Minor code refactoring

wwpdb/utils/nmr/ChemCompUtil.py

@@ -27,14 +27,16 @@
     from wwpdb.utils.nmr.io.ChemCompIo import ChemCompReader
     from wwpdb.utils.nmr.AlignUtil import (emptyValue,
                                            monDict3,
-                                           protonBeginCode)
+                                           protonBeginCode,
+                                           isReservedLigCode)
     cICc = ConfigInfoAppCc(getSiteId())
     CC_CVS_PATH = cICc.get_site_cc_cvs_path()
 except ImportError:
     from nmr.io.ChemCompIo import ChemCompReader
     from nmr.AlignUtil import (emptyValue,
                                monDict3,
-                               protonBeginCode)
+                               protonBeginCode,
+                               isReservedLigCode)
     CC_CVS_PATH = os.path.dirname(__file__) + '/ligand_dict'  # need to setup 'ligand_dict' CCD resource for NMR restraint processing
 
 
@@ -154,7 +156,7 @@ def updateChemCompDict(self, compId: str) -> bool:
             @return: True for successfully update CCD information or False for the case a given comp_id does not exist in CCD
         """
 
-        if compId in emptyValue:
+        if compId in emptyValue or isReservedLigCode(compId):
             return False
 
         compId = compId.upper()

wwpdb/utils/nmr/CifToNmrStar.py

@@ -4,11 +4,11 @@
 #
 # Updates:
 # 13-Oct-2021  M. Yokochi - code revision according to PEP8 using Pylint (DAOTHER-7389, issue #5)
-# 20-Apr-2022  M. Yokochi - enable to fix broken data block order of CIF formatted NMR-STAR using NMR-STAR schema (DAOTHER-7407, NMR restraint remediation)
+# 20-Apr-2022  M. Yokochi - enable to fix broken datablock order of CIF formatted NMR-STAR using NMR-STAR schema (DAOTHER-7407, NMR restraint remediation)
 # 28-Jul-2022  M. Yokochi - enable to fix format issue of CIF formatted NMR-STAR (You cannot have two loops with the same category in one saveframe. Category: '_Audit')
 # 27-Sep-2022  M. Yokochi - auto fill list ID and entry ID (NMR restraint remediation)
 # 13-Jun-2023  M. Yokochi - sort loops in a saveframe based on schema
-# 30-May-2024  M. Yokochi - resolve duplication of data block/saveframe name (DAOTHER-9437)
+# 30-May-2024  M. Yokochi - resolve duplication of datablock/saveframe name (DAOTHER-9437)
 # 25-Jun-2024  M. Yokochi - strip white spaces in a datablock name derived from the model file (DAOTHER-9511)
 # 07-Jan-2025  M. Yokochi - retrieve symbolic label representations (DAOTHER-1728, 9846)
 ##
@@ -62,23 +62,20 @@ def has_key_value(d: dict, key: Any) -> bool:
     return False
 
 
-def get_value_safe(d: Optional[dict] = None, key: Any = None) -> Any:
-    """ Return value of a given dictionary for a key.
-        @return: value for a key, None otherwise
+def get_value_safe(d: Optional[Union[dict, list, tuple]] = None, key: Optional = None, default: Optional = None) -> Any:
+    """ Return value of a given dictionary, list, or tuple for a key.
+        @return: value for a key, None (by default) otherwise
     """
 
     if d is None or key is None:
-        return None
-
-    if key not in d:
-        return None
+        return default
 
-    return d[key]
+    return d.get(key, default)
 
 
-def get_first_sf_tag(sf: pynmrstar.Saveframe, tag: str, default: str = '') -> str:
+def get_first_sf_tag(sf: pynmrstar.Saveframe, tag: str, default: str = '') -> Any:
     """ Return the first value of a given saveframe tag with decoding symbol notation.
-        @return: The first tag value, default string otherwise.
+        @return: The first tag value, '' (by default) otherwise.
     """
 
     if not isinstance(sf, pynmrstar.Saveframe) or tag is None:
@@ -92,11 +89,14 @@ def get_first_sf_tag(sf: pynmrstar.Saveframe, tag: str, default: str = '') -> st
     if not isinstance(array[0], str):
         return array[0]
 
