updater for custom preprocessing #132

Author: mojaie

src/coords.jl

@@ -90,11 +90,11 @@ function coords_from_sdf!(mol::SimpleMolGraph)
     zrange = nv(mol) == 0 ? (0, 0) : extrema(mol[i].coords[3] for i in vertices(mol))
     # Embed 3D coords to 2D
     push!(
-        mol.gprops.descriptors.coords2d,
+        mol[:descriptors].coords2d,
         [Point2d(mol[i].coords[1:2]...) for i in vertices(mol)])
     if zrange[2] - zrange[1] > 0.001  # 3D coords available
         push!(
-            mol.gprops.descriptors.coords3d,
+            mol[:descriptors].coords3d,
             [Point3d(mol[i].coords[1:3]...) for i in vertices(mol)])
     end
     # Bond style in 2D notation (wedges)
@@ -117,7 +117,7 @@ function coords_from_sdf!(mol::SimpleMolGraph)
             arr[i] = :none
         end
     end
-    push!(mol.gprops.descriptors.draw2d_bond_style, arr)
+    push!(mol[:descriptors].draw2d_bond_style, arr)
 end
 
 
@@ -172,9 +172,9 @@ draw2d_bond_style(mol::SimpleMolGraph) = draw2d_bond_style(mol, 1)
 
 function update_coords!(mol::SimpleMolGraph)
     # TODO: just remap nodes if still all existing vertices have coords.
-    empty!(mol.gprops.descriptors.coords2d)
-    empty!(mol.gprops.descriptors.coords3d)
-    empty!(mol.gprops.descriptors.draw2d_bond_style)
+    empty!(mol[:descriptors].coords2d)
+    empty!(mol[:descriptors].coords3d)
+    empty!(mol[:descriptors].draw2d_bond_style)
     if hasfield(vproptype(mol), :coords)
         if !any(isnothing(mol[i].coords) for i in vertices(mol))
             coords_from_sdf!(mol)
@@ -197,22 +197,9 @@ where n is atom count, which stores 2D coordinates (x, y) of each atoms.
 """
 coordgen(mol::SimpleMolGraph) = coordgen(
     mol.graph, atom_number(mol), bond_order(mol),
-    mol.gprops.stereocenter, mol.gprops.stereobond
+    mol[:stereocenter], mol[:stereobond]
 )
 
-function coordgen!(mol::ReactiveMolGraph)
-    # Initialize
-    empty!(mol.gprops.descriptors.coords2d)
-    empty!(mol.gprops.descriptors.draw2d_bond_style)
-    # TODO: unspecified stereochem in SMILES
-    coords, styles = coordgen(
-        mol.graph, atom_number(mol), bond_order(mol),
-        mol[:stereocenter], mol[:stereobond]
-    )
-    push!(mol.gprops.descriptors.coords2d, coords)
-    push!(mol.gprops.descriptors.draw2d_bond_style, styles)
-end
-
 function coordgen(
         g::SimpleGraph{T}, atomnum::Vector{Int}, bondorder_::Vector{Int},
         stereocenters::Dict{T,Tuple{T,T,T,Bool}},
@@ -284,3 +271,16 @@ function coordgen(
     # TODO: keep wave bond in SDFile
     return coords, styles
 end
+
+function coordgen!(mol::SimpleMolGraph)
+    # Initialize
+    empty!(mol[:descriptors].coords2d)
+    empty!(mol[:descriptors].draw2d_bond_style)
+    # TODO: unspecified stereochem in SMILES
+    coords, styles = coordgen(
+        mol.graph, atom_number(mol), bond_order(mol),
+        mol[:stereocenter], mol[:stereobond]
+    )
+    push!(mol[:descriptors].coords2d, coords)
+    push!(mol[:descriptors].draw2d_bond_style, styles)
+end

src/model/molgraph.jl

@@ -37,21 +37,22 @@ mutable struct MolState{T,F1,F2} <: AbstractState
     initialized::Bool
     has_updates::Bool
     has_new_edges::Bool  # as a SSSR recalculation flag
+    force_calculate::Bool  # ignore cached descriptors (temporary set when running auto-preprocess)
     on_init::F1
     on_update::F2
 end
 
 
 function MolState{T}(
-        ; initialized=false, has_updates=true, has_new_edges=true,
+        ; initialized=false, has_updates=true, has_new_edges=true, force_calculate=false,
         on_init=default_on_init!, on_update=default_on_update!) where T <: Integer
     return MolState{T,typeof(on_init),typeof(on_update)}(
-        initialized, has_updates, has_new_edges, on_init, on_update)
+        initialized, has_updates, has_new_edges, force_calculate, on_init, on_update)
 end
 
 
 Base.copy(state::T) where T <: MolState = T(
-    state.initialized, state.has_updates, state.has_new_edges,
+    state.initialized, state.has_updates, state.has_new_edges, state.force_calculate,
     state.on_init, state.on_update
 )
 
@@ -60,7 +61,12 @@ Base.copy(state::T) where T <: MolState = T(
 
 function get_descriptor(mol::ReactiveMolGraph, field::Symbol)
     dispatch_update!(mol)
-    return getproperty(mol.gprops.descriptors, field)
+    return getproperty(mol[:descriptors], field)
+end
+
+function has_descriptor(mol::ReactiveMolGraph, field::Symbol)
+    mol.state.force_calculate && return false
+    return hasproperty(mol[:descriptors], field)
 end
 
 
@@ -103,8 +109,10 @@ to recalculate descriptors. If there are no changes, just return the stored desc
 """
 function dispatch_update!(mol::ReactiveMolGraph)
     mol.state.has_updates || return
-    mol.state.has_updates = false  # call before update to avoid infinite roop
+    mol.state.force_calculate = true # to avoid infinite roop
     mol.state.on_update(mol)
+    mol.state.force_calculate = false
+    mol.state.has_updates = false  
     mol.state.has_new_edges = false
     return
 end
@@ -151,7 +159,7 @@ Custom `on_init` function is called inside this method.
 function initialize!(mol::ReactiveMolGraph)
     mol.state.initialized || mol.state.on_init(mol)
     mol.state.initialized = true
-    dispatch_update!(mol)  # just checking on-update callback errors
+    dispatch_update!(mol)  # check on-update callback errors
     return
 end
 
@@ -275,7 +283,6 @@ end
 
 
 function Graphs.rem_vertex!(mol::ReactiveMolGraph, v::Integer)
-    dispatch_update!(mol)
     nv_ = nv(mol)
     old_edges = collect(edges(mol))
     rem_vertex!(mol.graph, v) || return false
@@ -301,7 +308,6 @@ end
 
 function Graphs.rem_vertices!(mol::ReactiveMolGraph{T,V,E}, vs::Vector{T}) where {T,V,E}
     # TODO: if many vertices should be removed, induced_subgraph may be more efficient.
-    dispatch_update!(mol)
     old_edges = collect(edges(mol))
     vmap = rem_vertices!(mol.graph, vs)
     # remap vertex properties
@@ -330,7 +336,6 @@ end
 
 function _induced_subgraph(mol::T, vlist_or_elist) where {T<:ReactiveMolGraph}
     # In many cases, induced_subgraph(mol.graph, vlist_or_elist) is sufficient
-    dispatch_update!(mol)
     subg, vmap = induced_subgraph(mol.graph, vlist_or_elist)
     vps = Dict{eltype(T),vproptype(T)}()
     for v in vertices(subg)