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Patch/stereoapi #328

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merged 14 commits into from Jun 24, 2017
Merged

Patch/stereoapi #328

merged 14 commits into from Jun 24, 2017

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johnmay
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@johnmay johnmay commented Jun 3, 2017

Improvements to how we represent stereochemistry - backwards compatible but much of details are pushed down to the abstract API. More in the JavaDoc but essentially we describe stereochemistry with a focus (or maybe foci in future), two or more carriers, and a configuration.

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johnmay commented Jun 17, 2017

Rebased on master and added preliminary support for Atropisomers.

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egonw commented Jun 17, 2017

I'm reviewing the patch... think I'm done Tue/Wed or so...

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Hard to review the correctness of all new code, but will trust the author and the test suite. Looks like a great clean up, generalization. Some very minor comments/questions. Thanks!

* \ /
* a' b
* f: focus
* Ar: Aryl (carriers connected to either end of 'f')
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Is it necessarily an aromatic ring in those positions? All examples I can think of the have it, but if the a's and b's are sufficiently bulky, other Ar connectors might also "work", or is "atropisomerism" restricted to have aryl groups there?

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There's some good papers looking at it in drug discovery - no need to be aromatic.

See. LaPlante et al Revealing Atropisomer Axial Chirality in Drug Discovery

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Inversion barrier is lower though.

*/
public class Atropisomeric extends AbstractStereo<IBond,IAtom> {

public Atropisomeric(IBond focus, IAtom[] carriers, int value) {
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Missing JavaDoc?

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Yep will add in future commit thanks for spotting.

import java.util.List;
import java.util.Map;

abstract class AbstractStereo<F extends IChemObject, C extends IChemObject>
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I like the focus/carrier formalism.

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I think it's still possible to do better but it's in the right direction.

@egonw egonw merged commit 851842c into master Jun 24, 2017
@johnmay johnmay deleted the patch/stereoapi branch March 18, 2018 20:36
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2 participants