Molecule Ring & Functional Lifting (Graph to Combinatorial) - geometric-intelligence/TopoBench GitHub Wiki

Using QM9 dataset, we implement a lifting from a molecule graph to a combinatorial complex based on two points:

  • The ring information of the molecule. Rings will be represented as 2-cells in the combinatorial complex.
  • Its functional groups will be add as hyperedges in the complex, i.e., 1-cells that sometimes connect more than two 0-cells. The functional groups are found by the SMARTS patterns, predifenied patterns that are used to identify functional groups in molecules.

So far, to the best of our knowledge, it is the first implementation of a molecule as a combinatorial complex, combining both hypergraphs and cell complexes.

Here, the elements are the following:

  • Nodes: Atoms in the molecule.
  • Edges: Bonds between atoms.
  • Hyperedges: Clusters of atoms that are close to each other.
  • 2-cells: Rings in the molecule.

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Additionally, attributes inspired by those used in (Battiloro et al., 2024) are incorporated into the elements, enhancing the representation of the molecule. The attributes are:

  • Node: Atom type, atomic number, and chirality.
  • Edge: Bond type, conjugation and stereochemistry.
  • Rings: Ring size, aromaticity, heteroatoms, saturation, hydrophobicity, electrophilicity, nucleophilicity, and polarity.
  • Functional groups: Conjugation, hydrophobicity, electrophilicity, nucleophilicity, and polarity.

This pull request is done under the team formed by: Bertran Miquel Oliver, Manel Gil Sorribes, Alexis Molina

From https://github.com/pyt-team/challenge-icml-2024/pull/21