Merge pull request #6 from ReactionMechanismGenerator/updatepycall

use improved pycall syntax

Author: mjohnson541

src/Parse.jl

@@ -113,22 +113,22 @@ function getatomdictfromrdkit(mol)
     retrives the number of each type of atom and the number of bonds of an rdkit molecule
     """
     atmD = Dict{String,Int64}()
-    for atm in mol[:GetAtoms]()
-        v = elementdict[atm[:GetAtomicNum]()]
+    for atm in mol.GetAtoms()
+        v = elementdict[atm.GetAtomicNum()]
         if v in keys(atmD)
             atmD[v] += 1
         else
             atmD[v] = 1
         end
     end
-    nbonds = length(mol[:GetBonds]())
+    nbonds = length(mol.GetBonds())
     return atmD,nbonds
 end
 export getatomdictfromrdkit
 
-getatomdictsmiles(smiles) = getatomdictfromrdkit(Chem[:AddHs](Chem[:MolFromSmiles](smiles)))
+getatomdictsmiles(smiles) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromSmiles(smiles)))
 export getatomdictsmiles
-getatomdictinchi(inchi) = getatomdictfromrdkit(Chem[:AddHs](Chem[:MolFromInchi](inchi)))
+getatomdictinchi(inchi) = getatomdictfromrdkit(Chem.AddHs(Chem.MolFromInchi(inchi)))
 export getatomdictinchi
 
 function getspeciesradius(atomdict::Dict{String,Int64},nbonds::Int64)

src/fluxdiagrams.jl

@@ -42,13 +42,13 @@ function drawspc(spc::Species,path::String=".")
         end
     end
     if spc.inchi != ""
-        mol = molecule[:Molecule]()[:fromInChI](spc.inchi)
+        mol = molecule.Molecule().fromInChI(spc.inchi)
     elseif spc.smiles != ""
-        mol = molecule[:Molecule]()[:fromSMILES](spc.smiles)
+        mol = molecule.Molecule().fromSMILES(spc.smiles)
     else
         throw(error("no smiles or inchi for molecule $name"))
     end
-    mol[:draw](joinpath(path,fname))
+    mol.draw(joinpath(path,fname))
 end
 export drawspc
 
@@ -203,16 +203,16 @@ function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpo
         end
     end
 
-    graph = pydot[:Dot]("flux_diagram",graph_type="digraph",overlap="false")
-    graph[:set_rankdir]("LR")
-    graph[:set_fontname]("sans")
-    graph[:set_fontsize]("10")
+    graph = pydot.Dot("flux_diagram",graph_type="digraph",overlap="false")
+    graph.set_rankdir("LR")
+    graph.set_fontname("sans")
+    graph.set_fontsize("10")
 
     for index in nodes
         species = specieslist[index]
-        node = pydot[:Node](name=species.name)
-        node[:set_penwidth](maximumnodepenwidth)
-        graph[:add_node](node)
+        node = pydot.Node(name=species.name)
+        node.set_penwidth(maximumnodepenwidth)
+        graph.add_node(node)
 
         speciesindex = string(species.name,".png")
         imagepath = ""
@@ -228,22 +228,22 @@ function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpo
             end
         end
         if isfile(imagepath)
-            node[:set_image](imagepath)
-            node[:set_label](" ")
+            node.set_image(imagepath)
+            node.set_label(" ")
         end
     end
 
     for (reactantindex,productindex) in edges
         if reactantindex in nodes && productindex in nodes
             reactant = specieslist[reactantindex]
             product = specieslist[productindex]
-            edge = pydot[:Edge](reactant.name,product.name)
-            edge[:set_penwidth](maximumedgepenwidth)
-            graph[:add_edge](edge)
+            edge = pydot.Edge(reactant.name,product.name)
+            edge.set_penwidth(maximumedgepenwidth)
+            graph.add_edge(edge)
         end
     end
 
-    graph = pydot[:graph_from_dot_data](graph[:create_dot](prog="dot"))[1]
+    graph = pydot.graph_from_dot_data(graph.create_dot(prog="dot"))[1]
 
     for t in 1:length(ts)
         slope = -maximumnodepenwidth / log10(concentrationtol)
@@ -255,15 +255,15 @@ function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpo
                 species_string = string("\"",species.name,"\"")
             end
 
-            node = graph[:get_node](species_string)[1]
+            node = graph.get_node(species_string)[1]
             concentration = concentrations[index,t] / maxconcentration
             if concentration < concentrationtol
                 penwidth = 0.0
             else
                 penwidth = round((slope*log10(concentration)+maximumnodepenwidth)*1.0e3)/1.0e3
             end
 
-            node[:set_penwidth](penwidth)
+            node.set_penwidth(penwidth)
         end
 
         slope = -maximumedgepenwidth / log10(speciesratetolerance)
@@ -294,25 +294,25 @@ function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpo
                     product_string = string("\"",product.name,"\"")
                 end
 
