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Resolve test with modified output - one of these (assignDbStereo) cam…
…e from the beam algorithm change for assign up/down cis-trans indication.
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johnmay committed Aug 24, 2016
1 parent 9cece8b commit 6feb445
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Showing 2 changed files with 4 additions and 4 deletions.
Expand Up @@ -644,7 +644,7 @@ private void fixCarbonHCount(IAtomContainer mol) {
@Test
public void testPseudoAtom() throws Exception {
IAtom atom = new PseudoAtom("Star");
SmilesGenerator sg = new SmilesGenerator();
SmilesGenerator sg = new SmilesGenerator(SmiFlavor.Generic);
String smiles = "";
IAtomContainer molecule = new AtomContainer();
molecule.addAtom(atom);
Expand Down Expand Up @@ -673,7 +673,7 @@ public void testReactionSMILES() throws Exception {
methane.getAtom(0).setImplicitHydrogenCount(4);
gold.getAtom(0).setImplicitHydrogenCount(0);

SmilesGenerator sg = new SmilesGenerator();
SmilesGenerator sg = new SmilesGenerator(SmiFlavor.Generic);
String smiles = sg.create(reaction);
//logger.debug("Generated SMILES: " + smiles);
Assert.assertEquals("C>*>[Au]", smiles);
Expand Down Expand Up @@ -1215,7 +1215,7 @@ public void assignDbStereo() throws Exception {
String in = "C(/N)=C\\C=C\\1/N=C1";
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles(in);
Assert.assertEquals("C(\\N)=C/C=C/1\\N=C1", SmilesGenerator.isomeric().create(mol));
Assert.assertEquals("C(\\N)=C/C=C/1N=C1", SmilesGenerator.isomeric().create(mol));
}

@Test public void canonicalReactions() throws Exception {
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Expand Up @@ -2515,7 +2515,7 @@ public void atomBasedDbStereo() throws Exception {
@Test
public void atomBasedDbStereoReversing() throws Exception {
assertThat(SmilesGenerator.isomeric().create(load("[C@H](F)=[C@@H]F")),
is("F/C=C\\F"));
is("C(\\F)=C\\F"));
}

/**
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