In the following implementation, it appears that the rigid_group_atom_positions for non-standard amino acids are based on a single reference PDB structure, as suggested by the comments in the code:
https://github.com/hongliangduan/HighFold2/blob/main/alphafold/common/residue_constants.py#L471-L915
Could you please clarify how the atomic coordinates for each rigid group are computed from that reference structure? What steps are involved in determining those positions?
Additionally, I’m interested in extending support to other non-standard amino acids not currently listed in the file. Could you share any guidance or best practices for calculating the rigid_group_atom_positions for new residues?
In the following implementation, it appears that the rigid_group_atom_positions for non-standard amino acids are based on a single reference PDB structure, as suggested by the comments in the code:
https://github.com/hongliangduan/HighFold2/blob/main/alphafold/common/residue_constants.py#L471-L915
Could you please clarify how the atomic coordinates for each rigid group are computed from that reference structure? What steps are involved in determining those positions?
Additionally, I’m interested in extending support to other non-standard amino acids not currently listed in the file. Could you share any guidance or best practices for calculating the rigid_group_atom_positions for new residues?