make fragment compatible for rms

src/Parse.jl

@@ -165,7 +165,22 @@ 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)
+    _ , 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)
+        mol.assign_representative_molecule()
+        getatomdictfromrmg(mol.mol_repr)
+    else
+        @error("Unrecognizable molecule type $mol")
+    end
+end
 export getatomdictadjlist
 
 function getspeciesradius(atomdict,nbonds::Int64)
@@ -290,19 +305,25 @@ function readinputyml(fname::String)
                 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")
+                    catch e
+                        showerror(stdout, e)
+                        display(stacktrace(catch_backtrace()))
+                        @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"])
-                    catch
+                    catch e
+                        showerror(stdout, e)
+                        display(stacktrace(catch_backtrace()))
                         @warn("failed to generate molecular information from smiles for species $spcname")
                     end
                 elseif "inchi" in keys(d)
                     try
                         d["atomnums"],d["bondnum"],d["molecularweight"] = getatomdictinchi(d["inchi"])
-                    catch
+                    catch e
+                        showerror(stdout, e)
+                        display(stacktrace(catch_backtrace()))
                         @warn("failed to generate molecular information from inchi for species $spcname")
                     end
                 end

src/ReactionMechanismSimulator.jl

@@ -4,6 +4,7 @@ module ReactionMechanismSimulator
     const Chem = PyNULL()
     const Desc = PyNULL()
     const molecule = PyNULL()
+    const fragment = PyNULL()
     const pydot = PyNULL()
     const chemkin =PyNULL()
     const species = PyNULL()
@@ -29,6 +30,7 @@ module ReactionMechanismSimulator
             copy!(falloff,pyimport("rmgpy.kinetics.falloff"))
             copy!(chebyshev,pyimport("rmgpy.kinetics.chebyshev"))
             copy!(solvation,pyimport("rmgpy.data.solvation"))
+            copy!(fragment,pyimport("rmgpy.molecule.fragment"))
         catch e
             copy!(molecule,pyimport_conda("molecule.molecule","rmgmolecule","hwpang"))
             copy!(chemkin,pyimport_conda("molecule.chemkin","rmgmolecule","hwpang"))
@@ -40,6 +42,7 @@ module ReactionMechanismSimulator
             copy!(falloff,pyimport_conda("molecule.kinetics.falloff","rmgmolecule","hwpang"))
             copy!(chebyshev,pyimport_conda("molecule.kinetics.chebyshev","rmgmolecule","hwpang"))
             copy!(solvation,pyimport_conda("molecule.data.solvation","rmgmolecule","hwpang"))
+            copy!(fragment,pyimport_conda("molecule.molecule.fragment","rmgmolecule","hwpang"))
         end
         copy!(pydot,pyimport_conda("pydot","pydot"))
         copy!(os,pyimport_conda("os","os"))

src/Simulation.jl

@@ -319,7 +319,7 @@ end
 function rops(ssys::SystemSimulation, name, t)
     domains = getfield.(ssys.sims, :domain)
     ind = findfirst(isequal(name), ssys.names)
-    Nrxns = sum([length(sim.domain.phase.reactions) for sim in ssys.sims]) + sum([length(inter.reactions) for inter in ssys.interfaces if hasproperty(inter, :reactions)])
+    Nrxns = sum([length(sim.domain.phase.reactions) for sim in ssys.sims]) + sum(Vector{Int}([length(inter.reactions) for inter in ssys.interfaces if hasproperty(inter, :reactions)]))
     Nspcs = sum([length(getphasespecies(sim.domain.phase)) for sim in ssys.sims])
     cstot = zeros(Nspcs)
     vns = Array{Any,1}(undef, length(domains))

src/fluxdiagrams.jl

@@ -42,11 +42,20 @@ function drawspc(spc::Species,path::String=".")
         end
     end
     if spc.adjlist != ""
-        mol = molecule.Molecule().from_adjacency_list(spc.adjlist)
+        _ , 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 != ""
-        mol = molecule.Molecule().from_smiles(spc.smiles)
+        if occursin(r"R", spc.smiles) || occursin(r"L", spc.smiles)
+            mol = fragment.Fragment().from_smiles_like_string(spc.smiles)
+        else
+            mol = molecule.Molecule().from_smiles(spc.smiles)
+        end
     else
         throw(error("no smiles or inchi for molecule $name"))
     end

src/rmstest.jl

@@ -1,12 +1,15 @@
 using PyCall
 const Chem = PyNULL()
 const molecule = PyNULL()
+const fragment = PyNULL()
 const pydot = PyNULL()
 copy!(Chem,pyimport_conda("rdkit.Chem","rdkit","rmg"))
 try
     copy!(molecule, pyimport("rmgpy.molecule"))
+    copy!(fragment, pyimport("rmgpy.molecule.fragment"))
 catch e
     copy!(molecule, pyimport_conda("molecule.molecule", "rmgmolecule", "hwpang"))
+    copy!(fragment, pyimport_conda("molecule.molecule.fragment", "rmgmolecule", "hwpang"))
 end
 copy!(pydot,pyimport_conda("pydot","pydot","rmg"))