-                edge = graph[:get_edge](reactant_string,product_string)[1]
+                edge = graph.get_edge(reactant_string,product_string)[1]
 
                 speciesrate = speciesrates[reactantindex,productindex,t] / maxspeciesrate
                 if speciesrate < 0
-                    edge[:set_dir]("back")
+                    edge.set_dir("back")
                     speciesrate = -speciesrate
                 else
-                    edge[:set_dir]("forward")
+                    edge.set_dir("forward")
                 end
 
                 if speciesrate < speciesratetolerance
                     penwidth = 0.0
-                    edge[:set_dir]("none")
+                    edge.set_dir("none")
                 else
                     penwidth = round((slope*log10(speciesrate) + maximumedgepenwidth)*1.0e3)/1.0e3
                 end
 
-                edge[:set_penwidth](penwidth)
-                edge[:set_color](getcolor(speciesrates[reactantindex,productindex,t],maxspeciesrate,minspeciesrate,colorscheme))
+                edge.set_penwidth(penwidth)
+                edge.set_color(getcolor(speciesrates[reactantindex,productindex,t],maxspeciesrate,minspeciesrate,colorscheme))
 
             end
         end
@@ -324,10 +324,10 @@ function makefluxdiagrams(bsol,ts;centralspecieslist=Array{String,1}(),superimpo
             label = "t = 10^$tval s"
         end
 
-        graph[:set_label](label)
-        graph[:write_dot](joinpath(outputdirectory,"flux_diagram_$t.dot"))
-        graph[:write_png](joinpath(outputdirectory,"flux_diagram_$t.png"))
-        graph[:write_svg](joinpath(outputdirectory,"flux_diagram_$t.svg"))
+        graph.set_label(label)
+        graph.write_dot(joinpath(outputdirectory,"flux_diagram_$t.dot"))
+        graph.write_png(joinpath(outputdirectory,"flux_diagram_$t.png"))
+        graph.write_svg(joinpath(outputdirectory,"flux_diagram_$t.svg"))
     end
     return FluxDiagram(ts,outputdirectory)
 end

src/yml.jl

@@ -1,15 +1,15 @@
 function convertchemkin2yml(chemkinpath;spcdictpath="",output="chem.rms")
     if spcdictpath != ""
-        spcs,rxns = chemkin[:loadChemkinFile](chemkinpath,dictionaryPath=spcdictpath)
+        spcs,rxns = chemkin.loadChemkinFile(chemkinpath,dictionaryPath=spcdictpath)
     else
-        spcs,rxns = chemkin[:loadChemkinFile](chemkinpath)
+        spcs,rxns = chemkin.loadChemkinFile(chemkinpath)
     end
     writeyml(spcs,rxns;path=output)
 end
 
 function writeyml(spcs,rxns;path="chem.rms")
     D = getmechdict(spcs,rxns)
-    yaml[:dump](D,stream=pybuiltin("file")(path,"w"))
+    yaml.dump(D,stream=pybuiltin("file")(path,"w"))
 end
 
 function getmechdict(spcs,rxns)
@@ -24,103 +24,107 @@ function getmechdict(spcs,rxns)
 end
 
 function getradicals(obj::T) where {T}
-    sm = obj[:molecule][1][:toSMILES]()
+    sm = obj.molecule[1].toSMILES()
     if sm == "[O][O]"
         return 0
     else
-        return obj[:molecule][1][:multiplicity]-1
+        return obj.molecule[1].multiplicity-1
     end
 end
 
