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Update IPython notebooks #1735

Merged
merged 9 commits into from
Oct 26, 2019
Merged

Update IPython notebooks #1735

merged 9 commits into from
Oct 26, 2019

Commits on Oct 25, 2019

  1. Remove Species import from rmgpy.molecule.draw 

    It was leading to circular imports, and was only used for
an isinstance check, which was refactored
    @mliu49
    mliu49 committed Oct 25, 2019
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  2. Refactor entry sorting in kinetics rules 

    Main motivation is that None can no longer be compared to ints in
Python 3

This changes how the sorting process is implemented but maintains
the same behavior as before
    @mliu49
    mliu49 committed Oct 25, 2019
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  3. Adjust reaction template retrieval when parsing reaction comments 

    In cases where there may have been a line break in the middle of
the reaction template, which is very likely with automatically
generated families.
    @mliu49
    mliu49 committed Oct 25, 2019
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  4. Fix leftover uses of format in molecule.draw

    @mliu49
    mliu49 committed Oct 25, 2019
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  5. Update example model in ipython/data/parse_source

    @mliu49
    mliu49 committed Oct 25, 2019
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  6. Update IPython notebooks with Python 3 and RMG changes

    @mliu49
    mliu49 committed Oct 25, 2019
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  7. Standardize ipython notebook filenames

    @mliu49
    mliu49 committed Oct 25, 2019
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  8. Fix incorrect argument in call to RDKit 

    Was accidentally renamed
    @mliu49
    mliu49 committed Oct 25, 2019
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  9. Fix get_labeled_reactants_and_products for new families 

    The R_Recombination family was changed for auto tree generation
There is only a single template now, and duplicate * labels
This copies template handling from __generate_reactions
A unit test is also added
    @mliu49
    mliu49 committed Oct 25, 2019
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