Using Chemical Environments

ChemicalEnvironment usage examples

Here, we show how to use ChemicalEnvironments in detail. First, we will outline how they are structured with some example code snippets.

Demo jupyter notebook

The using_environments.ipynb jupyter notebook should be your first stop for interactively understanding and using ChemicalEnvironment. It includes all of the examples shown above and more in a jupyter notebook so you can play with the different method options.

Creating a ChemicalEnvironment

A ChemicalEnvironment can be creatied using SMIRKS strings. If a ChemicalEnvironment is created with no SMIRKS pattern, it is an empty structure. There are five subtypes of ChemicalEnvironment that match the types of parameters found in the SMIRNOFF format. If they are created with no SMIRKS pattern, their structure matches a generic for that parameter type—for example, [*:1]~[*:2] for a bond (that is any atom connected to any other atom by any bond). The five subtypes are listed below with their expected number of indexed atoms and the corresponding SMIRKS structure:

  • AtomChemicalEnvironment
    • expects 1 indexed atom
    • default/generic SMIRKS "[*:1]"
  • BondChemicalEnvironment
    • expects 2 indexed atoms
    • default/generic SMIRKS: "[*:1]~[*:2]"
  • AngleChemicalEnvironment
    • expects 3 indexed atoms
    • default/generic SMIRKS: "[*:1]~[*:2]~[*:3]"
  • TorsionChemicalEnvironment
    • expects 4 indexed atoms in a proper dihedral angle
    • default/generic SMIRKS: "[*:1]~[*:2]~[*:3]~[*:4]"
  • ImproperChemicalEnvironment
    • expects 4 indexed atoms in an improper dihedral angle
    • default/generic SMIRKS: "[*:1]~[*:2](~[*:3])~[*:4]"

Here is an example for initiating a chemical environment:

from openforcefield.typing.chemistry import environment as env
smirks = "[#6X3,#7;+0:1]~;@[#8;r:2]~;@[#6X3,#7;+0:3]"
angle = env.AngleChemicalEnvironment(smirks = smirks)

ANDtypes and ORtypes

After being initiated with a SMIRKS string, ChemicalEnvironments separate and store information about the fragment in a NetworkX graph. This information is stored in the same way a chemist might think about a fragment, that is there are atoms connected by bonds. The descriptors for both atoms and bonds are broken down into ORtypes, decorators OR’d together with a ‘,’ and ANDtypes, decorators AND’d to the end of an atom or bond with a ‘;’. ORtypes are further broken down into bases and decorators. A base is typically an atomic number or symbol.

As an example, consider atom 1 above (‘[#6X3,#7X2,#7X3;+0:1]’):

  • ORtypes (base, [list of decorators] )
    • ('#6', ['X3'])
    • ('#7', [])
  • ANDtypes
    • ['+0']

You can set and get ORtypes and ANDtypes for atoms and bonds. You can also addORtypes and addANDtypes for atoms and bonds. For example:

old_SMIRKS = angle.asSMIRKS()

new_ORtypes = [ ('#6', ['X3']), ('#7', ['X2']) ]
atom1.setORtypes(new_ORtypes)
print("New Atom 1: %s " % atom1.asSMIRKS())
# New Atom 1: [#6X3,#7X2;+0:1]

# Change atom2's AND and OR types with the add*type methods
atom2 = angle.selectAtom(2)
atom2.addANDtype('R1')
atom2.addORtype('#7', ['X3', '+0'])
print("New Atom 2: %s" % atom2.asSMIRKS())
# New Atom 2: [#8,#7+0X3;R1:2]

print("\nSMIRKS Before Changes: '%s'" % old_SMIRKS)
print("\nNew SMIRKS: '%s'" % angle.asSMIRKS())
# SMIRKS Before Changes: '[#6X3,#7;+0:1]~;@[#8;r:2]~;@[#6X3,#7;+0:3]'
# New SMIRKS: '[#6X3,#7X2:1]~;@[#8,#7+0X3;R1:2]~;@[#6X3,#7:3]'

Adding and removing atoms

You can add new atoms to an environment by specifying an atom to connect to and the OR and AND types for the new bond and new atom.

