updated tri hydro information

lifs-tools · Feb 23, 2024 · 2472b10 · 2472b10
1 parent 7430e6f
commit 2472b10
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/pygoslin/data/goslin/Goslin.g4 b/pygoslin/data/goslin/Goslin.g4
@@ -181,19 +181,20 @@ mediator_function_unknown_pos : mediator_functions;
 mediator_functions : mediator_mono_functions | mediator_di_functions | mediator_tri_functions;
 mediator_mono_functions: 'H' | 'Oxo' | 'oxo' | 'OXO' | 'keto' | 'Hp' | 'HP' | 'NO2' | 'K' | 'k' | 'hydroxy' | 'd' | 'deoxy' | 'beta';
 mediator_di_functions: 'E' | 'Ep' | 'EP' | 'DH' | 'DiH' | 'diH' | 'dihydro';
-mediator_tri_functions : 'triH' | 'trihydroxy';
+mediator_tri_functions : 'TriH' | 'triH' | 'trihydroxy';
 mediator_full_function : mediator_position_group '-' mediator_mono_functions | mediator_di_pos '-' mediator_di_functions | mediator_tri_pos '-' mediator_tri_functions | mediator_position_group mediator_mono_functions;
 mediator_db_function : mediator_double_bond_positions '-' mediator_mono_functions;
 mediator_double_bond_positions_full : '(' mediator_double_bond_positions ')';
 mediator_double_bond_positions : mediator_double_bond_position | mediator_double_bond_positions ',' mediator_double_bond_position;
 mediator_double_bond_position : mediator_double_bond_pos mediator_double_bond_ct;
 mediator_double_bond_pos : number;
 mediator_double_bond_ct : cistrans;
-mediator_di_pos: mediator_position_group mediator_separator mediator_position_group | mediator_position_group '(' mediator_position_group ')' | '(' mediator_position_group mediator_separator mediator_position_group ')' | mediator_position_group ',' mediator_position_group;
+mediator_di_pos: mediator_position_group mediator_separator mediator_position_group | mediator_position_group '(' mediator_position_group ')' | '(' mediator_position_group mediator_separator mediator_position_group ')';
 mediator_tri_pos: mediator_position_group mediator_separator mediator_position_group mediator_separator mediator_position_group | '(' mediator_position_group mediator_separator mediator_position_group mediator_separator mediator_position_group ')';
 mediator_position_group : mediator_position | mediator_position mediator_position_isotope | mediator_position '(' mediator_position_isotope ')' |  '(' mediator_position mediator_position_isotope ')';
 mediator_position : number;
 mediator_position_isotope : 'S' | 'R';
+mediator_separator : ',' | '-' | '_';
 
 trivial_mediator : 'AA' | 'ARA' | 'LA' | 'ALA' | 'DHA' | 'EPA' | 'Linoleic acid' | 'Arachidonic acid' | 'TXB1' | 'TXB2' | 'TXB3' | 'Resolvin D1' | 'Resolvin D2' | 'Resolvin D3' | 'Resolvin D5' | 'LTB4' | 'Mar1' | 'Maresin 1' | 'Palmitic acid' | 'PDX' | 'OA' | 'Oleic acid' | 'iPF2alpha-VI';
 

diff --git a/pygoslin/parser/GoslinParserEventHandler.py b/pygoslin/parser/GoslinParserEventHandler.py
@@ -270,7 +270,9 @@ def recursive_deletion(fg_name, fg, functional_groups):
                                     return True
 
                                 for fg_curr in fg_list_curr:
-                                    if recursive_deletion(fg_name, fg, fg_curr.functional_groups): break
+                                    if recursive_deletion(fg_name, fg, fg_curr.functional_groups): return True
+                            return False
+
                         if not recursive_deletion(fg_name, fg, self.current_fa.functional_groups):
                             if fg_name not in self.current_fa.functional_groups: self.current_fa.functional_groups[fg_name] = []
                             self.current_fa.functional_groups[fg_name].append(fg)
@@ -482,7 +484,6 @@ def new_fa(self, node):
 
 
     def append_fa(self, node):
-
         if type(self.current_fa.double_bonds) != int:
             if self.db_numbers > -1 and self.db_numbers != len(self.current_fa.double_bonds):
                 raise LipidException("Double bond count does not match with number of double bond positions")

diff --git a/pygoslin/parser/LipidBaseParserEventHandler.py b/pygoslin/parser/LipidBaseParserEventHandler.py
@@ -179,7 +179,7 @@ def resolve_fa_synonym(self, mediator_name):
         elif mediator_name in {"Linoleic acid", "LA"}:
             return FattyAcid("FA", 18, {9: "Z", 12: "Z"})
 
-        elif mediator_name in {"Arachidonic acid", "AA"}:
+        elif mediator_name in {"Arachidonic acid", "AA", "ARA"}:
             return FattyAcid("FA", 20, {5: "Z", 8: "Z", 11: "Z", 14: "Z"})
 
         elif mediator_name == "ALA":