Molecule Ring & Functional Lifting (Graph to Combinatorial)

[bertranMiquel]

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.

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

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[gbg141]

Hello @bertranMiquel! Thank you for your submission. As we near the end of the challenge, I am collecting participant info for the purpose of selecting and announcing winners. Please email me (or have one member of your team email me) at [email protected] so I can share access to the voting form. In your email, please include:

• your first and last name (as well as any other team members)
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• your pull request number (Molecule Ring & Functional Lifting (Graph to Combinatorial) #21)

Before July 12, make sure that your submission respects all Submission Requirements laid out on the challenge page. Any submission that fails to meet this criteria will be automatically disqualified.

[bertranMiquel]

Hi Guillermo, Answering to fulfill the submission requirements: - Name and last name of the participants: Bertran Miquel-Oliver, Manel Gil-Sorribes, Alexis Molina, Victor Guallar (all of them in cc) - Title: Molecule Ring & Functional Lifting - Input domain: Graph - Output domain: Combinatorial - Pull request: #21 <#21> Best, Bertran Missatge de Guillermo Bernárdez ***@***.***> del dia dl., 8 de jul. 2024 a les 19:15:

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Hello @bertranMiquel <https://github.com/bertranMiquel>! Thank you for your submission. As we near the end of the challenge, I am collecting participant info for the purpose of selecting and announcing winners. Please email me (or have one member of your team email me) at ***@***.*** so I can share access to the voting form. In your email, please include: - your first and last name (as well as any other team members) - the title of the method you implemented - the input domain of the method you implemented - the output domain of the method you implemented - your pull request number (#21 <#21>) Before July 12, make sure that your submission respects all Submission Requirements laid out on the challenge page <https://pyt-team.github.io/packs/challenge.html>. Any submission that fails to meet this criteria will be automatically disqualified. — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHTIUTRMPU4XPS7VOP2I7LLZLLCKFAVCNFSM6AAAAABKALBN72VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJUG42DQMRQGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>