Reintroduce ignore_homometallic_bonds, split from reduce_homometallic…

…_bonds
coudertlab · Feb 28, 2024 · dd7af43 · dd7af43
1 parent 25fd07f
commit dd7af43
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Showing 3 changed files with 20 additions and 16 deletions.
diff --git a/src/guessbonds.jl b/src/guessbonds.jl
@@ -71,8 +71,8 @@ function guess_bonds(pos, types, mat, options)
         typi = types[i]
         #ignoreifmetallic = typi === :C
         #ignoreifC = ismetal[atomic_numbers[typi]]
-        skiphomoatomic = typi ∈ options.ignore_homoatomic_bonds #||
-                        #  (options.ignore_homometallic_bonds && ismetal[atomic_numbers[typi]])
+        skiphomoatomic = typi ∈ options.ignore_homoatomic_bonds ||
+                         (options.ignore_homometallic_bonds && ismetal[atomic_numbers[typi]])
         acceptonlyO = options.structure === StructureType.Zeolite && typi !== :O
         acceptallbutO = options.structure === StructureType.Zeolite && typi === :O
         for j in (i+1):n

diff --git a/src/input.jl b/src/input.jl
@@ -1184,13 +1184,13 @@ function sanity_checks!(graph, pos, types, mat, options)
 end
 
 
-function _remove_homoatomic_bonds!(graph::PeriodicGraph{D}, types, targets, ignore_homometallic) where D
-    isempty(targets) && !ignore_homometallic && return Int[]
+function _remove_homoatomic_bonds!(graph::PeriodicGraph{D}, types, targets, reduce_homometallic) where D
+    isempty(targets) && !reduce_homometallic && return Int[]
     metallics = Int[]
     for i in 1:length(types)
         t = types[i]
         if t ∉ targets
-            ignore_homometallic && ismetal[atomic_numbers[t]] && push!(metallics, i)
+            reduce_homometallic && ismetal[atomic_numbers[t]] && push!(metallics, i)
             continue
         end
         rem_edges = PeriodicVertex{D}[]
@@ -1254,16 +1254,16 @@ function _remove_homometallic_bonds!(graph::PeriodicGraph{D}, types, metallics)
 end
 
 """
-    remove_homoatomic_bonds!(graph::PeriodicGraph, types, targets, ignore_homometallic)
+    remove_homoatomic_bonds!(graph::PeriodicGraph, types, targets, reduce_homometallic)
 
 Remove from the graph all bonds of the form X-X where X is an atom in `targets`.
 
 Also remove all such bonds where X is a metal if the two bonded atoms up to third
-neighbours otherwise, and if `ignore_homometallic` is `true`.
+neighbours otherwise, and if `reduce_homometallic` is `true`.
 """
-function remove_homoatomic_bonds!(graph::PeriodicGraph{D}, types, targets, ignore_homometallic) where D
-    metallics = _remove_homoatomic_bonds!(graph, types, targets, ignore_homometallic)
-    ignore_homometallic && _remove_homometallic_bonds!(graph, types, metallics)
+function remove_homoatomic_bonds!(graph::PeriodicGraph{D}, types, targets, reduce_homometallic) where D
+    metallics = _remove_homoatomic_bonds!(graph, types, targets, reduce_homometallic)
+    reduce_homometallic && _remove_homometallic_bonds!(graph, types, metallics)
 end
 
 
@@ -1443,7 +1443,7 @@ function finalize_checks(cell::Cell, pos::Vector{SVector{3,Float64}}, types::Vec
             end
         end
 
-        remove_homoatomic_bonds!(graph, types, options.ignore_homoatomic_bonds, options.ignore_homometallic_bonds)
+        remove_homoatomic_bonds!(graph, types, options.ignore_homoatomic_bonds, options.reduce_homometallic_bonds)
     end
 
     if isempty(attributions)

diff --git a/src/options.jl b/src/options.jl
@@ -350,7 +350,8 @@ These boolean options have a default value that may be determined by [`Bonding`]
 - `authorize_pruning`: remove colliding atoms in the input. Default is true.
 - `wider_metallic_bonds`: for bond detections, metals have a radius equal to 1.5× their Van
   der Waals radius. Default is false, unless [`StructureType`](@ref) is `MOF` or `Zeolite`.
-- `ignore_homometallic_bonds`: when guessing bonds, do not bond two metallic atoms of the
+- `ignore_homometallic_bonds`: remove all bonds between two metal atoms of the same kind.
+- `reduce_homometallic_bonds`: when guessing bonds, do not bond two metallic atoms of the
   same type if they are up to third neighbours anyway.
   Default is false, unless [`StructureType`](@ref) is `MOF`.
 - `ignore_metal_cluster_bonds`: do not bond two metallic clusters together if they share at
@@ -399,6 +400,7 @@ struct Options
     ignore_atoms::Set{Symbol}
     ignore_homoatomic_bonds::Set{Symbol}
     ignore_homometallic_bonds::Bool
+    reduce_homometallic_bonds::Bool
     ignore_low_occupancy::Bool
     export_input::String
     export_trimmed::String
@@ -443,7 +445,8 @@ struct Options
                        authorize_pruning=true,
                        ignore_atoms=Set{Symbol}(),
                        ignore_homoatomic_bonds=Set{Symbol}(),
-                       ignore_homometallic_bonds=nothing,
+                       ignore_homometallic_bonds=false,
+                       reduce_homometallic_bonds=nothing,
                        ignore_low_occupancy=false,
                        export_input=DOEXPORT[],
                        export_trimmed=false,
@@ -482,10 +485,10 @@ struct Options
         _export_net = ifbooltempdirorempty(export_net)
         _export_subnets = ifbooltempdirorempty(export_subnets)
 
-        _ignore_homometallic_bonds = if ignore_homometallic_bonds === nothing
+        _reduce_homometallic_bonds = if reduce_homometallic_bonds === nothing
             structure == StructureType.MOF
         else
-            ignore_homometallic_bonds
+            _reduce_homometallic_bonds
         end
 
         _wider_metallic_bonds = if wider_metallic_bonds === nothing
@@ -503,7 +506,8 @@ struct Options
             authorize_pruning,
             Set{Symbol}(ignore_atoms),
             Set{Symbol}(ignore_homoatomic_bonds),
-            _ignore_homometallic_bonds,
+            ignore_homometallic_bonds,
+            _reduce_homometallic_bonds,
             ignore_low_occupancy,
             _export_input,
             _export_trimmed,