 function obj2dict(obj,spcs;label="solvent")
     D = Dict([])
-    if pybuiltin("isinstance")(obj,species[:Species])
-        D["name"] = obj[:label]
+    if pybuiltin("isinstance")(obj,species.Species)
+        D["name"] = obj.label
         D["type"] = "Species"
-        D["smiles"] = obj[:molecule][1][:toSMILES]()
-        D["thermo"] = obj2dict(obj[:thermo],spcs)
+        if length(obj.molecule) == 0
+            println(obj)
+            println(obj.label)
+        end
+        D["smiles"] = obj.molecule[1].toSMILES()
+        D["thermo"] = obj2dict(obj.thermo,spcs)
         if D["smiles"] != "[O][O]"
-            D["radicalelectrons"] = obj[:molecule][1][:multiplicity]-1
+            D["radicalelectrons"] = obj.molecule[1].multiplicity-1
         else
             D["radicalelectrons"] = 0
         end
-    elseif pybuiltin("isinstance")(obj,nasa[:NASA])
-        D["polys"] = [obj2dict(k,spcs) for k in obj[:polynomials]]
+    elseif pybuiltin("isinstance")(obj,nasa.NASA)
+        D["polys"] = [obj2dict(k,spcs) for k in obj.polynomials]
         D["type"] = "NASA"
-    elseif pybuiltin("isinstance")(obj,nasa[:NASAPolynomial])
+    elseif pybuiltin("isinstance")(obj,nasa.NASAPolynomial)
         D["type"] = "NASApolynomial"
-        D["coefs"] = PyVector(obj[:coeffs])
-        D["Tmax"] = obj[:Tmax][:value_si]
-        D["Tmin"] = obj[:Tmin][:value_si]
-    elseif pybuiltin("isinstance")(obj,reaction[:Reaction])
-        D["reactants"] = [x[:label] for x in obj[:reactants]]
-        D["products"] = [x[:label] for x in obj[:products]]
-        D["kinetics"] = obj2dict(obj[:kinetics],spcs)
+        D["coefs"] = PyVector(obj.coeffs)
+        D["Tmax"] = obj.Tmax.value_si
+        D["Tmin"] = obj.Tmin.value_si
+    elseif pybuiltin("isinstance")(obj,reaction.Reaction)
+        D["reactants"] = [x.label for x in obj.reactants]
+        D["products"] = [x.label for x in obj.products]
+        D["kinetics"] = obj2dict(obj.kinetics,spcs)
         D["type"] = "ElementaryReaction"
-        D["radicalchange"] = sum([getradicals(x) for x in obj[:products]])-sum([getradicals(x) for x in obj[:reactants]])
-    elseif pybuiltin("isinstance")(obj,arrhenius[:Arrhenius])
+        D["radicalchange"] = sum([getradicals(x) for x in obj.products])-sum([getradicals(x) for x in obj.reactants])
+    elseif pybuiltin("isinstance")(obj,arrhenius.Arrhenius)
         D["type"] = "Arrhenius"
-        D["A"] = obj[:A][:value_si]
-        D["Ea"] = obj[:Ea][:value_si]
-        D["n"] = obj[:n][:value_si]
-    elseif pybuiltin("isinstance")(obj,arrhenius[:PDepArrhenius])
+        D["A"] = obj.A.value_si
+        D["Ea"] = obj.Ea.value_si
+        D["n"] = obj.n.value_si
+    elseif pybuiltin("isinstance")(obj,arrhenius.PDepArrhenius)
         D["type"] = "PdepArrhenius"
-        D["Ps"] = PyVector(obj[:pressures][:value_si])
-        D["arrs"] = [obj2dict(x,spcs) for x in obj[:arrhenius]]
-    elseif pybuiltin("isinstance")(obj,arrhenius[:MultiArrhenius])
+        D["Ps"] = PyVector(obj.pressures.value_si)
+        D["arrs"] = [obj2dict(x,spcs) for x in obj.arrhenius]
+    elseif pybuiltin("isinstance")(obj,arrhenius.MultiArrhenius)
         D["type"] = "MultiArrhenius"
-        D["arrs"] = [obj2dict(x,spcs) for x in obj[:arrhenius]]
-    elseif pybuiltin("isinstance")(obj,arrhenius[:MultiPDepArrhenius])
+        D["arrs"] = [obj2dict(x,spcs) for x in obj.arrhenius]
+    elseif pybuiltin("isinstance")(obj,arrhenius.MultiPDepArrhenius)
         D["type"] = "MultiPdepArrhenius"
-        D["parrs"] = [obj2dict(x,spcs) for x in obj[:arrhenius]]
-    elseif pybuiltin("isinstance")(obj,falloff[:ThirdBody])
+        D["parrs"] = [obj2dict(x,spcs) for x in obj.arrhenius]
+    elseif pybuiltin("isinstance")(obj,falloff.ThirdBody)
         D["type"] = "ThirdBody"
-        D["arr"] = obj2dict(obj[:arrheniusLow],spcs)
-        D["efficiencies"] = Dict([spcs[i][:label]=>float(val) for (i,val) in enumerate(obj[:getEffectiveColliderEfficiencies](spcs)) if val != 1])
