AutoChem

A Package of the AutoMech Suite

Andreas V. Copan, Kevin B. Moore III, Sarah N. Elliott, and Stephen J. Klippenstein

Overview

Autochem is a library of molecular toolkit packages, including automol, phydat, and transformations.

AutoMol

Automol provides the framework for any molecule object used across the AutoMech suite and facilitates the conversion between objects. Some of these objects are internal representations of well known objects in chemistry. Automol, however, also has its own molecular objects like our molecuar graph, which stores connectivity and stereo information. Perhaps the most novel features in automol are its transformation functions on any of these objects. Such tools enable us to search reaction profiles, set up scans along torsional angles, and identify configurations for alternative conformers. Our tutorials and code documentation demonstrate the extensive scope of functions within this toolkit.


SMILES string: 2D representation

Simplified molecular-input line-entry system (SMILES) are a standard convention in large scale chemistry. SMILES strings encode molecular connectivity.

Vinyl Radical (CH2CH)

C=[CH]


InChI string: 2D representation

IUPAC International Chemical Identifiers are also widely used in large scale chemistry. The string encodes atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information in various, and optional, layers.

Vinyl Radical (CH2CH)

InChI=1S/C2H3/c1-2/h1H,2H2


Graph object: 2D representation

The automol graph, designed for the AutoMech suite, gives atoms, their hydrogen valences, and their stereo parities as vertices with the atom connectivies as edges. The graph provides a 2D representation that is transformable and manipulable. For this reason, the graph object is essential to reaction identification. There are two implementations of the graph object, with trivial conversion between the two, with implicit and explicit hydrogen atoms

Vinyl Radical (CH2CH) Internal

Implicit

({ 0: (‘C’, 1, None), 1: (‘C’, 2, None)}, {frozenset({0, 1}): (1, None)})

Explicit

({ 0: (‘C’, 0, None), 1: (‘C’, 0, None), 2: (‘H’, 0, None), 3: (‘H’, 0, None), 4: (‘H’, 0, None)}, { frozenset({0, 1}): (1, None), frozenset({0, 2}): (1, None), frozenset({1, 3}): (1, None), frozenset({1, 4}): (1, None)})

Vinyl Radical (CH2CH) External

Implicit

atoms:

1: {symbol: C, implicit_hydrogen_valence: 1, stereo_parity: null}

2: {symbol: C, implicit_hydrogen_valence: 2, stereo_parity: null}

bonds:

1-2: {order: 1, stereo_parity: null}

Explicit

atoms:

1: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

2: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

3: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

4: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

5: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

bonds:

1-2: {order: 1, stereo_parity: null}

1-3: {order: 1, stereo_parity: null}

2-4: {order: 1, stereo_parity: null}

2-5: {order: 1, stereo_parity: null}


Geometry Object: 3D representation

Our most simple 3D representation of the molecule gives the location of its atoms in Cartesian coordinates. Externally, coordinates are in Angstrom and, internally, coordinates are in Bohr. Automol has simple conversions to/from the 2D descriptors from/to a geometry object using calls to RDkit and OpenBabel.

Vinyl Radical (CH2CH) Internal

((‘C’, (-1.7385058975595666, 0.2715876398092092, 0.7998932295794201)), (‘C’, (0.9772590604406942, 0.0027272925514021072, 0.028477437733657032)), (‘H’, (-3.250682519670039, -0.08885591643834877, -0.5801409688754181)), (‘H’, (2.160193047410571, 1.6990073384324165, -0.20556820450994961)), (‘H’, (1.8517363093783363, -1.8844663543546802, -0.04266149392770653)))

Vinyl Radical (CH2CH) External

C

-0.919978

0.143718

0.423285

C

0.517143

0.001443

0.015070

H

-1.720187

-0.047021

-0.306997

H

1.143125

0.899076

-0.108782

H

0.979897

-0.997217

-0.022575


Z-matrix object: 3D representation

The Z-matrix is a standard representation for a molecule in computational chemistry. It uses internal coordinates between atoms, specifying an atom a, its distance from atom b, the central angle a-b-c for a third atom c, and the dihedral angle a-b-c-d for a fourth atom d. Many possible Z-matices can represent a single molecule, but automol will choose a set of internal coordinates that captures the connections and torisonal angles along the backbone of the molecule. Automol provides functions to seamlessly convert between geometry and Z-matrix object and the 2D representations.

