valence check

Author: mojaie

assets/test/valence_err.mol

@@ -0,0 +1,25 @@
+
+  MJ250300                      
+
+ 10 10  0  0  0  0  0  0  0  0999 V2000
+   -0.1074   -1.0478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.7175   -1.0478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.9744   -0.2637    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3050    0.2229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
+   -0.3600   -0.2637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    0.3037    1.0479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.7593   -0.0099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+   -1.1447   -0.0091    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
+   -1.3184    0.8028    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
+   -1.7593   -0.5563    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  5  2  0  0  0  0
+  2  3  2  0  0  0  0
+  3  4  1  0  0  0  0
+  3  7  1  0  0  0  0
+  4  5  1  0  0  0  0
+  4  6  1  0  0  0  0
+  5  8  1  0  0  0  0
+  8  9  1  0  0  0  0
+  8 10  2  0  0  0  0
+M  END

src/property/valence.jl

@@ -122,6 +122,17 @@ apparent_valence!(mol::SimpleMolGraph) = set_descriptor!(
     mol, :apparent_valence, apparent_valence(mol.graph, bond_order(mol)))
 
 
+function formal_valence(symbol_arr::Vector{Symbol}, charge_arr::Vector{Int})
+    arr = fill(zero(Int), length(symbol_arr))
+    for i in 1:length(symbol_arr)
+        if haskey(LONEPAIR_COUNT, symbol_arr[i])
+            arr[i] = 4 - abs(LONEPAIR_COUNT[symbol_arr[i]] - charge_arr[i])
+        end
+    end
+    return arr
+end
+
+
 """
     valence(mol::SimpleMolGraph) -> Vector{Int}
 
@@ -142,22 +153,24 @@ end
 function valence(
         symbol_arr::Vector{Symbol}, charge_arr::Vector{Int},
         apparent_valence_arr::Vector{Int})
-    arr = fill(zero(Int), length(symbol_arr))
-    for i in 1:length(symbol_arr)
-        if haskey(LONEPAIR_COUNT, symbol_arr[i])
-            val = 4 - abs(LONEPAIR_COUNT[symbol_arr[i]] - charge_arr[i])
-            arr[i] = max(val, apparent_valence_arr[i])
-        else
-            arr[i] = apparent_valence_arr[i]
-        end
-    end
-    return arr
+    return max.(formal_valence(symbol_arr, charge_arr), apparent_valence_arr)
 end
 
 valence!(mol::SimpleMolGraph) = set_descriptor!(
     mol, :valence, valence(atom_symbol(mol), atom_charge(mol), apparent_valence(mol)))
 
 
+function check_valence!(mol::SimpleMolGraph)
+    av = apparent_valence(mol)
+    fv = formal_valence(atom_symbol(mol), atom_charge(mol))
+    comments = String[]
+    for i in vertices(mol)[av .> fv]
+         push!(comments, "unusual valence at #$(i) (actual $(av[i]), expected $(fv[i]))")
+    end
+    mol[:logs]["warning_valence"] = join(comments, "; ")
+end
+
+
 """
     explicit_hydrogens(mol::SimpleMolGraph) -> Vector{Int}
 

src/sdfilereader.jl

@@ -99,6 +99,7 @@ end
 
 
 function sdf_on_init!(mol::SimpleMolGraph)
+    check_valence!(mol)
     coords_from_sdf!(mol)
     stereocenter_from_sdf2d!(mol)
     stereobond_from_sdf2d!(mol)

src/smarts/base.jl

@@ -59,6 +59,7 @@ SMARTSParser{T,V,E}(smarts) where {T,V,E} = SMARTSParser{T,V,E}(
 
 
 function smiles_on_init!(mol::SimpleMolGraph)
+    check_valence!(mol)
     stereocenter_from_smiles!(mol)
     stereobond_from_smiles!(mol)
 end