Split implict ins_code of atom_site and allow safe retrieval from bot…

…h auth and label sequence schemes (2kny)
wwPDB · Mar 1, 2024 · 62a2de7 · 62a2de7
1 parent f9aa80f
commit 62a2de7
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Showing 14 changed files with 692 additions and 393 deletions.
diff --git a/wwpdb/utils/nmr/NmrDpUtility.py b/wwpdb/utils/nmr/NmrDpUtility.py
@@ -24959,7 +24959,111 @@ def fill_cs_row(lp, index, _row, prefer_auth_atom_name, coord_atom_site, _seq_ke
                     else:
                         resolved = False
 
-                    if not resolved:
+                    if not resolved and has_auth_seq and row[auth_asym_id_col] == 'UNMAPPED':  # 2kny: leave data as is
+
+                        is_valid, cc_name, _ = self.__getChemCompNameAndStatusOf(comp_id)
+                        comp_id_bmrb_only = not is_valid and cc_name is not None and 'processing site' in cc_name
+
+                        chain_id = row[chain_id_col]
+                        if chain_id in emptyValue:
+                            chain_id = 'A'
+
+                        if chain_id in copied_chain_ids:
+                            continue
+
+                        entity_id = None
+                        if (self.__combined_mode or (self.__bmrb_only and self.__internal_mode)) and entity_id_col != -1:
+                            try:
+                                entity_id = int(row[entity_id_col])
+                            except (ValueError, TypeError):
+                                entity_id = None
+
+                        seq_id = auth_seq_id
+
+                        _row[1], _row[2], _row[3], _row[4], _row[5] = chain_id, entity_id, seq_id, seq_id, comp_id
+
+                        # DAOTHER-9065
+                        if details_col != -1 and row[details_col] == 'UNMAPPED':
+                            if isinstance(_row[1], int) and str(_row[1]) in seq_id_offset_for_unmapped:
+                                offset = None
+                                if isinstance(_row[17], int):
+                                    offset = _row[3] - _row[17]
+                                elif isinstance(_row[17], str) and _row[17].isdigit():
+                                    offset = _row[3] - int(_row[17])
+                                if offset is not None and offset != seq_id_offset_for_unmapped[str(_row[1])]:
+                                    if isinstance(_row[17], int):
+                                        _row[3] = _row[17] + seq_id_offset_for_unmapped[str(_row[1])]
+                                        _row[4] = _row[3]
+                                    else:
+                                        _row[3] = int(_row[17]) + seq_id_offset_for_unmapped[str(_row[1])]
+                                        _row[4] = _row[3]
+                            elif isinstance(_row[1], str) and _row[1] in seq_id_offset_for_unmapped:
+                                offset = None
+                                if isinstance(_row[17], int):
+                                    offset = _row[3] - _row[17]
+                                elif isinstance(_row[17], str) and _row[17].isdigit():
+                                    offset = _row[3] - int(_row[17])
+                                if offset is not None and offset != seq_id_offset_for_unmapped[_row[1]]:
+                                    if isinstance(_row[17], int):
+                                        _row[3] = _row[17] + seq_id_offset_for_unmapped[_row[1]]
+                                        _row[4] = _row[3]
+                                    else:
+                                        _row[3] = int(_row[17]) + seq_id_offset_for_unmapped[_row[1]]
+                                        _row[4] = _row[3]
+                            elif trial == 0:
+                                regenerate_request = True
+
+                        atom_ids = self.__getAtomIdListInXplor(comp_id, atom_id)
+                        if len(atom_ids) == 0 or atom_ids[0] not in self.__csStat.getAllAtoms(comp_id):
+                            atom_ids = self.__getAtomIdListInXplor(comp_id, translateToStdAtomName(atom_id, comp_id, ccU=self.__ccU))
+                        len_atom_ids = len(atom_ids)
+                        if len_atom_ids == 0 or comp_id_bmrb_only:
+                            _row[6] = atom_id
+                            _row[7] = 'H' if atom_id[0] in pseProBeginCode else atom_id[0]
+                            if _row[7] in ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS:
+                                _row[8] = ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS[_row[7]][0]
+                        else:
+                            _row[6] = atom_ids[0]
+                            _row[19] = None
+                            fill_auth_atom_id = _row[18] not in emptyValue
+                            if self.__ccU.updateChemCompDict(comp_id):
+                                cca = next((cca for cca in self.__ccU.lastAtomList if cca[self.__ccU.ccaAtomId] == _row[6]), None)
+                                if cca is not None:
+                                    _row[7] = cca[self.__ccU.ccaTypeSymbol]
+                                    if _row[7] in ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS:
+                                        _row[8] = ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS[_row[7]][0]
+                                else:
+                                    _row[7] = 'H' if _row[6][0] in protonBeginCode else atom_id[0]
+                                    if _row[7] in ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS:
+                                        _row[8] = ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS[_row[7]][0]
+                            else:
+                                _row[7] = 'H' if atom_id[0] in pseProBeginCode else atom_id[0]
+                                if _row[7] in ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS:
+                                    _row[8] = ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS[_row[7]][0]
+
+                            if len_atom_ids > 1:
+                                __row = copy.copy(_row)
+                                lp.add_data(__row)
+
+                                for _atom_id in atom_ids[1:-1]:
+                                    __row = copy.copy(_row)
+
+                                    index += 1
+
+                                    __row[0] = index
+                                    __row[6] = _atom_id
+
+                                    lp.add_data(__row)
+
+                                index += 1
+
+                                _row[0] = index
+                                _row[6] = atom_ids[-1]
+
+                            if fill_auth_atom_id:
+                                _row[19] = _row[6]
+
+                    elif not resolved:
 
                         chain_id = row[chain_id_col]
                         if chain_id in emptyValue: