Tidy up structure matching functions

[mojaie]

(sub)structure matching methods will be integrated and renamed.

• structmatches(mol::UndirectedGraph, query::UndirectedGraph, matchtype::Symbol; kwargs...) now returns a lazy iterator that generate all isomorphism mappings between mol and query
  • mol should be GraphMol or SubgraphView{GraphMol}
  • query should be GraphMol, SubgraphView{GraphMol} or QueryMol
  • matchtype should be one of the followings
  • :exact: mol is isomorphic to query
  • :substruct: a subgraph of mol is monomorphic to query (typical substructure search)
  • :nodeinduced: a node-induced subgraph of mol is isomorphic to query
  • :edgeinduced: an edge-induced subgraph of mol is isomorphic to query
• isstructmatch(mol, query, matchtype; kwargs...) returns whether there is an isomorphism mapping between mol and query -> `!isempty(structmatches(mol, query, matchtype))

[mojaie]

After consideration, structure matching methods will be as follows:

• exactmatches(mol::UndirectedGraph, query::UndirectedGraph; kwargs...)
• substructmatches(mol::UndirectedGraph, query::UndirectedGraph; kwargs...)
• nodeinducedmatches(mol::UndirectedGraph, query::UndirectedGraph; kwargs...)
• edgeinducedmatches(mol::UndirectedGraph, query::UndirectedGraph; kwargs...)

These methods return a lazy iterator that generate node mappings (or edge mappings for edgeinducedmatches).

There will be some convenient methods, hasexactmatch, hassubstructmatch, hasnodeinducedmatch, hasedgeinducedmatch that returns whether the structures have matches or not.

Here is rough correspondence between the new method and the old one is as follows. structmatches -> exactmatches isstructmatch -> hasexactmatch substructmatches -> edgeinducedmatches issubstructmatch -> hasedgeinducedmatch querymatch, fastquerymatches -> substructmatches

vf2 isomorphism detection methods in MolecularGraph.Graph are also reconstructed and renamed.

See src/substructurematch.jl and src/graph/isomorphism/vf2.jl for details.

[mojaie]

• Maybe the performance of some structure matching operations increased significantly (e.g. functional group detection).
• substructure matching method has been changed from edge-induced subgraph isomorphism-based to monomorphism-based. This allows us to match single atom node queries.
• Anyway, I will update the tutorial soon.

[mojaie]

Merged d551ee55a9d3403de7ca4f5a967bb8e7fa12c685