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Use american spelling of flavour. #233

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merged 3 commits into from Aug 24, 2016
Merged

Use american spelling of flavour. #233

merged 3 commits into from Aug 24, 2016

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johnmay
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@johnmay johnmay commented Aug 24, 2016

Daniel pointed out it's best to stick to one form. Since Java uses Color, american spellings are preferential. Putting this in before there is a release.

* Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers. The
* ordering is not canonical.
*/
public static final int Default = Stereo | AtomicMass | CxSmiles;
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I need to read more about this (and we need a sentence + reference in https://github.com/cdk/cdk-paper-3), but is CXSMILES something people would expect as default?

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@johnmay johnmay Aug 24, 2016

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The default constructor is actually deprecated... telling the user to choose what you want. But CXSMILES is backwards compatible with SMILES. Toolkits that support it (ChemAxon,CDK,Indigo) can exchange more information, those that don't (RDKit,OpenBabel,etc) simply ignore. There is information loss when ignored, but for our purposes it allows better round tripping when serialising to SMILES, hence the default.

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OK, clear. Thanks for the clarification!

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All to be documented :-) - need to get sections added to paper first though.

@egonw egonw merged commit bb12f67 into master Aug 24, 2016
@johnmay johnmay deleted the patch/smiflags-spelling branch February 12, 2017 21:46
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2 participants