-    elseif pybuiltin("isinstance")(obj,falloff[:Lindemann])
+        D["arr"] = obj2dict(obj.arrheniusLow,spcs)
+        D["efficiencies"] = Dict([spcs[i].label=>float(val) for (i,val) in enumerate(obj.getEffectiveColliderEfficiencies(spcs)) if val != 1])
+    elseif pybuiltin("isinstance")(obj,falloff.Lindemann)
         D["type"] = "Lindemann"
-        D["arrhigh"] = obj2dict(obj[:arrheniusHigh],spcs)
-        D["arrlow"] = obj2dict(obj[:arrheniusLow],spcs)
-        D["efficiencies"] = Dict([spcs[i][:label]=>float(val) for (i,val) in enumerate(obj[:getEffectiveColliderEfficiencies](spcs)) if val != 1])
-    elseif pybuiltin("isinstance")(obj,falloff[:Troe])
+        D["arrhigh"] = obj2dict(obj.arrheniusHigh,spcs)
+        D["arrlow"] = obj2dict(obj.arrheniusLow,spcs)
+        D["efficiencies"] = Dict([spcs[i].label=>float(val) for (i,val) in enumerate(obj.getEffectiveColliderEfficiencies(spcs)) if val != 1])
+    elseif pybuiltin("isinstance")(obj,falloff.Troe)
         D["type"] = "Troe"
-        D["arrhigh"] = obj2dict(obj[:arrheniusHigh],spcs)
-        D["arrlow"] = obj2dict(obj[:arrheniusLow],spcs)
-        D["efficiencies"] = Dict([spcs[i][:label]=>float(val) for (i,val) in enumerate(obj[:getEffectiveColliderEfficiencies](spcs)) if val != 1])
-        D["a"] = obj[:alpha]
-        D["T1"] = obj[:T1][:value_si]
-        if !isa(obj[:T2],Nothing)
-            D["T2"] = obj[:T2][:value_si]
+        D["arrhigh"] = obj2dict(obj.arrheniusHigh,spcs)
+        D["arrlow"] = obj2dict(obj.arrheniusLow,spcs)
+        D["efficiencies"] = Dict([spcs[i].label=>float(val) for (i,val) in enumerate(obj.getEffectiveColliderEfficiencies(spcs)) if val != 1])
+        D["a"] = obj.alpha
+        D["T1"] = obj.T1.value_si
+        if !isa(obj.T2,Nothing)
+            D["T2"] = obj.T2.value_si
         else
             D["T2"] = 0.0
         end
-        D["T3"] = obj[:T3][:value_si]
-    elseif pybuiltin("isinstance")(obj,chebyshev[:Chebyshev])
+        D["T3"] = obj.T3.value_si
+    elseif pybuiltin("isinstance")(obj,chebyshev.Chebyshev)
         D["type"] = "Chebyshev"
-        n,m = size(obj[:coeffs][:value_si])
-        D["coefs"] = PyVector([PyVector(obj[:coeffs][:value_si][i,:]) for i in 1:n])
-        D["Tmin"] = obj[:Tmin][:value_si]
-        D["Tmax"] = obj[:Tmax][:value_si]
-        D["Pmin"] = obj[:Pmin][:value_si]
-        D["Pmax"] = obj[:Pmax][:value_si]
-    elseif pybuiltin("isinstance")(obj,wilhoit[:Wilhoit])
+        n,m = size(obj.coeffs.value_si)
+        D["coefs"] = PyVector([PyVector(obj.coeffs.value_si[i,:]) for i in 1:n])
+        D["Tmin"] = obj.Tmin.value_si
+        D["Tmax"] = obj.Tmax.value_si
+        D["Pmin"] = obj.Pmin.value_si
+        D["Pmax"] = obj.Pmax.value_si
+    elseif pybuiltin("isinstance")(obj,wilhoit.Wilhoit)
         D["type"] = "Wilhoit"
-        D["coefs"] = [obj[:a0],obj[:a1],obj[:a2],obj[:a3]]
-        D["Cp0"] = obj[:Cp0][:value_si]
-        D["Cpinf"] = obj[:CpInf][:value_si]
-        D["H0"] = obj[:H0][:value_si]
-        D["S0"] = obj[:S0][:value_si]
-        D["B"] = obj[:B][:value_si]
-    elseif pybuiltin("isinstance")(obj,solvation[:SolventData])
+        D["coefs"] = [obj.a0,obj.a1,obj.a2,obj.a3]
+        D["Cp0"] = obj.Cp0.value_si
+        D["Cpinf"] = obj.CpInf.value_si
+        D["H0"] = obj.H0.value_si
+        D["S0"] = obj.S0.value_si
+        D["B"] = obj.B.value_si
+    elseif pybuiltin("isinstance")(obj,solvation.SolventData)
         D["type"] = "Solvent"
         D["name"] = label
         dsub = dict()
         dsub["type"] = "RiedelViscosity"
-        dsub["A"] = obj[:A][:value_si]
-        dsub["B"] = obj[:B][:value_si]
-        dsub["C"] = obj[:C][:value_si]
-        dsub["D"] = obj[:D][:value_si]
-        dsub["E"] = obj[:E][:value_si]
+        dsub["A"] = obj.A.value_si
+        dsub["B"] = obj.B.value_si
+        dsub["C"] = obj.C.value_si
+        dsub["D"] = obj.D.value_si
+        dsub["E"] = obj.E.value_si
         D["mu"] = dsub
     elseif pybuiltin("is")(obj,pybuiltin("None"))
         return pybuiltin("None")