Merge branch 'release/0.4'

Project.toml

@@ -1,7 +1,7 @@
 name = "BiochemicalAlgorithms"
 uuid = "9d651bdf-8945-47d1-9188-34e269d8f7b5"
 authors = ["Andreas Hildebrandt <[email protected]> and contributors"]
-version = "0.4.5"
+version = "0.4.6"
 
 [deps]
 AutoHashEquals = "15f4f7f2-30c1-5605-9d31-71845cf9641f"

src/forcefields/common/forcefield.jl

@@ -47,7 +47,7 @@ end
 
 function _try_assign!(
         templates::Dict{String, AtomTypeTemplate{T}},
-        name::String,
+        name::AbstractString,
         atom::Atom{T};
         assign_typenames::Bool,
         overwrite_typenames::Bool,

src/substructures/smarts.jl

@@ -3,19 +3,19 @@ export
 
 struct SMARTSQuery
     query::String
-    query_graph::MolecularGraph.SMILESMolGraph
+    query_graph::MolecularGraph.SMARTSMolGraph
 
     function SMARTSQuery(query::String)
-        new(query, smartstomol(query))
+        new(query, MolecularGraph.smartstomol(query))
     end
 end
 
 function _to_substructure(name, mol, m; adjacent_bonds=false)
     matched_atoms = keys(m)
 
-    filter_atoms(
-            :number => n -> n ∈ matched_atoms, mol; 
-            name=name, adjacent_bonds=adjacent_bonds
+    filter_atoms(atom -> atom.number ∈ matched_atoms, mol;
+        name = name,
+        adjacent_bonds = adjacent_bonds
     )
 end
 

src/substructures/substructure.jl

@@ -27,7 +27,7 @@ end
     atoms::AtomTable{T},
     bonds::BondTable{T},
     properties::Properties = parent.properties
-) where {T, A} = Substructure{Float32, typeof(parent)}(name, parent, atoms, bonds, 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
     atom_view = filter(fn, atoms(mol))