Atom

class Atom(id, atomic_number, charge=0)[source]

Bases: object

An abstract base class for atoms.

A subclass is made for each element. The name of each subclass is the periodic table symbol of that element.

Atoms of a particular element can be made with this class or with the subclass representing that element.

Examples

Initialization.

Initialization of an Atom can happen in one of two ways. The atom can be initialized through the Atom class or through the class representing the element.

import stk

# h0 is an instance of the H class.
h0 = stk.Atom(id=0, atomic_number=1)

# h1 is also an instance of the H class.
h1 = stk.H(id=1)

When the class corresponding to the element is used directly, the atomic_number is not provided. Here are a few more examples.

# Both he0 and he1 are instances of the He class.
he0 = stk.Atom(id=2, atomic_number=2)
he1 = stk.He(id=3)

# Both c0 and c1 are instances of the
# C class.
c0 = stk.Atom(id=4, atomic_number=6)
c1 = stk.C(id=5)

Methods

`clone`()	Return a clone.
`get_atomic_number`()	Get the atomic number of the atom.
`get_charge`()	Get the charge of the atom.
`get_id`()	Get the id of the atom.
`with_id`(id)	Get a clone but with a different id.

__init__(id, atomic_number, charge=0)[source]

Initialize an Atom.

Parameters

id (int) – The id of the atom.
atomic_number (int) – The atomic number.
charge (int) – The formal charge.

clone()[source]

Return a clone.

Return type: Atom
Returns: The clone.

get_atomic_number()[source]

Get the atomic number of the atom.

Return type: int
Returns: The atomic number.

get_charge()[source]

Get the charge of the atom.

Return type: int
Returns: The charge.

get_id()[source]

Get the id of the atom.

Return type: int
Returns: The id.

with_id(id)[source]

Get a clone but with a different id.

Parameters: id (int) – The id of the clone.
Return type: Atom
Returns: A clone with a new id.