Substructures: allow strings to be passed as AbstractStrings

Signed-off-by: Thomas Kemmer <[email protected]>
hildebrandtlab · Dec 17, 2024 · 94d446e · 94d446e
1 parent d4d124a
commit 94d446e
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Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/src/substructures/smarts.jl b/src/substructures/smarts.jl
@@ -5,12 +5,12 @@ struct SMARTSQuery
     query::String
     query_graph::MolecularGraph.SMARTSMolGraph
 
-    function SMARTSQuery(query::String)
+    function SMARTSQuery(query::AbstractString)
         new(query, MolecularGraph.smartstomol(query))
     end
 end
 
-function _to_substructure(name, mol, m; adjacent_bonds=false)
+function _to_substructure(name::AbstractString, mol::AbstractAtomContainer, m; adjacent_bonds::Bool = false)
     matched_atoms = keys(m)
 
     filter_atoms(atom -> atom.number ∈ matched_atoms, mol;
@@ -19,7 +19,7 @@ function _to_substructure(name, mol, m; adjacent_bonds=false)
     )
 end
 
-function Base.match(query::SMARTSQuery, mol::AbstractAtomContainer; adjacent_bonds=false)
+function Base.match(query::SMARTSQuery, mol::AbstractAtomContainer; adjacent_bonds::Bool = false)
     mg_mol = convert(MolecularGraph.SDFMolGraph, mol)
     matches = MolecularGraph.substruct_matches(mg_mol, query.query_graph)
 

diff --git a/src/substructures/substructure.jl b/src/substructures/substructure.jl
@@ -1,17 +1,19 @@
-export Substructure, filter_atoms
+export
+    Substructure,
+    filter_atoms
 
 @auto_hash_equals struct Substructure{T<:Real, A<:AbstractAtomContainer{T}} <: AbstractAtomContainer{T}
     name::String
 
     parent::A
-    
+
     _atoms::AtomTable{T}
     _bonds::BondTable{T}
-    
+
     properties::Properties
 
     function Substructure{T,A}(
-        name::String,
+        name::AbstractString,
         parent::A,
         atoms::AtomTable{T},
         bonds::BondTable{T},
@@ -22,14 +24,14 @@ export Substructure, filter_atoms
 end
 
 @inline Substructure(
-    name::String,
+    name::AbstractString,
     parent::A,
     atoms::AtomTable{T},
     bonds::BondTable{T},
     properties::Properties = parent.properties
 ) where {T, A} = Substructure{T, typeof(parent)}(name, parent, atoms, bonds, properties)
 
-function filter_atoms(fn, mol::AbstractAtomContainer{T}; name="", adjacent_bonds=false) where T
+function filter_atoms(fn, mol::AbstractAtomContainer; name::AbstractString="", adjacent_bonds::Bool=false)
     atom_view = filter(fn, atoms(mol))
     idxset = Set(atom_view.idx)
     bond_view = filter(row ->