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Defines classes which represent bonds.

class Bond(atom1, atom2, order, periodicity=(0, 0, 0), **kwargs)¶

Bases: object

Represents an atomic bond.

atom1¶

The first atom in the bond.

Type: Atom

atom2¶

The second atom in the bond.

Type: Atom

order¶

The bond order.

Type: int

periodicity¶

The directions across which the bond is periodic. For example, (1, 0, -1) means that when going from atom1 to atom2 the bond is periodic across the x axis in the positive direction, is not periodic across the y axis and is periodic across the z axis in the negative direction.

Type: tuple of int

Examples

Adding additional attributes.

Each bond can be given additional attributes. For example

import stk

bond1 = stk.Bond(stk.H(0), stk.H(1), 1)
bond1.attr1 = 12.2
bond1.attr2 = 'something'

A Bond can also initialized with additional attributes directly

bond2 = stk.Bond(
    atom1=stk.C(2),
    atom2=stk.C(3),
    order=1,
    attr1=123,
    attr2='hi'
)

bond2.attr1  # Holds 123.
bond2.attr2  # Holds 'hi'.

Printing

To print a brief summary of a bond you can run

# Prints Bond(C(2), C(3), 1).
print(bond2)

To print a complete description of a bond, including additional attributes, you can run

# Prints Bond(C(2), C(3), 1, attr1=123, attr2='hi')
print(repr(bond2))

If the atoms have additional attributes, they will be printed too

# Add a custom attribute to an atom.
bond2.atom1.alpha = 1

# Prints Bond(C(2, alpha=1), C(3), 1, attr1=123, attr2='hi')
print(repr(bond2))

If private attributes were added to a bond, they will not be printed

bond2._attr3 = 'private'
# Prints Bond(C(2, alpha=1), C(3), 1, attr1=123, attr2='hi')
print(repr(bond2))

Methods

`clone`(self[, atom_map])	Return a clone.
`is_periodic`(self)	Return `True` if the bond is periodic.

__init__(self, atom1, atom2, order, periodicity=(0, 0, 0), **kwargs)¶

Initialize a Bond.

atom1

The first atom in the bond.

Type: Atom

atom2

The second atom in the bond.

Type: Atom

order

The bond order.

Type: int

periodicity

The directions across which the bond is periodic. For example, (1, 0, -1) means that when going from atom1 to atom2 the bond is periodic across the x axis in the positive direction, is not periodic across the y axis and is periodic across the z axis in the negative direction.

Type: tuple of int, optional

**kwargs

Additional attributes to be added to the bond.

Type: object, optional

clone(self, atom_map=None)¶

Return a clone.

Private attributes are not passed to the clone.

Parameters: atom_map (dict, optional) – If the clone should hold different Atom instances, then a dict should be provided, which maps atoms in the current Bond to the atoms which should be used in the clone. Only atoms which need to be remapped need to be present in the atom_map.
Returns: The clone.
Return type: Bond

Examples

import stk

c0 = stk.C(0)
c1 = stk.C(1)
bond = stk.Bond(c0, c1, 1, custom_attr=12, _private_attr=1)

# bond_clone holds c0 and c1 in its atom1 and atom2
# attributes, respectively. It also has a custom_attr
# with a value of 12 but it does not have a _private_attr
# attribute.
bond_clone = bond.clone()

It is possible to make sure that the clone holds different atoms

li2 = stk.Li(2)
n3 = stk.N(3)

# clone2 is also a clone, except that it holds
# li2 in the atom2 attribute. Its atom1 attribute still
# holds c0.
clone2 = bond.clone(atom_map={
    c1: li2
})

# clone3 is also a clone, except that it holds n3 and
# li2 in its atom1 and atom2 attributes, respectively.
clone3 = bond.clone(atom_map={
    c0: n3,
    c1: li2
})

is_periodic(self)¶

Return True if the bond is periodic.

Returns: True if the bond is periodic.
Return type: bool