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Hydrolysis families and tests#770

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LeenFahoum wants to merge 78 commits intomainReactionMechanismGenerator/ARC:mainfrom hydrolysisReactionMechanismGenerator/ARC:hydrolysisCopy head branch name to clipboard

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Commits on Feb 4, 2025

• Minor: CI style modifications

  

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• Minor: Fixed typo in Arkane test

  

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• Minor: Removed debug print from species test

  

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• Minor: Modifications to ARC's executable

  

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• Minor: Style modifications to mapping engine

  

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

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• 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 family module

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• Tests: Added 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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• Modifications to Scheduler

  

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• Removed the rmgdb module

  

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• TMP: commented out NMD tests, they are dealt with in a different PR

  

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• TMP: Skip NMD in ts check, it is dealt with in a different PR

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• Removed unnecessary functions from mapping engine

  

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• Removed _check_r_n_p_symbols_between_rmg_and_arc_rxns from common

  

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• Updated Heuristics TS search

  

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• Removed rmgdb from main

  

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• Tests: Updated heuristics tests

  

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• Modifications to mapping engine

  

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• Tests: Modifications to mapping engine tests

  

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• Modifications to mapping driver

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• Tests: Modifications to mapping driver tests

  

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• Tests: Modifications to reaction tests

  

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• Added check_molecule_list_order() to species converter

  

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• Added RMG thermo and kinetics scripts

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• Modified the trype of the species rmg_thermo attribute

  

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• Modified the type of the Reaction rmg_kinetics attribute

  

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• Updated processor to use RMG's scripts instead of RMG's API

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• Updated plotter for RMG's parsed data

  

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• Tests: Updated H atomtype in common tests to H0

  

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• Removed rmg_reaction from reaction

  

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• Tests: Removed rmg_reaction from reaction tests

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• Tests: Minor: Fix isotope SMILES in conformers tests

  

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• Removed utilization of .rmg_reaction from ARC's modules

  

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• Todo: fix plotter

  

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• tmp cache

  

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• f autotst ts

  

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• tmp cache

  

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• f kinbot tst

  

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• Check species type in Reaction

  

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• f scripts

  

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• Added calculate_arrhenius_rate_coefficient() to common

  

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• Tests: calculate_arrhenius_rate_coefficient

  

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• Updated plotter to use calculate_arrhenius_rate_coefficient()

  

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• f common

  

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• f plotter

  

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• f processor

  

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• f reation

  

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• TMP

  

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• f rxn

  

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• TMP

  

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• Exclude hidden and underscore files from ARC families list

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• Added different hydrolysis arc families groups

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• Added tests for arc families groups

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• Added is_water function

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• test for is_water function

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Commits on Feb 5, 2025

• Add electronegativity-based neighbor selection and YAML data

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• tests for get_neighbors_by_electronegativity()

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Commits on Feb 6, 2025

• Add functions to retrieve, and count matching dihedral angles

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• tests for all dihedral functions

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• Add TS guess generation for hydrolysis reaction families

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• Add unit tests for TS guess generation in hydrolysis reaction families

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• Minor update in ether hydrolysis family definition

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• minor: typo fix

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