Fix atom name conversion (DT|T):H5(#|%|*) should be mapped to H71/H72…

…/H73, THM:H7(#|%|*) should be mapped to HM51/HM52/HM53 (8ht7)
wwPDB · Nov 29, 2024 · fffac99 · fffac99
1 parent c10eba7
commit fffac99
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/wwpdb/utils/nmr/NEFTranslator/NEFTranslator.py b/wwpdb/utils/nmr/NEFTranslator/NEFTranslator.py
@@ -137,7 +137,8 @@
     from wwpdb.utils.nmr.CifToNmrStar import CifToNmrStar
     from wwpdb.utils.nmr.mr.ParserListenerUtil import (ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS,
                                                        ALLOWED_AMBIGUITY_CODES,
-                                                       translateToStdResName)
+                                                       translateToStdResName,
+                                                       translateToStdAtomName)
 except ImportError:
     from nmr.AlignUtil import (LEN_LARGE_ASYM_ID, LOW_SEQ_COVERAGE,
                                emptyValue, trueValue, monDict3,
@@ -152,7 +153,8 @@
     from nmr.CifToNmrStar import CifToNmrStar
     from nmr.mr.ParserListenerUtil import (ISOTOPE_NUMBERS_OF_NMR_OBS_NUCS,
                                            ALLOWED_AMBIGUITY_CODES,
-                                           translateToStdResName)
+                                           translateToStdResName,
+                                           translateToStdAtomName)
 
 
 __package_name__ = 'wwpdb.utils.nmr'
@@ -6683,7 +6685,7 @@ def get_valid_star_atom_for_ligand_remap(self, comp_id, atom_id, coord_atom_site
 
         if details is not None and comp_id not in monDict3 and self.__csStat.peptideLike(comp_id) and atom_id[0] in ('H', 'C', 'N', 'O', 'P')\
            and len_atom_id > 1 and atom_id[1] in ('A', 'B', 'G', 'D', 'E', 'Z', 'H')\
-           and (atom_id[0] != 'H' or (atom_id[0] == 'H' and atom_id[-1] not in ('%', '#'))):
+           and (atom_id[0] != 'H' or (atom_id[0] == 'H' and atom_id[-1] not in ('%', '*'))):
             grk_atoms = self.__ccU.getAtomsBasedOnGreekLetterSystem(comp_id, atom_id)
             if len(grk_atoms) > 0:
                 atom_list = []
@@ -7011,6 +7013,10 @@ def get_valid_star_atom_in_xplor(self, comp_id, atom_id, details=None, leave_unm
             if '#' in atom_id:
                 atom_id = atom_id.replace('#', '%')
 
+            if atom_id[-1] in ('%', '*') and atom_id[-2] != "'" and self.__csStat.getTypeOfCompId(comp_id)[1]:
+                atom_id = translateToStdAtomName(atom_id[:-1], refCompId=comp_id, ccU=self.__ccU) + atom_id[-1]
+                print(atom_id)
+
             if atom_id[0] in ('1', '2', '3'):
                 atom_list, ambiguity_code, details = self.get_valid_star_atom(comp_id, atom_id, details, leave_unmatched, methyl_only)
                 if details is None:
@@ -7349,7 +7355,7 @@ def get_valid_star_atom(self, comp_id, atom_id, details=None, leave_unmatched=Tr
 
             if details is not None and comp_id not in monDict3 and self.__csStat.peptideLike(comp_id) and atom_id[0] in ('H', 'C', 'N', 'O', 'P')\
                and len_atom_id > 1 and atom_id[1] in ('A', 'B', 'G', 'D', 'E', 'Z', 'H')\
-               and (atom_id[0] != 'H' or (atom_id[0] == 'H' and atom_id[-1] not in ('%', '#'))):
+               and (atom_id[0] != 'H' or (atom_id[0] == 'H' and atom_id[-1] not in ('%', '*'))):
                 grk_atoms = self.__ccU.getAtomsBasedOnGreekLetterSystem(comp_id, atom_id)
                 if len(grk_atoms) > 0:
                     atom_list = []

diff --git a/wwpdb/utils/nmr/mr/ParserListenerUtil.py b/wwpdb/utils/nmr/mr/ParserListenerUtil.py
@@ -2183,7 +2183,7 @@ def translateToStdAtomName(atomId, refCompId=None, refAtomIdList=None, ccU=None,
             elif refCompId in ('DT', 'T') and atomId.startswith('H5'):  # 2lsz
                 if atomId in ('H51', 'H52', 'H53'):
                     return 'H7' + atomId[-1]
-                if atomId in 'H5':
+                if atomId in ('H5', 'H5%', 'H5#', 'H5*'):
                     return 'H7'
             elif refCompId in ('DT', 'T') and (atomId.startswith('C5') or atomId == 'CM'):  # 7dju, 7pdu
                 return 'C7'
@@ -2193,7 +2193,7 @@ def translateToStdAtomName(atomId, refCompId=None, refAtomIdList=None, ccU=None,
                 if atomId.startswith('H7'):
                     if atomId in ('H71', 'H72', 'H73'):
                         return 'HM5' + atomId[-1]
-                    if atomId in 'H7':
+                    if atomId in ('H7', 'H7%', 'H7#', 'H7*'):
                         return 'HM5'
                 if atomId in ('C7', 'CM'):  # 7png, 7pdu
                     return 'C5M'