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Added a module for working with RMG reaction families #754

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Added a module for working with RMG reaction families #754

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Commits on Jul 29, 2024

  1. Minor: CI style modifications

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  2. Removed RMG-Py and RMG-database repo paths from common 

    were used to report the git branch and commit of the repos
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  3. Relocated reaction into a sub module

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  4. Added RMG_DB_PATH to settings

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  5. Added clean_text() to common

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  6. Tests: common.clean_text()

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  7. Added hydrolysis as an ARC reaction family 

    ARC reaction families are families for which only a template/recipe is given without kinetic data. They can be used by ARC to atom-map a reaction and search for a transition state just like RMG families. They have the same format as the `group.py` file in RMG reaction families, only here the files are named by the family label. ARC families should be located under ARC/data/families/ to be discovered by ARC.

Also added ARC_FAMILIES_PATH to settings
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  8. Added the reaction family module

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  9. Tests: Added reaction family tests

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  10. Removed rmgdb from reaction

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  11. Tests: Adaptations to reaction tests

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  12. Corrected import in arkane test

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  13. Don't consider additional TS conformers if there's just one

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  14. Removed the determine_family() function from the rmgdb module 

    It is obsolete now
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  15. Don't use RMGDatabase to determine reaction family 

    Currently the rmgdb module is only used by processor which will be dealt with in a different PR
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  16. Tests: Removed RMGDatabase from tests

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  17. Modifications to how reaction family is used in ARC 

    It is no longer an object, no need to call family.label
No need to call determine_family() since family is now a property of reaction
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  18. Make family a property of reaction

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  19. Tests: Adaptations to ARC tests

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  20. f! fam

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  21. f! fam test

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  22. fam

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  23. f! tst

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  24. f tst

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  25. f fam

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  26. TMP

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  27. Removed hard-coded no-mol-perception for triplet O2/S2 

    Solved by PR #756
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  28. Tests: Perceive triplet O2 properly

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  29. f! fam resonance

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  30. f! fam tests

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Commits on Aug 8, 2024

  1. TMP

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Commits on Aug 11, 2024

  1. TMP

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Commits on Aug 12, 2024

  1. TMP

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Commits on Oct 10, 2024

  1. f!

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    alongd committed Oct 10, 2024
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Commits on Oct 30, 2024

  1. Added add_atom_to_zmat()

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    alongd committed Oct 30, 2024
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Commits on Oct 31, 2024

  1. f! engine

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    alongd committed Oct 31, 2024
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