added trivial mediator db information

pygoslin/data/goslin/Goslin.g4

@@ -180,7 +180,7 @@ mediator_functional_group_clear: mediator_full_function | mediator_function_unkn
 mediator_function_unknown_pos : mediator_functions;
 mediator_functions : mediator_mono_functions | mediator_di_functions;
 mediator_mono_functions: 'H' | 'Oxo' | 'oxo' | 'OXO' | 'Hp' | 'HP' | 'NO2';
-mediator_di_functions: 'E' | 'Ep' | 'DH' | 'DiH' | 'diH';
+mediator_di_functions: 'E' | 'Ep' | 'EP' | 'DH' | 'DiH' | 'diH';
 mediator_full_function : mediator_position_group '-' mediator_mono_functions | mediator_di_pos '-' mediator_di_functions;
 mediator_di_pos: mediator_position_group ',' mediator_position_group | mediator_position_group '_' mediator_position_group | mediator_position_group '(' mediator_position_group ')';
 mediator_position_group : mediator_position | mediator_position mediator_position_isotope | mediator_position '(' mediator_position_isotope ')';

pygoslin/data/goslin/trivial_mediators.csv

@@ -0,0 +1,106 @@
+9S-HpODE	10,12
+13-Oxo-ODE	9,11
+9S-HOTrE	10,12,15
+13S-HpODE	9,11
+13R-HODE	9,11
+9(10)-EpOME	12
+12(13)-EpOME	9
+13S-HOTrE	9,11,15
+12,13S-EOT	9,11,15
+8R-HpOME	9
+13R-HpOME	11
+13S-HpOME	11
+12R-HpOME	13
+12S-HpOME	13
+14R-HpOME	12
+14S-HpOME	12
+12R-HpOME	13
+12S-HpOME	13
+10R-HpOME	11
+7-HpOME	5
+8-HpOME	6
+9-HpOME	7
+11-HpOME	9
+12-HpOME	10
+10R-HOME	11
+10S-HOME	11
+12R-HOME	13
+12S-HOME	13
+11R-HOME	12
+11S-HOME	12
+12R-HOME	10
+12S-HOME	10
+12R-HOME	13
+12S-HOME	13
+13R-HOME	11
+13S-HOME	11
+11R-HOME	12
+11S-HOME	12
+6-HpOME	7
+13-HpOME	14
+8R-HpODE	9,12
+13S-HpOTrE	9,11,14
+11S-HpODE	9,12
+9-HODE	10,12
+9S-HODE	10,12
+12R-HODE	9,15
+13R-HODE	9,11
+8R-HOME	9
+7S,8S-DiHODE	9,12
+7S,8S-DiHOME	9
+7S,8S-DiHOTrE	9,12,15
+8S-HODE	9,12
+13S-HODE	9,11
+9,10-DiHOME	12
+12,13-DiHOME	9
+9-OxoODE	10,12
+12,13S-EpODE	9,11
+12S,13R-EpOME	9
+9R,10S-EpOME	12
+8R-HODE	9,12
+17R,18S-EpETE	5,8,11,14
+5S,12R-diHETE	6,8,10,14
+12S-HHTrE	5,8,10
+15-HETrE	8,11,13
+5-HETrE	6,8,11
+8-HETrE	9,11,14
+12-oxoHT	5,8,10
+20-HETE	5,8,11,14
+5S-HpETE	6,8,11,14
+15S-HpETE	5,8,11,13
+11R-HETE	5,8,12,14
+8R-HpETE	5,9,11,14
+5,12-DiHETE	6,8,10,14
+8-HETE	5,9,11,14
+9-HETE	5,7,11,14
+11-HETE	5,8,12,14
+12-HETE	5,8,10,14
+12(S)-HETE	5,8,10,14
+12-HETE	5,8,10,14
+15-HETE	5,8,11,13
+15(R)-HETE	5,8,11,13
+5S,11R-DiHETE	6,8,12,14
+15-HPETE	5,8,11,13
+16-HETE	5,8,11,14
+19-HETE	5,8,11,14
+5,15-DiHETE	6,8,11,13
+5-HPETE	6,8,11,14
+13R-HETE	5,8,11,14
+11-HEPE	5,8,12,14,17
+14R,15S-EpETrE	5,8,11
+5,6-EET	8,11,14
+8,9-EET	5,11,14
+11,12-EET	5,8,14
+14,15-EET	5,8,11
+14S,15R-EpETrE	5,8,11
+11S,12R-EpETrE	5,8,14
+11R,12S-EpETrE	5,8,14
+5R,6S-EpETrE	8,11,14
+5S,6R-EpETrE	8,11,14
+8R,9S-EpETrE	5,11,14
+8S,9R-EpETrE	5,11,14
+17,18-diHEPE	5,8,11,13,15
+17R,18R-diHEPE	5,8,11,13,15
+17,18-diHEPE	5,8,11,13,15
+17R,18S-diHEPE	5,8,11,13,15
+10S,17S-DiHDoHE	4,7,11,13,15,19

