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

`__init__`(molecule)	Constructor.
`charge`([property_map, is_lambda1])	Return the charge.
`coordinates`([property_map])	Return the coordinates of the atoms in the molecule.
`copy`()	Return a copy of this object.
`getAtoms`()	Return a list containing the atoms in the molecule.
`getAxisAlignedBoundingBox`([property_map])	Get the axis-aligned bounding box enclosing the object.
`getResidues`()	Return a list containing the residues in the molecule.
`isAmberWater`()	Whether this is an AMBER format water molecule.
`isGromacsWater`()	Whether this is a GROMACS format water molecule.
`isMerged`()	Whether this molecule has been merged with another.
`isWater`()	Whether this is a water molecule.
`makeCompatibleWith`(molecule[, property_map, …])	Make this molecule compatible with passed one, i.e.
`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.
`number`()	Return the number of the molecule.
`search`(query)	Search the molecule for atoms and residues.
`toSystem`()	Convert a single Molecule to a System.
`translate`(vector[, property_map])	Translate the object.

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

coordinates(property_map={})¶

Return the coordinates of the atoms in the molecule.

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: [coordinates] – The coordinates of the atoms in the molecule.
Return type: [class:Coordinate]

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: Atom, Residue, Molecule, Molecules, System

getAtoms()¶

Return a list containing the atoms in the molecule.

Returns: atoms – The list of atoms in the molecule.
Return type: [Atom]

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: [Residue]

isAmberWater()¶

Whether this is an AMBER format water molecule.

Returns: is_amber_water – Whether this molecule is an AMBER format water.
Return type: bool

isGromacsWater()¶

Whether this is a GROMACS format water molecule.

Returns: is_gromacs_water – Whether this molecule is a GROMACS format water.
Return type: bool

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

makeCompatibleWith(molecule, property_map={}, overwrite=True, rename_atoms=False, verbose=False)¶

Make this molecule compatible with passed one, i.e. match atoms and add all additional properties from the passed molecule while preserving the topology and naming/numbering convention of this molecule.

Parameters

molecule (Sire.Mol.Molecule, Molecule, Sire.System.System, System) – The molecule, or system of molecules, to match with.
property_map (dict) – A map between property names and user supplied names.
overwrite (bool) – Whether to overwrite any duplicate properties.
rename_atoms (bool) – Whether to rename atoms if they have changed.
verbose (bool) – Whether to report status updates to stdout.

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: [Atom, Residue, …]

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” }