changed amine to amide and added ether bond

lifs-tools · Dec 15, 2021 · 9624c79 · 9624c79
1 parent cc8544e
commit 9624c79
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Showing 5 changed files with 18 additions and 12 deletions.
diff --git a/cppgoslin/domain/LipidEnums.h b/cppgoslin/domain/LipidEnums.h
@@ -95,7 +95,7 @@ struct LipidClassMeta {
 
 
 typedef map<LipidClass, LipidClassMeta> ClassMap;
-enum LipidFaBondType { NO_FA, UNDEFINED_FA, ESTER, ETHER_PLASMANYL, ETHER_PLASMENYL, ETHER_UNSPECIFIED, LCB_REGULAR, LCB_EXCEPTION, AMINE};
+enum LipidFaBondType { NO_FA, UNDEFINED_FA, ESTER, ETHER_PLASMANYL, ETHER_PLASMENYL, ETHER, ETHER_UNSPECIFIED, LCB_REGULAR, LCB_EXCEPTION, AMIDE};
 
 static const set<LipidFaBondType> LCB_STATES {LCB_REGULAR, LCB_EXCEPTION};
 

diff --git a/src/domain/FattyAcid.cpp b/src/domain/FattyAcid.cpp
@@ -263,12 +263,12 @@ void FattyAcid::compute_elements(){
             elements->at(ELEMENT_H) = (2 * num_carbon - 1 - 2 * num_double_bonds + 2); // hydrogen
         }
 
-        else if (lipid_FA_bond_type == ETHER_PLASMANYL){
+        else if (lipid_FA_bond_type == ETHER_PLASMANYL || lipid_FA_bond_type == ETHER){
             elements->at(ELEMENT_H) = ((num_carbon + 1) * 2 - 1 - 2 * num_double_bonds); // hydrogen
         }
 
-        else if (lipid_FA_bond_type == AMINE)
-            elements->at(ELEMENT_H) = (2 * num_carbon + 1 - 2 * num_double_bonds); // hydrogen
+        else if (lipid_FA_bond_type == AMIDE)
+            elements->at(ELEMENT_H) = (2 * num_carbon + 1 - 2 * num_double_bonds) - 1; // hydrogen
 
         else {
             throw LipidException("Mass cannot be computed for fatty acyl chain with this bond type");

diff --git a/src/domain/LipidSpecies.cpp b/src/domain/LipidSpecies.cpp
@@ -163,5 +163,10 @@ ElementTable* LipidSpecies::get_elements(){
     elements->at(ELEMENT_O) -= -additional_fa + info->num_ethers + headgroup->sp_exception + hydrochain;
     elements->at(ELEMENT_H) += -additional_fa + remaining_H + 2 * info->num_ethers + 2 * hydrochain;
 
+    if (contains_val(meta.special_cases, "Amide")){
+        elements->at(ELEMENT_O) -= meta.max_num_fa;
+        elements->at(ELEMENT_H) += meta.max_num_fa;
+    }
+
     return elements;
 }
diff --git a/src/parser/FattyAcidParserEventHandler.cpp b/src/parser/FattyAcidParserEventHandler.cpp
@@ -512,7 +512,7 @@ void FattyAcidParserEventHandler::set_fatty_acyl_type(TreeNode *node) {
     else if (contains_val(acetate_set, t)) headgroup = "WE";
     else if (t == "ne"){
         headgroup = "HC";
-        fatty_acyl_stack.back()->lipid_FA_bond_type = AMINE;
+        fatty_acyl_stack.back()->lipid_FA_bond_type = ETHER;
     }
     else {
         headgroup = t;
@@ -1057,9 +1057,7 @@ void FattyAcidParserEventHandler::add_wax_ester(TreeNode *node) {
     FattyAcid *fa = fatty_acyl_stack.back();
     fatty_acyl_stack.pop_back();
 
-    fa->name += "1";
-    fa->lipid_FA_bond_type = AMINE;
-    fatty_acyl_stack.back()->name += "2";
+    fa->lipid_FA_bond_type = ETHER;
     fatty_acyl_stack.insert(fatty_acyl_stack.begin(), fa);
 }
 
@@ -1110,9 +1108,8 @@ void FattyAcidParserEventHandler::add_amine(TreeNode *node) {
     FattyAcid *fa = fatty_acyl_stack.back();
     fatty_acyl_stack.pop_back();
 
-    fa->name += "1";
-    fatty_acyl_stack.back()->name += "2";
-    fa->lipid_FA_bond_type = AMINE;
+    fa->lipid_FA_bond_type = AMIDE;
+    fatty_acyl_stack[fatty_acyl_stack.size() - 1]->lipid_FA_bond_type = AMIDE;
     fatty_acyl_stack.insert(fatty_acyl_stack.begin(), fa);
 }
 

diff --git a/src/parser/LipidBaseParserEventHandler.cpp b/src/parser/LipidBaseParserEventHandler.cpp
@@ -110,7 +110,11 @@ Headgroup* LipidBaseParserEventHandler::prepare_headgroup_and_checks(){
     if (contains_val(LipidClasses::get_instance().lipid_classes, headgroup->lipid_class)){
 
         if (contains_val(LipidClasses::get_instance().lipid_classes.at(headgroup->lipid_class).special_cases, "HC")){
-            fa_list->front()->lipid_FA_bond_type = AMINE;
+            fa_list->front()->lipid_FA_bond_type = ETHER;
+        }
+
+        if (contains_val(LipidClasses::get_instance().lipid_classes.at(headgroup->lipid_class).special_cases, "Amide")){
+            for (auto fatty : *fa_list) fatty->lipid_FA_bond_type = AMIDE;
         }
 
         int max_num_fa = LipidClasses::get_instance().lipid_classes.at(headgroup->lipid_class).max_num_fa;