BioSimSpace._SireWrappers.Bond

class BioSimSpace._SireWrappers.Bond(bond)

A class for storing a bond.

__init__(bond)

Constructor.

Parameters

bond (Sire.MM.Bond, Bond) – A Sire or BioSimSpace Bond object.

Methods

__init__(bond)

Constructor.

atom0()

Return the first atom in the bond.

atom1()

Return the first atom in the bond.

charge([property_map, is_lambda1])

Return the charge.

coordinates([property_map])

Return the coordinates of the atoms in the bond.

copy()

Return a copy of this object.

energy()

Return the energy of the bond.

getAtoms()

Return a list containing all of the atoms in the bond.

getAxisAlignedBoundingBox([property_map])

Get the axis-aligned bounding box enclosing the object.

length()

Return the length of the bond

moleculeNumber()

Return the number of the molecule to which this bond belongs.

nAtoms()

Return the number of atoms in the bond.

name()

Return the name of the bond.

search(query[, property_map])

Search the bond for atoms and bonds.

toMolecule()

Convert a single Residue to a Molecule.

translate(vector[, property_map])

Translate the object.

atom0()

Return the first atom in the bond.

Returns

atom – The atom

Return type

Atom

atom1()

Return the first atom in the bond.

Returns

atom – The atom

Return type

Atom

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 bond.

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 bond.

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

object – A copy of the object.

Return type

Atom, Residue, Molecule, Molecules, System

energy()

Return the energy of the bond. This assumes that an energy expression has been assigned to this bond.

Returns

energy – The energy of the bond

Return type

Energy

getAtoms()

Return a list containing all of the atoms in the bond.

Returns

atoms – The list of atoms in the bond.

Return type

[Atoms]

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.

length()

Return the length of the bond

Returns

length – The length of the bond

Return type

Length

moleculeNumber()

Return the number of the molecule to which this bond belongs.

Returns

number – The number of the molecule to which the bond belongs.

Return type

int

nAtoms()

Return the number of atoms in the bond.

Returns

num_atoms – The number of atoms in the system.

Return type

int

name()

Return the name of the bond.

Returns

name – The name of the bond.

Return type

str

search(query, property_map={})

Search the bond for atoms and bonds.

Parameters
  • query (str) – The search query.

  • 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

results – A list of objects matching the search query.

Return type

[Atom]

Examples

Search for all oxygen or hydrogen atoms.

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

Search for atom index 23.

>>> result = bond.search("atomidx 23")
toMolecule()

Convert a single Residue to a Molecule.

Returns

system

Return type

Molecule

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” }