1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
Overview
========
Python implementations of the `MolSSI QCSchema <https://github.com/MolSSI/QCSchema>`_
are available within QCElemental. These models use `Pydantic <https://pydantic-docs.helpmanual.io>`_
as their base to provide serialization, validation, and manipluation.
Basics
--------
Model creation occurs with a ``kwargs`` constructor as shown by equivalent operations below:
.. code-block:: python
>>> mol = qcel.models.Molecule(symbols=["He"], geometry=[0, 0, 0])
>>> mol = qcel.models.Molecule(**{"symbols":["He"], "geometry": [0, 0, 0]})
A list of all available fields can be found by querying the ``fields`` attribute:
.. code-block:: python
>>> mol.fields.keys()
dict_keys(['symbols', 'geometry', ..., 'id', 'extras'])
These attributes can be accessed as shown:
.. code-block:: python
>>> mol.symbols
['He']
Note that these models are typically immutable:
.. code-block:: python
>>> mol.symbols = ["Ne"]
TypeError: "Molecule" is immutable and does not support item assignment
To update or alter a model the ``copy`` command can be used with the ``update`` kwargs:
.. code-block:: python
>>> mol.copy(update={"symbols": ["Ne"]})
< Geometry (in Angstrom), charge = 0.0, multiplicity = 1:
Center X Y Z
------------ ----------------- ----------------- -----------------
Ne 0.000000000000 0.000000000000 0.000000000000
>
Serialization
-------------
All models can be serialized back to their dictionary counterparts through the ``dict`` function:
.. code-block:: python
>>> mol.dict()
{'symbols': ['He'], 'geometry': array([[0., 0., 0.]])}
JSON representations are supported out of the box for all models:
.. code-block:: python
>>> mol.json()
'{"symbols": ["He"], "geometry": [0.0, 0.0, 0.0]}'
Raw JSON can also be parsed back into a model:
.. code-block:: python
>>> mol.parse_raw(mol.json())
< Geometry (in Angstrom), charge = 0.0, multiplicity = 1:
Center X Y Z
------------ ----------------- ----------------- -----------------
He 0.000000000000 0.000000000000 0.000000000000
>
The standard ``dict`` operation returns all internal representations which may be classes or other complex structures.
To return a JSON-like dictionary the ``dict`` function can be used:
.. code-block:: python
>>> mol.dict(encoding='json')
{'symbols': ['He'], 'geometry': [0.0, 0.0, 0.0]}
|
