add tests for cdxml

Author: hhaensel

test/cdxml.jl

@@ -0,0 +1,90 @@
+
+@testset "cdxmlreader" begin
+
+@testset "aromatic ring" begin
+    # cdxml codes aromaticity via bond order 1.5
+    cdxml_string = """
+    <?xml version="1.0" encoding="UTF-8"?>
+    <CDXML>
+        <page>
+        <fragment id="1">
+            <n id="2" Element="6" p="100 100"/>
+            <n id="3" Element="6" p="120 110"/>
+            <n id="4" Element="6" p="120 130"/>
+            <n id="5" Element="6" p="100 140"/>
+            <n id="6" Element="6" p="80 130"/>
+            <n id="7" Element="6" p="80 110"/>
+            <b id="8" B="2" E="3" Order="1.5"/>
+            <b id="9" B="3" E="4" Order="1.5"/>
+            <b id="10" B="4" E="5" Order="1.5"/>
+            <b id="11" B="5" E="6" Order="1.5"/>
+            <b id="12" B="6" E="7" Order="1.5"/>
+            <b id="13" B="7" E="2" Order="1.5"/>
+        </fragment>
+        </page>
+    </CDXML>
+    """
+
+    mol = cdxmltomol(IOBuffer(cdxml_string))
+    @test atom_symbol(mol) == fill(:C, 6)
+    @test sum(bond_order(mol)) == 6 * 1.5
+    @test mol[1].coords == [100, 100, 0]
+
+    benzene_cdxml_aromatic = mol
+    cdxml_string = """
+    <?xml version="1.0" encoding="UTF-8"?>
+    <CDXML>
+        <page>
+        <fragment id="1">
+            <n id="2" Element="6" p="100 100"/>
+            <n id="3" Element="6" p="120 110"/>
+            <n id="4" Element="6" p="120 130"/>
+            <n id="5" Element="6" p="100 140"/>
+            <n id="6" Element="6" p="80 130"/>
+            <n id="7" Element="6" p="80 110"/>
+            <b id="8" B="2" E="3" Order="1"/>
+            <b id="9" B="3" E="4" Order="2"/>
+            <b id="10" B="4" E="5" Order="1"/>
+            <b id="11" B="5" E="6" Order="2"/>
+            <b id="12" B="6" E="7" Order="1"/>
+            <b id="13" B="7" E="2" Order="2"/>
+        </fragment>
+        </page>
+    </CDXML>
+    """
+    benzene_cdxml_classic = cdxmltomol(IOBuffer(cdxml_string))
+    @test has_exact_match(benzene_cdxml_aromatic, benzene_cdxml_classic)
+    
+    benzene_smiles = smilestomol("c1ccccc1")
+    @test has_exact_match(benzene_cdxml_aromatic, benzene_smiles)
+end
+
+
+@testset "stereo bond" begin
+    cdxml_string = """
+    <?xml version="1.0" encoding="UTF-8"?>
+    <CDXML>
+    <page>
+        <fragment id="1">
+        <n id="2" Element="6" p="100 100"/>
+        <n id="3" Element="17" p="110 95"/>
+        <n id="4" Element="35" p="110 105"/>
+        <n id="5" Element="1" p="90 95"/>
+        <n id="6" Element="1" p="90 105"/>
+        <b id="7" B="2" E="3" Display="WedgeBegin"/>
+        <b id="8" B="2" E="4" Display="Hash"/>
+        <b id="9" B="2" E="5"/>
+        <b id="10" B="2" E="6"/>
+        </fragment>
+    </page>
+    </CDXML>
+    """
+
+    mol = cdxmltomol(IOBuffer(cdxml_string))
+    @test [b.notation for (_, b) in mol.eprops] == [1, 6, 0, 0]
+    @test bond_order(mol) == fill(1, 4)
+    @test atom_symbol(mol) == [:C, :Cl, :Br, :H, :H]
+    @test mol[2].coords == [110, 95, 0]
+end
+
+end # cdxmlreader

test/runtests.jl

@@ -87,6 +87,7 @@ include("./smarts/smarts.jl")
 include("sdfilereader.jl")
 include("sdfilewriter.jl")
 include("json.jl")
+include("cdxml.jl")
 
 include("stereo.jl")
 include("preprocess.jl")