Add a reader for cdxml format (#145)

* support cdxml format

* implement stereo-bonds via 'notation' analog to sdfilereader

* add has_isaromatic for CDXML

* add tests for cdxml

* correct handling of WedgeHashEnd

* switch from LightXML to EzXML

---------

Co-authored-by: hhaensel <helmut.haensel@gmx.com>

Author: hhaensel

Project.toml

@@ -10,6 +10,7 @@ DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
@@ -35,6 +36,7 @@ DelimitedFiles = "1"
 GeometryBasics = "0.5"
 Graphs = "1.12"
 JSON = "1"
+EzXML = "1"
 MakieCore = "0.9,0.10"
 OrderedCollections = "1.8"
 RDKitMinimalLib = "1.2"

src/MolecularGraph.jl

@@ -52,6 +52,8 @@ include("./model/atom.jl")
 include("./model/bond.jl")
 include("./model/molgraph.jl")
 include("./model/query.jl")
+include("./model/cdxml.jl")
+export cdxmltomol, cdxmltomols
 
 include("./graph/operators.jl")
 include("./graph/traversals.jl")
@@ -66,11 +68,11 @@ include("./graph/isomorphism_clique.jl")
 
 export
     ATOMTABLE, ATOMSYMBOLMAP, ATOM_COVALENT_RADII, ATOM_VANDERWAALS_RADII,
-    SDFAtom, SMILESAtom, CommonChemAtom,
+    SDFAtom, SMILESAtom, CommonChemAtom, CDXMLAtom,
     atom_number, atom_symbol, atom_charge, multiplicity, isotope,
-    SDFBond, SMILESBond, CommonChemBond,
+    SDFBond, SMILESBond, CommonChemBond, CDXMLBond,
     bond_order,
-    MolGraph, SDFMolGraph, SMILESMolGraph, CommonChemMolGraph,
+    MolGraph, SDFMolGraph, SMILESMolGraph, CommonChemMolGraph, CDXMLMolGraph,
     QueryMolGraph, QueryAtom, QueryBond
 
 export