component of the merged molecule at lambda = 1. Returns None if this isn’t a merged molecule.

Return type

Molecule

nAtoms()

Return the number of atoms in the molecule.

Returns

num_atoms – The number of atoms in the molecule.

Return type

int

nChains()

Return the number of chains in the molecule.

Returns

num_chains – The number of chains in the molecule.

Return type

int

nResidues()

Return the number of residues in the molecule.

Returns

num_residues – The number of residues in the molecule.

Return type

int

toSystem()

Convert a single Molecule to a System.

Returns

system

Return type

System

translate(vector, property_map={})

Translate the molecule.

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” }