better handling for SP without explicit OH description

lifs-tools · Jun 10, 2022 · b52123a · b52123a
1 parent a388642
commit b52123a
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Showing 2 changed files with 29 additions and 8 deletions.
diff --git a/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java b/parsers/src/main/java/org/lifstools/jgoslin/domain/FattyAcid.java
@@ -34,11 +34,12 @@
  * @author Nils Hoffmann
  */
 public class FattyAcid extends FunctionalGroup {
-
+
+    public static final Set<String> fgExceptions = new HashSet<>(Arrays.asList("acyl", "alkyl", "cy", "cc", "acetoxy"));
+    public static final Set<LipidFaBondType> LCB_STATES = new HashSet<>(Arrays.asList(LipidFaBondType.LCB_REGULAR, LipidFaBondType.LCB_EXCEPTION));
     protected int numCarbon;
     protected LipidFaBondType lipidFaBondType;
-    private final Set<String> fgExceptions = new HashSet<>(Arrays.asList("acyl", "alkyl", "cy", "cc", "acetoxy"));
-
+
     public FattyAcid(String _name, KnownFunctionalGroups knownFunctionalGroups) {
         this(_name, 0, null, null, LipidFaBondType.ESTER, 0, knownFunctionalGroups);
     }

diff --git a/parsers/src/main/java/org/lifstools/jgoslin/parser/ShorthandParserEventHandler.java b/parsers/src/main/java/org/lifstools/jgoslin/parser/ShorthandParserEventHandler.java
@@ -110,7 +110,8 @@ public ShorthandParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)
                     entry("carbohydrate_structural_pre_event", this::setCarbohydrateStructural),
                     entry("carbohydrate_isomeric_pre_event", this::setCarbohydrateIsomeric),
                     // fatty acyl events
-                    entry("lcb_post_event", this::setLcb),
+                    entry("lcb_pre_event", this::newLcb),
+                    entry("lcb_post_event", this::addFattyAcylChain),
                     entry("fatty_acyl_chain_pre_event", this::newFattyAcylChain),
                     entry("fatty_acyl_chain_post_event", this::addFattyAcylChain),
                     entry("carbon_pre_event", this::setCarbon),
@@ -128,6 +129,7 @@ public ShorthandParserEventHandler(KnownFunctionalGroups knownFunctionalGroups)
                     entry("func_group_count_pre_event", this::setFunctionalGroupCount),
                     entry("stereo_type_fg_pre_event", this::setFunctionalGroupStereo),
                     entry("molecular_func_group_name_pre_event", this::setSnPositionFuncGroup),
+                    entry("fa_db_only_post_event", this::addDiHydroxyl),
                     // set cycle events
                     entry("func_group_cycle_pre_event", this::setCycle),
                     entry("func_group_cycle_post_event", this::addCycle),
@@ -323,10 +325,10 @@ private void setCarbohydrateIsomeric(TreeNode node) {
         tmp.put("func_group_head", 1);
     }
 
-    private void setLcb(TreeNode node) {
-        FattyAcid fa = faList.get(faList.size() - 1);
-        fa.setName("LCB");
-        fa.setType(LipidFaBondType.LCB_REGULAR);
+    private void newLcb(TreeNode node) {
+        newFattyAcylChain(node);
+        currentFas.getLast().setName("LCB");
+        ((FattyAcid)currentFas.getLast()).setType(LipidFaBondType.LCB_REGULAR);
     }
 
     private void newFattyAcylChain(TreeNode node) {
@@ -422,6 +424,24 @@ private void setFunctionalGroup(TreeNode node) {
         gd.put("fg_ring_stereo", "");
     }
 
+
+    private void addDiHydroxyl(TreeNode node) {
+        if (!FattyAcid.LCB_STATES.contains(((FattyAcid)currentFas.getLast()).getLipidFaBondType())) return;
+        int num_h = 1;
+
+        if (FattyAcid.fgExceptions.contains(headGroup) && !headgroupDecorators.isEmpty()) {
+            num_h -= 1;
+        }
+
+        FunctionalGroup functional_group = knownFunctionalGroups.get("OH");
+        functional_group.setCount(num_h);
+        if (!currentFa.getFunctionalGroupsInternal().containsKey("OH")) {
+            currentFa.getFunctionalGroupsInternal().put("OH", new ArrayList<>());
+        }
+        currentFa.getFunctionalGroupsInternal().get("OH").add(functional_group);
+    }
+
+
     private void addFunctionalGroup(TreeNode node) {
         Dictionary gd = (Dictionary) tmp.get(faI());
         String fg_name = (String) gd.get("fg_name");