TODO: Questions that arise when studying how to convert a PDB file to a CIF file

[asdfefbhjy]

protenix\data\utils.py: pdb_to_cif()

understand how the hetero atoms are related to the protein in a PDB file
bytedance#157 (comment)

[asdfefbhjy]

protenix tojson --input examples/7pzb.pdb --out_dir ./output

protenix\data\utils.py: pdb_to_cif()

/content/Protenix/protenix/data/utils.py
resname_seq:
 ['ARG', 'SER', 'SER', 'ALA', 'PHE', 'TRP', 'ARG', 'SER', 'PHE', 'PRO', 'ILE', 'PHE', 'GLU', 'GLU', 'PHE', 'ASP', 'SER', 'GLU', 'THR', 'LEU', 'CYS', 'GLU', 'LEU', 'SER', 'GLY', 'ILE', 'ALA', 'SER', 'TYR', 'ARG', 'LYS', 'TRP', 'SER', 'ALA', 'GLY', 'THR', 'VAL', 'ILE', 'PHE', 'GLN', 'ARG', 'GLY', 'ASP', 'GLN', 'GLY', 'ASP', 'TYR', 'MET', 'ILE', 'VAL', 'VAL', 'VAL', 'SER', 'GLY', 'ARG', 'ILE', 'LYS', 'LEU', 'SER', 'LEU', 'PHE', 'THR', 'PRO', 'GLN', 'GLY', 'ARG', 'GLU', 'LEU', 'MET', 'LEU', 'ARG', 'GLN', 'HIS', 'GLU', 'ALA', 'GLY', 'ALA', 'LEU', 'PHE', 'GLY', 'GLU', 'MET', 'ALA', 'LEU', 'LEU', 'ASP', 'GLY', 'GLN', 'PRO', 'ARG', 'SER', 'ALA', 'ASP', 'ALA', 'THR', 'ALA', 'VAL', 'THR', 'ALA', 'ALA', 'GLU', 'GLY', 'TYR', 'VAL', 'ILE', 'GLY', 'LYS', 'LYS', 'ASP', 'PHE', 'LEU', 'ALA', 'LEU', 'ILE', 'THR', 'GLN', 'ARG', 'PRO', 'LYS', 'THR', 'ALA', 'GLU', 'ALA', 'VAL', 'ILE', 'ARG', 'PHE', 'LEU', 'CYS', 'ALA', 'GLN', 'LEU', 'ARG', 'ASP', 'THR', 'THR', 'ASP', 'ARG', 'LEU', 'GLU', 'THR', 'ILE', 'ALA', 'LEU', 'TYR', 'ASP', 'LEU', 'ASN', 'ALA', 'ARG', 'VAL', 'ALA', 'ARG', 'PHE', 'PHE', 'LEU', 'ALA', 'THR', 'LEU', 'ARG', 'GLN', 'ILE', 'HIS', 'GLY', 'SER', 'GLU', 'MET', 'PRO', 'GLN', 'SER', 'ALA', 'ASN', 'LEU', 'ARG', 'LEU', 'THR', 'LEU', 'SER', 'GLN', 'THR', 'ASP', 'ILE', 'ALA', 'SER', 'ILE', 'LEU', 'GLY', 'ALA', 'SER', 'ARG', 'PRO', 'LYS', 'VAL', 'ASN', 'ARG', 'ALA', 'ILE', 'LEU', 'SER', 'LEU', 'GLU', 'GLU', 'SER', 'GLY', 'ALA', 'ILE', 'LYS', 'ARG', 'ALA', 'ASP', 'GLY', 'ILE', 'ILE', 'CYS', 'CYS', 'ASN', 'VAL', 'GLY', 'ARG', 'LEU', 'LEU', 'SER', 'ILE', 'ALA', 'ASP', 'PRO', 'GLU']



