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.

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” }