Fix AttributeError exception of isReservedLigCode() and rename io/Che…

…mCompIo.py -> io/ChemCompReader.py

wwpdb/utils/nmr/AlignUtil.py

@@ -95,7 +95,7 @@ def isReservedLigCode(compId: str) -> bool:
     """
     if compId in reservedLigCode:
         return True
-    if len(compId) == 2 and compId[0].isdigit() and compId[1].digit() and compId != '00':
+    if len(compId) == 2 and compId[0].isdigit() and compId[1].isdigit() and compId != '00':
         return True
     return False
 

wwpdb/utils/nmr/ChemCompUtil.py

@@ -24,15 +24,17 @@
 try:
     from wwpdb.utils.config.ConfigInfo import getSiteId
     from wwpdb.utils.config.ConfigInfoApp import ConfigInfoAppCc
-    from wwpdb.utils.nmr.io.ChemCompIo import ChemCompReader
+    from wwpdb.utils.nmr.io.ChemCompReader import (ChemCompReader,
+                                                   ccd_id_pattern)
     from wwpdb.utils.nmr.AlignUtil import (emptyValue,
                                            monDict3,
                                            protonBeginCode,
                                            isReservedLigCode)
     cICc = ConfigInfoAppCc(getSiteId())
     CC_CVS_PATH = cICc.get_site_cc_cvs_path()
 except ImportError:
-    from nmr.io.ChemCompIo import ChemCompReader
+    from nmr.io.ChemCompReader import (ChemCompReader,
+                                       ccd_id_pattern)
     from nmr.AlignUtil import (emptyValue,
                                monDict3,
                                protonBeginCode,
@@ -58,7 +60,7 @@ def __init__(self, verbose: bool = False, log: IO = sys.stderr):
         self.lastAtomList = None
         self.lastBonds = None
 
-        # taken from wwpdb.utils.nmr.io.ChemCompIo
+        # taken from wwpdb.utils.nmr.io.ChemCompReader
         _chemCompAtomDict = [
             ('_chem_comp_atom.comp_id', '%s', 'str', ''),
             ('_chem_comp_atom.atom_id', '%s', 'str', ''),
@@ -114,7 +116,7 @@ def __init__(self, verbose: bool = False, log: IO = sys.stderr):
         cTerminalAtomFlag = next(d for d in _chemCompAtomDict if d[0] == '_chem_comp_atom.pdbx_c_terminal_atom_flag')
         self.ccaCTerminalAtomFlag = _chemCompAtomDict.index(cTerminalAtomFlag)
 
-        # taken from wwpdb.utils.nmr.io.ChemCompIo
+        # taken from wwpdb.utils.nmr.io.ChemCompReader
         _chemCompBondDict = [
             ('_chem_comp_bond.comp_id', '%s', 'str', ''),
             ('_chem_comp_bond.atom_id_1', '%s', 'str', ''),
@@ -156,7 +158,8 @@ 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 or isReservedLigCode(compId):
+        if compId in emptyValue or not isinstance(compId, str)\
+           or not ccd_id_pattern.match(compId) or isReservedLigCode(compId):
             return False
 
         compId = compId.upper()

wwpdb/utils/nmr/NmrDpUtility.py

@@ -614,7 +614,7 @@
 
 possible_typo_for_comment_out_pattern = re.compile(r'\s*([13])$')
 
-sparky_assignment_pattern = re.compile(r'[0-9A-Za-z_\+\*\?\'\"]+-[0-9A-Za-z_\+\*\?\'\"]+\S*')
+sparky_assignment_pattern = re.compile(r'[\w\+\*\?\'\"]+-[\w\+\*\?\'\"]+\S*')
 
 comment_code_mixed_set = {'#', '!'}
 

wwpdb/utils/nmr/io/ChemCompIo.py → wwpdb/utils/nmr/io/ChemCompReader.py

@@ -1,5 +1,5 @@
 ##
-# File: ChemCompIo.py
+# File: ChemCompReader.py
 # Date: 31-May-2010  John Westbrook
 #
 # Update:
@@ -19,7 +19,7 @@
 
 import sys
 import os
-import traceback
+import re
 
 from mmcif.io.PdbxReader import PdbxReader
 from typing import IO, List, Optional
@@ -33,6 +33,9 @@
                                isReservedLigCode)
 
