Evaluation issue

[Luchixiang]

Hi. Firstly thanks for your great work. I'm trying to evaluate the performance of the model. I read the predicted cif file and the ground truth cif file using 'from protenix.data.parser import MMCIFParser' and get the structure using the get_structure function. But the len(atom_array) of the predicted structure and ground truth structure differ (the predicted one is larger than the gt one). Do you have any idea of this issue?

Also, looking forward to releasing the evaluation code.

Thanks

[cloverzizi]

Hi @Luchixiang

During inference, all atoms are constructed from sequence information. Occasionally, the ground truth CIF file may have some missing atoms or residues. As a result, you might notice that the predicted structure contains more atoms than the ground truth structure. When evaluating, you can check if the (residue_id, atom_name) of the corresponding chain in the predicted structure appears in the ground truth structure. At evaluation, you should ignore any atoms that do not appear in the ground truth structure.