fragment_capping: An Integer Linear Program (ILP) for predicting Lewis structures and applications to capping molecular fragments and enumerating tautomers

Introduction

This python module implements several graph-based Integer Linear Programs (ILPs) which are described in the paper:

Caron, Bertrand; Engler, Martin; Mark, Alan E. and Klau, Gunnar W.
An Integer Linear Program (ILP) for predicting Lewis structures and applications to capping molecular fragments and enumerating tautomers

Standard-dependencies

See requirements.txt. Install dependencies by running make setup.

• Python >=3.6
• pulp
• networkx
• numpy

Non-standard dependencies

• graph_tool: Efficient network-analysis with Python
• chem_graph_tool: Helper library to use graph_tool with chemical structure files (PDB format).
• chemistry_helpers: Helper library for interacting with chemical structure files (PDB files, etc.)
• OpenBabel: The Open Source Chemistry Toolbox

All Python module should be located in your PYTHONPATH.

Algorithms and examples

Lewis structure prediction

Given a complete molecular graph, returns the best Lewis structure of a molecule by distributing valence electrons to minimise the sum of absolute charge of the molecule and respecting relative atomic electronegativities.

from fragment_capping.helpers.molecule import Molecule, Atom

molecule = Molecule(
	atoms=[
		Atom(element='C', capped=True, index=1, valence=2, coordinates=(0, 0, 0)),
		Atom(element='O', capped=True, index=2, valence=1, coordinates=(1, 0, 0)),
		Atom(element='O', capped=True, index=3, valence=1, coordinates=(-1, 0, 0)),
	],
	bonds=[(1, 2), (1, 3)],
	name='CO2',
)

molecule.assign_bond_orders_and_charges_with_ILP()

print(molecule.mol2())

Fragment capping

Given a partial molecule graph (fragment), find the smallest, most aliphatic, least charged molecule containing this fragment.

from fragment_capping.helpers.molecule import Molecule, Atom

fragment = Molecule(
	atoms=[
		Atom(element='C', capped=False, index=1, valence=None, coordinates=[0, 0, 0]),
		Atom(element='O', capped=True, index=2, valence=1, coordinates=(1, 0, 0)),
	],
	bonds=[(1, 2)],
	name='CO',
)

fragment.get_best_capped_molecule_with_ILP()

print(fragment.mol2())

Tautomer enumeration

Tautomers are compounds that readily interconvert by the movement of an atom (usually hydrogen) or group of atoms from one site to another within the molecular structure (Katritzky et al., 2010). Given a molecule, enumerate all possible tautomers.

from fragment_capping.helpers.molecule import Molecule, Atom

molecule = Molecule(
	atoms=[
		Atom(element='C', capped=True, index=1, valence=3, coordinates=(0, 0, 0)),
		Atom(element='O', capped=True, index=2, valence=1, coordinates=(1, 0, 0)),
		Atom(element='H', capped=True, index=3, valence=1, coordinates=(0, 1, 0)),
		Atom(element='H', capped=True, index=4, valence=1, coordinates=(0, -1, 0)),
	],
	bonds=[(1, 2), (1, 3), (1, 4)],
	name='CH2O',
)

for tautomer in molecule.get_all_tautomers():
	print(tautomer.mol2())