Make trimming depend on the new "trim" option

Author: Liozou

src/clustering.jl

@@ -1406,7 +1406,7 @@ function _collapse_clusters(crystal::Crystal{Nothing}, clusters::Clusters, onlyn
         atts = clusters.attributions[s]
         neigh0 = neighbors(crystal.pge.g, s)
         # @show s, atts
-        @toggleassert length(neigh0) ≥ 2
+        @toggleassert !crystal.options.trim || length(neigh0) ≥ 2
         typisnotC = crystal.types[s] !== :C
         for x in neigh0
             d = x.v
@@ -1511,7 +1511,7 @@ function _find_clusters(c::Crystal{T}, guess::Bool, separate_metals::Bool)::Tupl
 end
 
 function find_clusters(_c::Crystal{T}) where T
-    c = trim_monovalent(_c)
+    c = _c.options.trim ? trim_monovalent(_c) : _c
     structure = c.options.structure
     clusterings = c.options.clusterings
     ret = Vector{Tuple{Crystal{Nothing},Union{Int,Clusters}}}(undef, length(clusterings))
@@ -1549,6 +1549,7 @@ transformed into a new vertex, for each targeted clustering.
 """
 function collapse_clusters(crystal::Crystal)
     crystalclusters::Vector{Tuple{Crystal{Nothing},Union{Int,Clusters}}} = find_clusters(crystal)
+    # @show only(crystalclusters)[2]
     ret = Vector{Crystal{Nothing}}(undef, length(crystalclusters))
     alreadyexported = false
     for (i, (cryst, clust)) in enumerate(crystalclusters)

src/options.jl

@@ -387,6 +387,10 @@ These boolean options have a default value that may be determined by [`Bonding`]
   Default is false, unless [`StructureType`](@ref) is `MOF` or `Zeolite`.
 - `unify_sbu_decomposition`: apply the same rule to decompose both periodic and finite SBUs.
   Default is false.
+- `trim`: remove vertices with zero or one neighbor and transform vertices with exactly two
+  neighbors into an edge, iteratively until convergence. Default is true and must be left
+  to true if the topology needs to be compared to databases of topologies, which all use
+  this convention.
 - `force_warn`: force printing warning and information even during `..._dataset` function
   calls. Default is false.
 - `label_for_type`: use the atom label instead of its type. Default is false.
@@ -450,6 +454,7 @@ struct Options
     cluster_simple_pe::Bool
     split_O_vertex::Bool
     unify_sbu_decomposition::Bool
+    trim::Bool
     separate_metals::Union{Nothing,Bool}
     premerge_metalbonds::Bool
     max_polyhedron_radius::Int
@@ -500,6 +505,7 @@ struct Options
                        cluster_simple_pe=true,
                        split_O_vertex=nothing,
                        unify_sbu_decomposition=false,
+                       trim=true,
                        separate_metals=nothing,
                        premerge_metalbonds=true,
                        max_polyhedron_radius=4,
@@ -585,6 +591,7 @@ struct Options
             cluster_simple_pe,
             _split_O_vertex,
             unify_sbu_decomposition,
+            trim,
             separate_metals,
             premerge_metalbonds,
             max_polyhedron_radius,

src/types.jl

@@ -497,8 +497,10 @@ end
     trimmed_crystal(c::Crystal{Nothing})
 
 Rebuild the crystal after trimming its graph according to [`trim_topology`](@ref CrystalNets.trim_topology).
+Does nothing if `c.options.trim` is unset.
 """
 function trimmed_crystal(c::Crystal{Nothing})
+    c.options.trim || return c
     g = deepcopy(c.pge.g)
     remove_metal_cluster_bonds!(g, c.types, c.options)
     vmap, graph = trim_topology(g)
@@ -768,7 +770,11 @@ end
 
 
 function _collect_net!(ret::Vector{<:CrystalNet{D}}, encountered, idx, c, clustering) where D
-    vmap, graph = trim_topology(c.pge.g)
+    vmap, graph = if c.options.trim
+        trim_topology(c.pge.g)
+    else
+        collect(1:length(c.types)), c.pge.g
+    end
     types = c.types[vmap]
     idx > 1 && c.options.track_mapping isa Vector{Int} && c.options.keep_single_track && throw(ArgumentError("Cannot keep a single mapping track for multiple sub-nets. Please use keep_single_track=true only on single components with a single clustering."))
     opts = rev_permute_mapping!(c.options, vmap, length(c.types))