lucidrains/alphafold3-pytorch

Atom at the origin cause incorrect res_atom_elements results

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#296 opened on Sep 26, 2024

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good first issue

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Description

Hello lucidrain, firstly thank you very much for the pytorch reproduction of alphafold3.

In file inputs.py function extract_canonical_molecules_from_biomolecule_chains

in some cif_file, certain key ion coordinates are set to the origin, which causes this line of code res_atom_positions = atom_positions[res_ligand_atom_mask] can not get the corresponding result correctly, its return res_atom_elements is null.

when use in later function create_mol_from_atom_positions_and_types, it raise an exception ValueError: The length of atom_elements and xyz_coordinates must be the same.

You can reproduce this problem using the 1qyl_assembly1.cif file as input, which has two vanadium ions that are each at the origin with 25% probability.

Contributor guide

Research direction
Investigate how atom positions at the origin affect the `res ligand atom mask` in `extract canonical molecules from biomolecule chains`. Trace the logic to understand why positions at origin lead to an empty `res atom positions` and subsequent error in `create mol from atom positions and types`. Use the 1qyl assembly1.cif file as a test case.
Tech stack
pythonpytorch
Domain
aimachine learning
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
3
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1-3 hours
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Clear
Prerequisites
PythonGitPyTorch
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
60