Patch/radical bugs #319
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Patch/radical bugs #319
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Rebased now the delta/gamma is swapped |
…nverse. Difficult to generate a test case but included now.
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Okay now done correctly :-) |
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The SMILES makes it clear the gamma one is probably broken... will look into it another point |
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Sorry delta one broken... hard to keep track of these swaps. The test case is currently a no-op: However it does do what's expected: String smi = "[CH](C)CCCCCCC |^1:0|";
SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer mol = smipar.parseSmiles(smi);
IAtomContainerSet reactants = new AtomContainerSet();
reactants.addAtomContainer(mol);
List<IReactionProcess> processes = Arrays.<IReactionProcess>asList(new RadicalSiteRrAlphaReaction(),
new RadicalSiteRrBetaReaction(),
new RadicalSiteRrGammaReaction(),
new RadicalSiteRrDeltaReaction());
SmilesGenerator smigen = new SmilesGenerator();
for (IReactionProcess process : processes) {
for (IReaction reaction : process.initiate(reactants, null).reactions()) {
System.out.println(smigen.create(reaction) + " " + process.getClass().getSimpleName());
}
}produces |
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Whilst reviewing #315 I found some problems with the radical CXSMILES and hydrogen suppression. I've also updated the equality check to use canonical SMILES. Can also make it much easier to show what the reactions are doing (may add another commit).