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Unimol kinetics#164

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mjohnson541 wants to merge 27 commits intomasterReactionMechanismGenerator/RMG-database:masterfrom unimol_kineticsReactionMechanismGenerator/RMG-database:unimol_kineticsCopy head branch name to clipboard

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Commits

Commits on Feb 17, 2017

• Add labels to backbone atoms of intra_OH_migration groups

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  4e48fa3

• Made all backbone end subgraphs isomorphic to general end group Y_rad_out in intra_OH_migration

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• Add labels for backbone between end groups in Intra_Disproportionation

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• Add backbones labels and standardized end groups for Birad_recombination family

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• Standardized use of rad_add_intra in backbones of Intra_RH_Add_Endocyclic

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• Add backbone labels for Cyclic_Ether_Formation

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• Added tree to Cyclic_Ether_Formation so that it follows backbone;end;end archetype

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• Removed extra labels from Y_rad_intra end group of Cyclic_Ether_Formation

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• Standardized end groups on backbones to be general for Cyclic_Ether_Formation

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• Removed a top level OR end group and replaced it with its only child

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• intra_H_migration database reorganization, too specific backbone groups changed, some backbone groups renamed

  

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• improve atomtyping and labeling in intrasubstitutionCS_cyclization

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• intra_substitutionCS_isomerization fixing, removed extraneous labels, fixed labels under CJ-3 and SJ-3

  

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• reorganization of intra_substitutionCS_cyclization removal of redundant branches, removal of redundant groups, general restructuring and simplification

  

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  8a28b29

• reorganization of intra_substitutionCS_isomerization removal of redundant branches, removal of redundant groups, general restructuring and simplification

  

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  455754b

• intra_substitutionS_cyclization, removed extraneous labels, changed *4 R!H’s to *4 R in the XSYJ tree to match S-RR

  

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• intra_substitutionS_isomerization fixes, removed extraneous labels, replaced R with R!H in S-RR to match XSR3J tree

  

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  86b12ce

• reorganization of intra_substitutionS_isomerization removal of redundant branches, removal of redundant groups, general restructuring and simplification

  

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• Change top level node S-RR to use *2R!H in intra_substitutionS_cyclization

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• Added in Nitrogen to the *2 and *3 options in the backbone, eliminated the _D, _T, _CO subgroups that were really just changes in the multiplebond_intra tree

  

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• Intra_R_Add_ExoTetCyclic fixes, removed Cs/O entries related tot eh *2,*3 end of the backbone and made remaining entries general enough to accommodate the component groups

  

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• Inra_R_Add_Endocyclic fixes, Generalized the doublebond_intra *2 and *3’s appropriately, eliminated unnecessary _D, _T and _CO groups that involved changes to the doublebond_intra section of the ba…

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• Intra_RH_Add_Exocyclic fixes, removed extraneous labels, removed all _D and _T backbone forms that restricted the doublebond_intra end group and suitably generalized the other backbone forms so tha…

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• Reorganization of the Ketoenol group

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Commits on Feb 19, 2017

• Add 'boundaryAtom' attribute to all unimolecular families

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• addition of a database test for unimolecular groups having multiple trees, checks that end group labels are consistent throughout each end group tree, that the backbone has all labels present in th…

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• reorganization of the intra_substitutionS_cyclization group to meet tests after group formatting fixes, combination of redundant branches and minor restructuring, changes in generality

  

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