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Hydrolysis families and tests#770

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LeenFahoum wants to merge 43 commits intomainReactionMechanismGenerator/ARC:mainfrom hydrolysisReactionMechanismGenerator/ARC:hydrolysisCopy head branch name to clipboard

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Commits on Nov 6, 2024

• Minor: CI style modifications

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• Removed RMG-Py and RMG-database repo paths from common

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  283dd12

• Relocated reaction into a sub module

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• Added RMG_DB_PATH to settings

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• Added clean_text() to common

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• Tests: common.clean_text()

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• Added hydrolysis as an ARC reaction family

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• Added the reaction family module

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• Tests: Added reaction family tests

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• Removed rmgdb from reaction

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• Tests: Adaptations to reaction tests

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• Corrected import in arkane test

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

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• Removed the determine_family() function from the rmgdb module

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• Don't use RMGDatabase to determine reaction family

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• Tests: Removed RMGDatabase from tests

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• Modifications to how reaction family is used in ARC

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• Make family a property of reaction

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• Tests: Adaptations to ARC tests

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• f! fam

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• f! fam test

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• fam

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• f! tst

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• f tst

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• f fam

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• TMP

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

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• Tests: Perceive triplet O2 properly

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• f! fam resonance

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• f! fam tests

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• TMP

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• TMP

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• TMP

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• f!

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• Call hydrolysis function (still doesn't exist)

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• Temporary commit

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Commits on Nov 11, 2024

• Add condition to filter ARC families by excluding hidden files and directories

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• Filter ARC families to exclude hidden files and directories

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  40467e1

Commits on Nov 13, 2024

• new ester__hydrolysis family

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• new imine hydrolysis family

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• new nitrite hydrolysis family

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• new ether hydrolysis family

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• tests for new hydrolysis families

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