Hydrolysis families and tests #770
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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
f family f family f! family f! family f! family init
f fam test f! fam tst f! fam test
It is obsolete now
Currently the rmgdb module is only used by processor which will be dealt with in a different PR
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
ester, nitrile, ether, and imine hydrolysis
ester, nitrile, ether,, and imine hydrolysis
identifies if a given molecule is water
-Implemented neighbour selection using electronegativity and bond order. -Added electronegativity.yml for element values.
Implemented three functions—`get_matching_dihedrals`, `find_matching_dihedral`, and `count_all_possible_dihedrals`—to identify dihedral angles in the Z-matrix based on specified atom indices. These functions provide flexible capabilities for retrieving, counting, and limiting dihedral angles matches.
get_matching_dihedrals() , find_matching_dihedral() , and count_all_possible_dihedrals
Implemented TS guess generation for hydrolysis reaction families, including ester, imine, ether, and nitrile hydrolysis. The approach uses z-matrix manipulation, dihedral angle adjustments, and electronegativity-based heuristics to generate TS structures.
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new hydrolysis families and tests