make Fragment parsed by adjacency list

ReactionMechanismGenerator · Oct 4, 2023 · d330613 · d330613
1 parent ad91e7b
commit d330613
Showing 1 changed file with 14 additions and 6 deletions.
diff --git a/src/Parse.jl b/src/Parse.jl
@@ -165,7 +165,15 @@ getatomdictsmiles(smiles) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(s
 export getatomdictsmiles
 getatomdictinchi(inchi) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromInchi(inchi)))
 export getatomdictinchi
-getatomdictadjlist(adjlist) = getatomdictfromrmg(molecule.Molecule().from_adjacency_list(adjlist))
+function getatomdictadjlist(adjlist)
+    try
+        getatomdictfromrmg(molecule.Molecule().from_adjacency_list(adjlist))
+    catch
+        mol = species.Species().from_adjacency_list(adjlist).molecule[1]
+        mol.assign_representative_molecule()
+        getatomdictfromrmg(mol.mol_repr)
+    end
+end
 export getatomdictadjlist
 
 function getspeciesradius(atomdict,nbonds::Int64)
@@ -288,11 +296,11 @@ function readinputyml(fname::String)
             #attempt to generate molecular information from rdkit if possible
             if !("atomnums" in keys(d)) || !("bondnum" in keys(d)) || !("molecularweight" in keys(d))
                 if "adjlist" in keys(d)
-                    try
-                        d["atomnums"],d["bondnum"],d["molecularweight"] = getatomdictadjlist(d["adjlist"])
-                    catch
-                         @warn("failed to generate molecular information from smiles for species $spcname")
-                    end
+                    # try
+                    d["atomnums"],d["bondnum"],d["molecularweight"] = getatomdictadjlist(d["adjlist"])
+                    # catch
+                    #      @warn("failed to generate molecular information from adjlist for species $spcname")
+                    # end
                 elseif "smiles" in keys(d)
                     try
                         d["atomnums"],d["bondnum"],d["molecularweight"] = getatomdictsmiles(d["smiles"])