Merge pull request #239 from hwpang/fix_fragment

Fix fragment smiles parser and refactor fragment adjlist parser

Author: mjohnson541

src/Parse.jl

@@ -161,24 +161,28 @@ function getatomdictfromrmg(mol)
     molecularweight = mol.get_molecular_weight()
     return atmD,nbonds,molecularweight
 end
-getatomdictsmiles(smiles) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
+function getatomdictsmiles(smiles)
+    if occursin(r"R", smiles) || occursin(r"L", smiles)
+        mol = fragment.Fragment().from_smiles_like_string(smiles)
+        mol.assign_representative_molecule()
+        getatomdictfromrmg(mol.mol_repr)
+    else
+        getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
+    end
+end
+
 export getatomdictsmiles
 getatomdictinchi(inchi) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromInchi(inchi)))
 export getatomdictinchi
 function getatomdictadjlist(adjlist)
     _ , cutting_label_list = fragment.Fragment().detect_cutting_label(adjlist)
     if isempty(cutting_label_list)
         mol = molecule.Molecule().from_adjacency_list(adjlist)
+        getatomdictfromrmg(mol)
     else
         mol = fragment.Fragment().from_adjacency_list(adjlist)
-    end
-    if pybuiltin(:isinstance)(mol, molecule.Molecule)
-        getatomdictfromrmg(mol)
-    elseif pybuiltin(:isinstance)(mol, fragment.Fragment)
         mol.assign_representative_molecule()
         getatomdictfromrmg(mol.mol_repr)
-    else
-        @error("Unrecognizable molecule type $mol")
     end
 end
 export getatomdictadjlist

src/TestParse.jl

@@ -9,3 +9,13 @@ s = r.products[1]
 @test getEnthalpy(s.thermo,1000.0) ≈ 20677.0 rtol=1e-4
 @test getEnthalpy(out["phase"]["Species"][5].thermo,1000.0) ≈ 20677.2 rtol=1e-4
 end;
+
+@testset "Read fragment input from file" begin
+    out = readinput("../src/testing/minimal_rmg_fragment.rms")
+    fragment = out["phase"]["Species"][5]
+
+    # check that fragment structure is parsed correctly and the representative molecule is assigned
+    @test fragment.atomnums["C"] == 18
+    @test fragment.molecularweight ≈ 0.25046 rtol=1e-4
+    @test fragment.radius ≈ 4.66375e-10 rtol=1e-4
+end;