BioSimSpace._SireWrappers.Molecule¶

class BioSimSpace._SireWrappers.Molecule(molecule)

A container class for storing a molecule.

__init__(molecule)

Constructor.

Parameters

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

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). __gt__ Return self>value. __hash__() Hash operator. __init__(molecule) Constructor. __init_subclass__ This method is called when a class is subclassed. __le__ Return self<=value. __lt__ Return self

Attributes

 __dict__ __doc__ __module__ __weakref__ list of weak references to the object (if defined)
charge(property_map={}, is_lambda1=False)

Return the 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 object is peturbable.

Returns

charge – The 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
getAtoms()

Return a list containing the atoms in the molecule.

Returns

atoms – The list of atoms in the molecule.

Return type
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.

getResidues()

Return a list containing the residues in the molecule.

Returns

residues – The list of residues in the molecule.

Return type
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

number()

Return the number of the molecule. Each molecule has a unique identification number.

Returns

mol_num – The unique number of the molecule.

Return type

int

search(query)

Search the molecule 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

Examples

Search for all residues named ALA.

>>> result = molecule.search("resname ALA")


Search for all oxygen or hydrogen atoms.

>>> result = molecule.search("element oxygen or element hydrogen")


Search for atom index 23.

>>> result = molecule.search("atomidx 23")

toSystem()

Convert a single Molecule to a System.

Returns

system

Return type

System

translate(vector, property_map={})

Translate the object.

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” }