Vinyl Radical (CH2CH) Internal

((‘C’, (None, None, None), (None, None, None), (None, None, None)), (‘C’, (0, None, None), (‘R1’, None, None), (2.4533342041496025, None, None)), (‘H’, (0, 1, None), (‘R2’, ‘A2’, None), (2.04887881761982, 2.106806084047999, None)), (‘H’, (0, 1, 2), (‘R3’, ‘A3’, ‘D3’), (2.048878892080454, 2.106806109048073, 3.1415931294947175)), (‘X’, (1, 0, 2), (‘R4’, ‘A4’, ‘D4’), (1.8897261254578281, 1.5707963267948968, 1.4901161193847656e-08)), (‘H’, (1, 4, 0), ((‘R5’, ‘A5’, ‘D5’), ((2.0154889471042523, 1.5707962916270888, 3.141592595877844)))


Reaction object: 2D representation

The reaction object in automol is made up of the reaction class string, (e.g., hydrogen abstraction, beta-scission, hydrogen migration, addition, insertion, substitution), two graphs – one describing the forward transformation from reactant to product molecules and one describing the backward transformation from product to reactant molecules – and lists of the keys that identify either the atom vertices from reactant or product molecules. Forming bonds, in these graphs, are given a value of 0.1, while breaking bonds are given a value of 0.9. The transition state itself can be represented as a Z-matrix or Geometry.

CH2CH + CH4 = CH2CH2 + CH3

reaction class: hydrogen abstraction

forward TS atoms:

1: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

2: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

3: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

4: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

5: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

6: {symbol: X, implicit_hydrogen_valence: 0, stereo_parity: null}

7: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

8: {symbol: X, implicit_hydrogen_valence: 0, stereo_parity: null}

9: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

10: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

11: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

12: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

forward TS bonds:

1-2: {order: 1, stereo_parity: null}

1-3: {order: 1, stereo_parity: null}

1-4: {order: 0.9, stereo_parity: null}

1-5: {order: 1, stereo_parity: null}

4-6: {order: 0, stereo_parity: null}

4-7: {order: 0.1, stereo_parity: null}

7-8: {order: 0, stereo_parity: null}

7-9: {order: 1, stereo_parity: null}

7-10: {order: 1, stereo_parity: null}

9-11: {order: 1, stereo_parity: null}

9-12: {order: 1, stereo_parity: null}

reactants keys:

  • [1, 2, 3, 4, 5, 6]

  • [7, 8, 9, 10, 11, 12]

backward TS atoms:

1: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

2: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

3: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

4: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

5: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

6: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

7: {symbol: C, implicit_hydrogen_valence: 0, stereo_parity: null}

8: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

9: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

10: {symbol: H, implicit_hydrogen_valence: 0, stereo_parity: null}

backward TS bonds:

1-2: {order: 1, stereo_parity: null}

1-3: {order: 1, stereo_parity: null}

1-4: {order: 0.9, stereo_parity: null}

2-5: {order: 1, stereo_parity: null}

2-6: {order: 1, stereo_parity: null}

4-7: {order: 0.1, stereo_parity: null}

7-8: {order: 1, stereo_parity: null}

7-9: {order: 1, stereo_parity: null}

7-10: {order: 1, stereo_parity: null}

products keys:

  • [1, 2, 3, 4, 5, 6]

  • [7, 8, 9, 10]

PhyDat

PhyDat stores physical data and constants used across AutoMech suite.

Transformations

author: Christoph Gohlke

site: https://www.lfd.uci.edu/~gohlke/

Calculate homogeneous transformation matrices for translating, rotating, reflecting, scaling, shearing, projecting, orthogonalizing, and superimposing 3D homogeneous coordinates, convert between rotation matrices, Euler angles, and quaternions, decompose transformation matrices, and provide an Arcball control object.

Getting Started

Installation

>>> conda install autochem -c auto-mech

Tutorial

The first step is to make sure the installation was successful by importing some of the modules in each package

>>> import automol
>>> import phydat
>>> import transformations

Then we can move on to using the autochem modules:

  • Automol Tutorial: Automol Tutorial Hub

    • ioformat-tutorial-doc

    • autoparse-tutorial-doc

    • autoread-tutorial-doc

  • PhyDat tutorial

  • Transformations tutorial

Documentation