pymatgen.core.bonds module

This class implements definitions for various kinds of bonds. Typically used in Molecule analysis.

class CovalentBond(site1: pymatgen.core.sites.Site, site2: pymatgen.core.sites.Site)

Bases: object

Defines a covalent bond between two sites.

Initializes a covalent bond between two sites.

Parameters

• site1 (Site) – First site.

• site2 (Site) – Second site.

get_bond_order(tol: float = 0.2, default_bl: Optional[float] = None) → float

The bond order according the distance between the two sites :param tol: Relative tolerance to test.

(1 + tol) * the longest bond distance is considered to be the threshold length for a bond to exist. (1 - tol) * the shortest bond distance is considered to be the shortest possible bond length Defaults to 0.2.

Parameters

default_bl – If a particular type of bond does not exist, use this bond length as a default value (bond order = 1). If None, a ValueError will be thrown.

Returns

Float value of bond order. For example, for C-C bond in benzene, return 1.7.

static is_bonded(site1, site2, tol: float = 0.2, bond_order: Optional[float] = None, default_bl: Optional[float] = None)

Test if two sites are bonded, up to a certain limit. :param site1: First site :type site1: Site :param site2: Second site :type site2: Site :param tol: Relative tolerance to test. Basically, the code

checks if the distance between the sites is less than (1 + tol) * typical bond distances. Defaults to 0.2, i.e., 20% longer.

Parameters

• bond_order – Bond order to test. If None, the code simply checks against all possible bond data. Defaults to None.

• default_bl – If a particular type of bond does not exist, use this bond length. If None, a ValueError will be thrown.

Returns

Boolean indicating whether two sites are bonded.

property length

Length of the bond.

get_bond_length(sp1, sp2, bond_order: float = 1)

Get the bond length between two species.

Parameters

• sp1 (Species) – First specie.

• sp2 (Species) – Second specie.

• bond_order – For species with different possible bond orders, this allows one to obtain the bond length for a particular bond order. For example, to get the C=C bond length instead of the C-C bond length, this should be set to 2. Defaults to 1.

Returns

Bond length in Angstrom. If no data is available, the sum of the atomic radius is used.

get_bond_order(sp1, sp2, dist: float, tol: float = 0.2, default_bl: Optional[float] = None)

Calculate the bond order given the distance of 2 species

Parameters

• sp1 (Species) – First specie.

• sp2 (Species) – Second specie.

• dist – Their distance in angstrom

• tol (float) – Relative tolerance to test. Basically, the code checks if the distance between the sites is larger than (1 + tol) * the longest bond distance or smaller than (1 - tol) * the shortest bond distance to determine if they are bonded or the distance is too short. Defaults to 0.2.

• default_bl – If a particular type of bond does not exist, use this bond length (bond order = 1). If None, a ValueError will be thrown.

Returns

Float value of bond order. For example, for C-C bond in benzene, return 1.7.

obtain_all_bond_lengths(sp1, sp2, default_bl: Optional[float] = None)

Obtain bond lengths for all bond orders from bond length database

Parameters

• sp1 (Species) – First specie.

• sp2 (Species) – Second specie.

• default_bl – If a particular type of bond does not exist, use this bond length as a default value (bond order = 1). If None, a ValueError will be thrown.

Returns

A dict mapping bond order to bond length in angstrom