 
+ccd_id_pattern = re.compile(r'(\w{1,3}|\w{5})')
+
+
 class ChemCompReader:
     """ Accessor methods chemical component definition data files
     """
@@ -134,7 +137,8 @@ def setCompId(self, compId: str) -> bool:
         """ Set chemical component definition data file path of the input chemical component
         """
 
-        if compId in emptyValue:
+        if compId in emptyValue or not isinstance(compId, str)\
+           or not ccd_id_pattern.match(compId) or isReservedLigCode(compId):
             return False
 
         self.__ccU = compId.upper()
@@ -144,11 +148,8 @@ def setCompId(self, compId: str) -> bool:
         self.__filePath = os.path.join(self.__topCachePath, hashKey, self.__ccU, self.__ccU + '.cif')
 
         if not os.access(self.__filePath, os.R_OK):
-
-            if self.__verbose and len(compId) in (3, 5) and compId[-1] not in ('+', '-')\
-               and not isReservedLigCode(compId):
+            if self.__verbose:
                 self.__lfh.write(f"+{self.__class_name__}.setCompId() ++ Error  - Missing file {self.__filePath}\n")
-
             return False
 
         return True
@@ -159,28 +160,24 @@ def setFilePath(self, filePath: str, compId: Optional[str] = None) -> bool:
 
         try:
 
-            if compId in emptyValue:
+            if compId in emptyValue or not isinstance(compId, str)\
+               or not ccd_id_pattern.match(compId) or not isReservedLigCode(compId):
                 return False
 
             self.__ccU = str(compId).upper()
 
             self.__filePath = filePath
 
             if not os.access(self.__filePath, os.R_OK):
-
-                if self.__verbose and len(compId) in (3, 5) and compId[-1] not in ('+', '-')\
-                   and not isReservedLigCode(compId):
+                if self.__verbose:
                     self.__lfh.write(f"+{self.__class_name__}.setFilePath() ++ Error  - Missing file {self.__filePath}\n")
-
                 return False
 
             return True
 
         except Exception as e:
-
             if self.__verbose:
                 self.__lfh.write(f"+{self.__class_name__}.setFilePath() ++ Error  - Set {self.__filePath} failed {str(e)}\n")
-
             return False
 
     def getAtomList(self) -> List[list]:
@@ -226,8 +223,9 @@ def __getComp(self) -> bool:
 
             return self.__setDataBlock(block)
 
-        except Exception:
-            traceback.print_exc(file=sys.stdout)
+        except Exception as e:
+            if self.__verbose:
+                self.__lfh.write(f"+{self.__class_name__}.__getComp() ++ Error  - {str(e)}\n")
             return False
 
     def __getDataBlock(self, filePath: str, blockId: Optional[str] = None):
@@ -261,8 +259,9 @@ def __getDataBlock(self, filePath: str, blockId: Optional[str] = None):
 
             return None
 
-        except Exception:
-            traceback.print_exc(file=self.__lfh)
+        except Exception as e:
+            if self.__verbose:
+                self.__lfh.write(f"+{self.__class_name__}.__getDataBlock() ++ Error  - {str(e)}\n")
             return None
 
     def __setDataBlock(self, dataBlock) -> bool:

wwpdb/utils/nmr/mr/IsdMRParserListener.py

@@ -374,7 +374,7 @@ def __init__(self, verbose: bool = True, log: IO = sys.stdout,
 
         self.distRestraints = 0      # ISD: Distance restraints
 
-        self.atom_sele_pat = re.compile(r'([A-Z][0-9A-Z]{2})(\d+)([A-Z][A-Z0-9]*)')
+        self.atom_sele_pat = re.compile(r'([A-Z][0-9A-Z]{2})(\d+)([A-Z][0-9A-Z]*)')
 
         self.sfDict = {}
 

wwpdb/utils/nmr/mr/SybylMRParserListener.py

@@ -374,7 +374,7 @@ def __init__(self, verbose: bool = True, log: IO = sys.stdout,
 
         self.distRestraints = 0      # SYBYL: Distance restraints
 
-        self.atom_sele_pat = re.compile(r'([A-Z][0-9A-Z]{2})(\d+)\.([A-Z][A-Z0-9]*)')
+        self.atom_sele_pat = re.compile(r'([A-Z][0-9A-Z]{2})(\d+)\.([A-Z][0-9A-Z]*)')
 
         self.sfDict = {}