-    if array[0] == '$':
-        return default
-
     value = array[0]
 
+    while value.startswith('$$'):
+        value = value[1:]
+
+    if len(value) == 0 or value == '$':
+        return default
+
     return value if len(value) < 2 or value[0] != '$' else value[1:]
 
 
@@ -107,9 +107,16 @@ def set_sf_tag(sf: pynmrstar.Saveframe, tag: str, value: Any):
     tagNames = [t[0] for t in sf.tags]
 
     if isinstance(value, str):
+
         if len(value) == 0:
             value = None
 
+        while value.startswith('$$'):
+            value = value[1:]
+
+        if len(value) == 0 or value == '$':
+            value = None
+
     if tag not in tagNames:
         sf.add_tag(tag, value)
         return

wwpdb/utils/nmr/NmrDpReport.py

@@ -1855,7 +1855,7 @@ def updateNonStandardResidueByExptlData(self, chain_id: str, seq_id: int, conten
             #     if self.__verbose:
             #         self.__lfh.write(f'+{self.__class_name__}.updateNonStandardResidueByExptlData() ++ Error  - Unknown seq_id {seq_id}\n')
             #     raise KeyError(f"+{self.__class_name__}.updateNonStandardResidueByExptlData() ++ Error  - Unknown seq_id {seq_id}")
-            #
+
         except StopIteration:
             if self.__verbose:
                 self.__lfh.write(f'+{self.__class_name__}.updateNonStandardResidueByExptlData() ++ Error  - Unknown chain_id {chain_id}')

wwpdb/utils/nmr/NmrDpUtility.py

@@ -10591,7 +10591,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
 
                         s = re.split('[ ()]', _line)
 
-                        _t_lower = ""
+                        _t_lower = ''
 
                         for t in s:
 
@@ -10678,7 +10678,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
 
                         s = re.split('[ ()=]', _line)
 
-                        _t_lower = ""
+                        _t_lower = ''
 
                         for t in s:
 
@@ -11740,7 +11740,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
             if not is_aux_amb and not is_aux_gro and not is_aux_cha and not has_chem_shift and not has_dist_restraint and not has_dihed_restraint and not has_rdc_restraint\
                and not has_plane_restraint and not has_hbond_restraint and not has_ssbond_restraint and not valid:
 
-                hint = ""
+                hint = ''
                 if len(concat_nmr_restraint_names(content_subtype)) == 0:
                     if file_type in ('nm-res-xpl', 'nm-res-cns') and not has_rdc_origins:
                         hint = 'assign ( segid $ and resid # and name $ ) ( segid $ and resid # and name $ ) #.# #.# #.#'
@@ -11762,7 +11762,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
 
             elif is_aux_amb and not has_amb_coord and not has_topology:
 
-                subtype_name = ""
+                subtype_name = ''
                 if has_chem_shift:
                     subtype_name += "Assigned chemical shifts, "
                 if has_dist_restraint:
@@ -11802,7 +11802,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
 
             elif is_aux_gro and not has_topology:
 
-                subtype_name = ""
+                subtype_name = ''
                 if has_chem_shift:
                     subtype_name += "Assigned chemical shifts, "
                 if has_dist_restraint:
@@ -11836,7 +11836,7 @@ def __detectContentSubTypeOfLegacyMr(self) -> bool:
 
             elif is_aux_cha and not has_topology:
 
-                subtype_name = ""
+                subtype_name = ''
                 if has_chem_shift:
                     subtype_name += "Assigned chemical shifts, "
                 if has_dist_restraint:

wwpdb/utils/nmr/ann/BMRBAnnTasks.py

@@ -11,9 +11,9 @@
 import copy
 import pynmrstar
 
-from typing import IO, List, Optional
 from packaging import version
 from operator import itemgetter
+from typing import IO, List, Optional
 
 try:
     from wwpdb.utils.nmr.ChemCompUtil import ChemCompUtil

wwpdb/utils/nmr/ann/OneDepAnnTasks.py

@@ -14,6 +14,7 @@
 import collections
 
 from typing import IO, List
+
 from wwpdb.utils.align.alignlib import PairwiseAlign  # pylint: disable=no-name-in-module
 
 try: