Interprete XPLOR-NIH distance restraints using 'donor' and 'acceptor'…

… terms as XPLOR-NIH HBDB restraints (2n7j)
wwPDB · Jun 17, 2024 · dea0ad8 · dea0ad8
1 parent 384a6b1
commit dea0ad8
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diff --git a/wwpdb/utils/nmr/mr/XplorMRParserListener.py b/wwpdb/utils/nmr/mr/XplorMRParserListener.py
@@ -1844,6 +1844,8 @@ def enterNoe_assign(self, ctx: XplorMRParser.Noe_assignContext):  # pylint: disa
         self.paramagCenter = None
         self.__has_nx = False
 
+        self.donor_columnSel = self.acceptor_columnSel = -1
+
     # Exit a parse tree produced by XplorMRParser#noe_assign.
     def exitNoe_assign(self, ctx: XplorMRParser.Noe_assignContext):  # pylint: disable=unused-argument
 
@@ -1910,6 +1912,17 @@ def exitNoe_assign(self, ctx: XplorMRParser.Noe_assignContext):  # pylint: disab
                             self.exitTenso_assign(ctx)
                             return
 
+            if self.donor_columnSel != -1 and self.acceptor_columnSel != -1 and len(self.atomSelectionSet) == 2:
+                self.distRestraints -= 1
+                self.hbondRestraints += 1
+                if self.__cur_subtype_altered:
+                    self.distStatements -= 1
+                    if self.hbondStatements == 0:
+                        self.hbondStatements += 1
+                self.__cur_subtype = 'hbond'
+                self.exitHbond_db_assign(ctx)
+                return
+
             self.__cur_subtype = 'dist'  # to get consistent number of statement
 
             target = self.numberSelection[0]

diff --git a/wwpdb/utils/nmr/mr/XplorMRReader.py b/wwpdb/utils/nmr/mr/XplorMRReader.py
@@ -219,6 +219,11 @@ def parse(self, mrFilePath, cifFilePath=None, isFilePath=True,
 
 
 if __name__ == "__main__":
+    reader = XplorMRReader(True)
+    reader.setDebugMode(True)
+    reader.parse('../../tests-nmr/mock-data-remediation/2n7j/2n7j-corrected.mr',
+                 '../../tests-nmr/mock-data-remediation/2n7j/2n7j.cif')
+
     reader = XplorMRReader(True)
     reader.setDebugMode(True)
     reader.parse('../../tests-nmr/mock-data-remediation/2n05/2n05-corrected.mr',