Avoid using species as Species doesn't work in rmgmolecule

ReactionMechanismGenerator · Oct 14, 2023 · 1bbc02e · 1bbc02e
1 parent 2ad8713
commit 1bbc02e
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/src/Parse.jl b/src/Parse.jl
@@ -166,7 +166,12 @@ export getatomdictsmiles
 getatomdictinchi(inchi) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromInchi(inchi)))
 export getatomdictinchi
 function getatomdictadjlist(adjlist)
-    mol = species.Species().from_adjacency_list(adjlist).molecule[1]
+    _ , cutting_label_list = fragment.Fragment().detect_cutting_label(adjlist)
+    if isempty(cutting_label_list)
+        mol = molecule.Molecule().from_adjacency_list(adjlist)
+    else
+        mol = fragment.Fragment().from_adjacency_list(adjlist)
+    end
     if pybuiltin(:isinstance)(mol, molecule.Molecule)
         getatomdictfromrmg(mol)
     elseif pybuiltin(:isinstance)(mol, fragment.Fragment)

diff --git a/src/fluxdiagrams.jl b/src/fluxdiagrams.jl
@@ -42,7 +42,12 @@ function drawspc(spc::Species,path::String=".")
         end
     end
     if spc.adjlist != ""
-        mol = species.Species().from_adjacency_list(spc.adjlist).molecule[1]
+        _ , cutting_label_list = fragment.Fragment().detect_cutting_label(spc.adjlist)
+        if isempty(cutting_label_list)
+            mol = molecule.Molecule().from_adjacency_list(spc.adjlist)
+        else
+            mol = fragment.Fragment().from_adjacency_list(spc.adjlist)
+        end
     elseif spc.inchi != ""
         mol = molecule.Molecule().from_inchi(spc.inchi)
     elseif spc.smiles != ""

diff --git a/src/rmstest.jl b/src/rmstest.jl
@@ -7,11 +7,9 @@ const pydot = PyNULL()
 copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
 try
     copy!(molecule, pyimport("rmgpy.molecule"))
-    copy!(species, pyimport("rmgpy.species"))
     copy!(fragment, pyimport("rmgpy.molecule.fragment"))
 catch e
     copy!(molecule, pyimport_conda("molecule.molecule", "rmgmolecule", "hwpang"))
-    copy!(species, pyimport_conda("molecule.species", "rmgmolecule", "hwpang"))
     copy!(fragment, pyimport_conda("molecule.molecule.fragment", "rmgmolecule", "hwpang"))
 end
 copy!(pydot,pyimport_conda("pydot","pydot","rmg"))