mstk.topology.Bond

class mstk.topology.Bond(atom1, atom2, order=0)

A bond between two atoms.

Unlike BondTerm in ForceField, the atoms are not sorted in connectivity because the properties of atoms (name, type, etc…) are prone to changing. It’s better to sort them when compare bonds or match force field parameters.

Parameters:

• atom1 (Atom) –

• atom2 (Atom) –

• order (int, Optional) –

atom1

Type:

Atom

atom2

Type:

Atom

order

The integer bond order. See Bond.Order

Type:

int

Methods

__init__(atom1, atom2[, order])
equals(other)	Check if two bonds represent the same connectivity.
evaluate([cell])	Evaluate the length of this bond

Attributes

atoms	The atoms forming this bond
is_aromatic
is_conjugated
is_drude	Whether or not this bond is a Drude dipole bond
is_rotatable
name	Name of this bond
order
rdbond	The rdkit.Chem.Bond object associated with this bond.

class Order

Enumerator of integer bond orders

The bonds in aromatic rings are in kekulized form.

UNSPECIFIED = 0

unspecified bond order

SINGLE = 1

order of single bond

DOUBLE = 2

order of double bond

TRIPLE = 3

order of triple bond

equals(other)

Check if two bonds represent the same connectivity. Return True if they contain the identical atoms, regardless of the sequence and bond order.

Parameters:

other (Bond) –

Returns:

equal

Return type:

bool

property order

property name

Name of this bond

Returns:

name

Return type:

str

property atoms

The atoms forming this bond

Returns:

atoms

Return type:

tuple of Atom

property is_drude

Whether or not this bond is a Drude dipole bond

Returns:

is

Return type:

bool

evaluate(cell=None)

Evaluate the length of this bond

Parameters:

box (UnitCell, Optional) –

Returns:

value

Return type:

float

property rdbond

The rdkit.Chem.Bond object associated with this bond.

Returns:

rdbond

Return type:

rdkit.Chem.Bond

property is_aromatic

property is_conjugated

property is_rotatable