resname_seq:
 ['ARG', 'SER', 'SER', 'ALA', 'PHE', 'TRP', 'ARG', 'SER', 'PHE', 'PRO', 'ILE', 'PHE', 'GLU', 'GLU', 'PHE', 'ASP', 'SER', 'GLU', 'THR', 'LEU', 'CYS', 'GLU', 'LEU', 'SER', 'GLY', 'ILE', 'ALA', 'SER', 'TYR', 'ARG', 'LYS', 'TRP', 'SER', 'ALA', 'GLY', 'THR', 'VAL', 'ILE', 'PHE', 'GLN', 'ARG', 'GLY', 'ASP', 'GLN', 'GLY', 'ASP', 'TYR', 'MET', 'ILE', 'VAL', 'VAL', 'VAL', 'SER', 'GLY', 'ARG', 'ILE', 'LYS', 'LEU', 'SER', 'LEU', 'PHE', 'THR', 'PRO', 'GLN', 'GLY', 'ARG', 'GLU', 'LEU', 'MET', 'LEU', 'ARG', 'GLN', 'HIS', 'GLU', 'ALA', 'GLY', 'ALA', 'LEU', 'PHE', 'GLY', 'GLU', 'MET', 'ALA', 'LEU', 'LEU', 'ASP', 'GLY', 'GLN', 'PRO', 'ARG', 'SER', 'ALA', 'ASP', 'ALA', 'THR', 'ALA', 'VAL', 'THR', 'ALA', 'ALA', 'GLU', 'GLY', 'TYR', 'VAL', 'ILE', 'GLY', 'LYS', 'LYS', 'ASP', 'PHE', 'LEU', 'ALA', 'LEU', 'ILE', 'THR', 'GLN', 'ARG', 'PRO', 'LYS', 'THR', 'ALA', 'GLU', 'ALA', 'VAL', 'ILE', 'ARG', 'PHE', 'LEU', 'CYS', 'ALA', 'GLN', 'LEU', 'ARG', 'ASP', 'THR', 'THR', 'ASP', 'ARG', 'LEU', 'GLU', 'THR', 'ILE', 'ALA', 'LEU', 'TYR', 'ASP', 'LEU', 'ASN', 'ALA', 'ARG', 'VAL', 'ALA', 'ARG', 'PHE', 'PHE', 'LEU', 'ALA', 'THR', 'LEU', 'ARG', 'GLN', 'ILE', 'HIS', 'GLY', 'SER', 'GLU', 'MET', 'PRO', 'GLN', 'SER', 'ALA', 'ASN', 'LEU', 'ARG', 'LEU', 'THR', 'LEU', 'SER', 'GLN', 'THR', 'ASP', 'ILE', 'ALA', 'SER', 'ILE', 'LEU', 'GLY', 'ALA', 'SER', 'ARG', 'PRO', 'LYS', 'VAL', 'ASN', 'ARG', 'ALA', 'ILE', 'LEU', 'SER', 'LEU', 'GLU', 'GLU', 'SER', 'GLY', 'ALA', 'ILE', 'LYS', 'ARG', 'ALA', 'ASP', 'GLY', 'ILE', 'ILE', 'CYS', 'CYS', 'ASN', 'VAL', 'GLY', 'ARG', 'LEU', 'LEU', 'SER', 'ILE', 'ALA', 'ASP', 'PRO']



resname_seq:
 ['DC', 'DT', 'DA', 'DG', 'DG', 'DT', 'DA', 'DA', 'DC', 'DA', 'DT', 'DT', 'DA', 'DC', 'DT', 'DC', 'DG', 'DC', 'DG']



resname_seq:
 ['DG', 'DC', 'DG', 'DA', 'DG', 'DT', 'DA', 'DA', 'DT', 'DG', 'DT', 'DT', 'DA', 'DC']



resname_seq:
 ['DC', 'DT', 'DA', 'DG', 'DG', 'DT', 'DA', 'DA', 'DC', 'DA', 'DT', 'DT', 'DA', 'DC']



resname_seq:
 ['DG', 'DT', 'DA', 'DA', 'DT', 'DG', 'DT', 'DT', 'DA', 'DC']



resname_seq:
 ['PCG']



resname_seq:
 ['PCG']



resname_seq:
 ['HOH']



resname_seq:
 ['HOH']



resname_seq:
 ['HOH']

[asdfefbhjy]

I don't understand why we need the following code. A dsDNA has 2 identical single strand. Is this possible ? If so, should we assign different "entity id" to each single strand ? Or should we assign one shared "entity id" to both single strand ?

        if (
            all([name in DNA_STD_RESIDUES for name in resname_seq])
            and resname_str in seq_to_entity_id
        ):
            resname_seq = resname_seq[::-1]
            resname_str = "_".join(resname_seq)
            atom_index[c_start:c_stop] = atom_index[c_start:c_stop][::-1]

The following are some excerpts from the DeepSeek answer:

Same label_entity_id = Same molecule (e.g., two chains of hemoglobin α will share an ID).

Different label_entity_id = Different molecules (e.g., protein vs. DNA vs. ligand).

Prevents duplicate entities (e.g., two identical DNA strands must share an ID).

Helps in structural comparisons (e.g., aligning chains with the same entity_id).

[asdfefbhjy]

    w = CIFWriter(atom_array=atom_array, entity_poly_type=entity_poly_type)
    w.save_to_cif(
        output_fname,
        entry_id=entry_id or os.path.basename(output_fname),
        include_bonds=True,
    )

The definition of CIFWriter says that the parameter entity_poly_type should have the type dict[str, str], but the provided entity_poly_type has the type dict[int, str]

entity_poly_type:
 {1: 'polypeptide(L)', 2: 'polypeptide(L)', 3: 'polydeoxyribonucleotide', 4: 'polydeoxyribonucleotide', 5: 'polydeoxyribonucleotide', 6: 'polydeoxyribonucleotide'}
 

[asdfefbhjy]

        if count["prot"] >= 2 and count["dna"] == 0 and count["rna"] == 0:
            entity_poly_type[entity_id] = "polypeptide(L)"
        elif count["dna"] >= 2 and count["rna"] == 0 and count["prot"] == 0:
            entity_poly_type[entity_id] = "polydeoxyribonucleotide"
        elif count["rna"] >= 2 and count["dna"] == 0 and count["prot"] == 0:
            entity_poly_type[entity_id] = "polyribonucleotide"
        else:
            # other entity type: ignoring
            continue

Should we change continue to entity_poly_type[entity_id] = "Ignored" ?