You can also remove existing atoms with the function removeAtom which returns True if the atom was removed and False if it was not. There are two conditions which will always results in the atom not being removed:

  • The atom is indexed, has a ':number' at the end
  • The atom is connected to more than one atom. Note, in these cases the removeAtom function returns false and the chemical graph remains unchanged. When an atom is removed the bond connecting it is also removed.
atom3 = angle.selectAtom(3)

alpha_ORtypes = [('#8', ['X2', 'H1'])]
alpha_ANDtypes = ['R0']
alpha_bondANDtypes = ['!@']
alpha = angle.addAtom(atom3, bondANDtypes = alpha_bondANDtypes,
                      newORtypes = alpha_ORtypes, newANDtypes = alpha_ANDtypes)
print("Alpha Atom SMIRKS: %s" % alpha.asSMIRKS())
# Alpha Atom SMIRKS: [#8X2H1;R0]

beta_ORtypes = [('#1', [])]
beta = angle.addAtom(alpha, newORtypes = beta_ORtypes)
print("Beta Atom SMIRKS: %s" % beta.asSMIRKS())
# Beta Atom SMIRKS: [#1]

print("New overall SMIRKS: %s" % angle.asSMIRKS())
# New overall SMIRKS: [#6X3,#7X2:1]~;@[#8,#7+0X3;R1:2]~;@[#6X3,#7:3]~;!@[#8X2H1;R0]~[#1]

removed = angle.removeAtom(beta)
print("The hydrogen beta to atom3 was remove: ", removed)
# The hydrogen beta to atom3 was remove:  True
print("Updated SMIRKS string: %s" % angle.asSMIRKS())
# print("Updated SMIRKS string: %s" % angle.asSMIRKS())

Other ChemicalEnvironment Methods

Selecting atoms and bonds

# when given an integer selectAtom or selectBond returns that atom or bond with that index
# otherwise it returns a random atom or bond that meets the specified requirement
# If no atom or bond with that type is found then None is returned
alpha = angle.selectAtom('alpha')
atom4 = angle.selectAtom(4) # None, angle has 3 indexed atoms
beta_bond = angle.selectBond('beta') # bond between an alpha and beta atom

Getting information about an atom or bond in an environment (i.e. isAlpha() returns a boolean)

# Check if the alpha atom above is any of the following
angle.isIndexed(alpha) # False
angle.isUnindexed(alpha) # True
angle.isAlpha(alpha) # True
angle.isBeta(alpha) # False
# NOTE - These methods can take an atom or a bond as an argument

Get atoms or bonds in each type of position, for example getIndexedAtoms() or getAlphaBonds()

# We will print the SMIRKS for each indexed atom:
all_atoms = angle.getAtoms()
indexed_list = angle.getIndexedAtoms() # list of indexed atoms
unindexed_list = angle.getUnindexedAtoms() # list of atoms with no index
alpha_list = angle.getAlphaAtoms()
beta_list = angle.getBetaAtoms
# Note - Atoms can be replaced with Bonds in each of the above examples

Report the minimum order of a bond with Bond.getOrder. SMIRKS strings can match multiple types of bonds, for example "[*]-,;,=[*]" describes any two atoms connected by a single, aromatic, or double bond. The getOrder function returns the minimum order for the bond, 1, in this case.

bond1 = angle.selectBond(1)
bond1.getOrder() # returns 1

Report the valence and bond order around an atom can be reported with getValence() and getBondOrder().

atom3 = angle.selectAtom(3)
angle.getValence(atom3) # number of neighbors atom 3 has
angle.getBondOrder(atom3) # total bond order around atom 3

Get a bond between two atoms (or determine if the atoms are bonded) with getBond(atom1, atom2):

# Check for bonds between each pair of indexed atoms
A = 1
B = 2
atomA = angle.selectAtom(A)
atomB = angle.selectAtom(B)
bondAB = angle.getBond(atomA, atomB) # returns None if no bond found

Get atoms bound to a specified atom with getNeighbors():

# get the neighbors for each indexed atom
atomA = angle.selectAtom(A)
neighbor_list = angle.getNeighbors(atomA)

Aspects of SMIRKS not yet implemented

Types of SMIRKS patterns that cannot be read into ChemicalEnvironment:

  • SMIRKS for multiple molecules. The symbol '.' can be used in SMIRKS to denote fragments in separate molecules, ChemicalEnvironment will fail if the given pattern has multiple molecules.
  • Similarly, SMIRKS for reactions are not parseable into ChemicalEnvironment. These are denoted with '>>' to indicate the fragment changing in a reaction.

Making Monte Carlo proposals in chemical perception space with ChemicalEnvironment

Here, our goal is to show how to use ChemicalEnvironment to make “moves” in chemical perception space. First, a list of weighted moves were generated and saved to output files. Then, a seconds notebook is used to make these moves in chemical space.

These notebooks were generated in the early planning stages for smirky, the first attempt at sampling chemical perception for SMIRNOFF parameter types.

  • create_move_types_and_weights.ipynb - used to create lists of moves and their probabilities based on the type of parameter (vdw, bond, angle, torsion, improper). Created the text files moveTrees.uniq.*.txt where * refers to the parameter type.
  • moves_using_environments.ipynb - uses the moveTrees.uniq.*.txt files to illustrate how to make moves in chemical perception space.

For a more thorough and automated tool for using ChemicalEnvironments to make changes to chemical perception see smirky, a tool we developed to rediscover SMIRNOFF parameters.