pygoslin/parser/GoslinParserEventHandler.py

@@ -420,8 +420,13 @@ def build_lipid(self, node):
         if self.plasmalogen != "" and self.lcb == None and len(self.fa_list) > 0:
             self.fa_list[0].lipid_FA_bond_type = LipidFaBondType.ETHER_PLASMANYL if self.plasmalogen == "O" else LipidFaBondType.ETHER_PLASMENYL
 
+
         headgroup = self.prepare_headgroup_and_checks()
-
+
+        if self.trivial_mediator and node.get_text() in trivial_mediators:
+            self.fa_list[0].double_bonds = {p: "" for p in trivial_mediators[node.get_text()]}
+            self.level = LipidLevel.FULL_STRUCTURE
+
         lipid = LipidAdduct()
         lipid.adduct = self.adduct
         lipid.lipid = self.assemble_lipid(headgroup)
@@ -518,4 +523,11 @@ def add_heavy_component(self, node):
         self.adduct.heavy_elements[self.heavy_element] += self.heavy_element_number
 
 
-
+trivial_mediators = {}
+tm_dir_name = path.dirname(pygoslin.__file__)
+tm_file_name = path.join(tm_dir_name, "data", "goslin", "trivial_mediators.csv")
+with open(tm_file_name, mode = "rt", encoding= "utf-8") as tm_infile:
+    for line in tm_infile:
+        tokens = line.strip().split("\t")
+        if len(tokens) != 2: continue
+        trivial_mediators[tokens[0]] = [int(p) for p in tokens[1].split(",")]

pygoslin/parser/LipidBaseParserEventHandler.py

@@ -87,21 +87,6 @@ def sp_regular_lcb(self):
 
 
     def prepare_headgroup_and_checks(self, allow_class_shift = True):
-        # checking if head group is a glyco-sphingolipid
-        """
-        hg = self.head_group.lower()
-        if hg in glyco_table:
-            for carbohydrate in glyco_table[hg]:
-                try:
-                    
-                    functional_group = get_functional_group(carbohydrate)
-                    functional_group.elements[Element.O] -= 1
-                    self.headgroup_decorators.append(functional_group)
-                except Exception:
-                    raise LipidParsingException("Carbohydrate '%s' unknown" % carbohydrate)
-            self.head_group = "Cer"
-        """
-
 
         headgroup = HeadGroup(self.head_group, self.headgroup_decorators, self.use_head_group)
         if self.use_head_group: return headgroup

setup.py

@@ -63,6 +63,6 @@
     python_requires = '>=3.5',
     include_package_data = True,
     package_data = {
-        '': ['data/goslin/*.g4', 'data/goslin/*.G4', 'data/goslin/lipid-list.csv', 'data/goslin/functional-groups.csv'],
+        '': ['data/goslin/*.g4', 'data/goslin/*.G4', 'data/goslin/lipid-list.csv', 'data/goslin/functional-groups.csv', 'data/goslin/trivial_mediators.csv'],
     }
 )