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SMILES extension and depiction of multipart reactions #986

Merged
merged 18 commits into from
Aug 1, 2023
Merged

SMILES extension and depiction of multipart reactions #986

merged 18 commits into from
Aug 1, 2023

Commits on Jul 26, 2023

  1. SMILES extension to store a multi-step reaction.

    @johnmay
    johnmay committed Jul 26, 2023
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  2. Use ReactionManipulator to simplify the CXSMILES layer application

    @johnmay
    johnmay committed Jul 26, 2023
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  3. Some refactoring to make it easy to lay out multiple reactions.

    @johnmay
    johnmay committed Jul 26, 2023
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  4. Simplify the layout of reactions with a common method for both vector… 

    … graphics and raster images.
    @johnmay
    johnmay committed Jul 26, 2023
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  5. Allow the ReactionBounds to determine the final arrow size. Padding i… 

    …s also now scaled like bond length.
    @johnmay
    johnmay committed Jul 26, 2023
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  6. Preliminary depiction for reaction sets.

    @johnmay
    johnmay committed Jul 26, 2023
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  7. Minor formatting change, wrap the parameters.

    @johnmay
    johnmay committed Jul 26, 2023
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  8. Detect a sequence of reactions and lay them out without replicating t… 

    …he intermediate compounds.
    @johnmay
    johnmay committed Jul 26, 2023
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  9. Fix a corner case now we have a null arrow.

    @johnmay
    johnmay committed Jul 26, 2023
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  10. Handle CXSMILES on multistep reaction SMILES.

    @johnmay
    johnmay committed Jul 26, 2023
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  11. Fix typo, we need to grab all the product labels not just the first one

    @johnmay
    johnmay committed Jul 26, 2023
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  12. Fix an issue with PDF rescaling, MM_TO_POINT when dimensions are auto… 

    …matic.
    @johnmay
    johnmay committed Jul 26, 2023
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  13. AtomNumber in reactions has been wrong for a while, track the number … 

    …with a counter class and ensure in sequence reactions they are numbered correctly (i.e. no gaps).

The highlighting should also be cleared after all the bounds are generated
    @johnmay
    johnmay committed Jul 26, 2023
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Commits on Jul 27, 2023

  1. Fix a corner case with empty reactants/products.

    @johnmay
    johnmay committed Jul 27, 2023
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  2. Improved positioning of the parts below the arrow (currently just the… 

    … conditions)
    @johnmay
    johnmay committed Jul 27, 2023
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  3. Fix SVG,PX unit spacing. Now padding is scaled we need to unscale it … 

    …first.
    @johnmay
    johnmay committed Jul 27, 2023
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  4. Cleanup some code smells.

    @johnmay
    johnmay committed Jul 27, 2023
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  5. Ensure scaling works correctly for raster images.

    @johnmay
    johnmay committed Jul 27, 2023
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