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make fragment compatible for rms #216

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merged 8 commits into from
Oct 17, 2023
Merged

make fragment compatible for rms #216

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17c09e1
Import fragment module
hwpang Oct 15, 2023
194ef9b
Add type to avoid error when summarizing over an empty list
hwpang Oct 15, 2023
288be53
Should be adjlist, not smiles. Fix indentation.
hwpang Oct 15, 2023
d844ee8
Generalize fluxdiagram to handle both mol and fragment adjlist
hwpang Oct 15, 2023
76bd4a8
Generalize fluxdiagram to handle both mol and fragment smiles
hwpang Oct 15, 2023
4e8274c
Generalize parser to get atom dict. Assign representative mol to give…
hwpang Oct 15, 2023
cd89bcd
Add fragment module for rmstest
hwpang Oct 15, 2023
5459c28
Show error trace in the wild try catch block
hwpang Oct 15, 2023
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31 changes: 26 additions & 5 deletions src/Parse.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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
Expand Down
3 changes: 3 additions & 0 deletions src/ReactionMechanismSimulator.jl
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Expand Up @@ -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()
Expand All @@ -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"))
Expand All @@ -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"))
Expand Down
2 changes: 1 addition & 1 deletion src/Simulation.jl
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Expand Up @@ -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)]))
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Nspcs = sum([length(getphasespecies(sim.domain.phase)) for sim in ssys.sims])
cstot = zeros(Nspcs)
vns = Array{Any,1}(undef, length(domains))
Expand Down
13 changes: 11 additions & 2 deletions src/fluxdiagrams.jl
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Expand Up @@ -42,11 +42,20 @@ function drawspc(spc::Species,path::String=".")
end
end
if spc.adjlist != ""
mol = molecule.Molecule().from_adjacency_list(spc.adjlist)
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Can we do this one with Species the same way you do later?

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Yep! Done.

_ , 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
Expand Down
3 changes: 3 additions & 0 deletions src/rmstest.jl
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@@ -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"))

Expand Down
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