Unimol kinetics #164
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Unimol kinetics #164
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@mjohnson541, thanks for your PR! By analyzing the history of the files in this pull request, we identified @connie, @faribas and @jwallen to be potential reviewers. |
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…_out in intra_OH_migration
…end archetype This also reduces the total number of groups and makes it more flexible to add more groups.
…tion *4/*5 depending on which version was a label reserved for backbones that now should not be in any end groups after commit
This now conforms to the fact that end groups must be groups without removing any relevant groups.
…ps changed, some backbone groups renamed
-removed extraneous labels -changed backbone Cs and Ss specificity to C and S to accommodate the C and S trees
… fixed labels under CJ-3 and SJ-3
…nt branches, removal of redundant groups, general restructuring and simplification
…dant branches, removal of redundant groups, general restructuring and simplification
…4 R!H’s to *4 R in the XSYJ tree to match S-RR
…eplaced R with R!H in S-RR to match XSR3J tree
…ant branches, removal of redundant groups, general restructuring and simplification
…ation Also made equivalent change in all backbone groups
…d the _D, _T, _CO subgroups that were really just changes in the multiplebond_intra tree
…2,*3 end of the backbone and made remaining entries general enough to accommodate the component groups
…*3’s appropriately, eliminated unnecessary _D, _T and _CO groups that involved changes to the doublebond_intra section of the backbone
…_D and _T backbone forms that restricted the doublebond_intra end group and suitably generalized the other backbone forms so that they matched the end groups
the tree is now broken up from one tree for R1=R2-O-R4 into trees for R1, R2 and R4 respectively (with an additional one level backbone tree), the rules have been sorted into the new tree structure
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This attribute states the most inward atom labels that overlaps between the end groups and backbones. It is useful for helping to separate the backbone from the end group for unit-testing.
…rees, checks that end group labels are consistent throughout each end group tree, that the backbone has all labels present in the end groups and labels indicating the shortest path between end groups, and that each end group subgraph in each entry in the backbone tree is the top level of the corresponding end group tree
…ests after group formatting fixes, combination of redundant branches and minor restructuring, changes in generality
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Closing this pull request to break it up into smaller ones for easier review |
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Unimolecular Group formatting changes and testing.
A new test requires that end group labels are consistent throughout each end group tree, that the backbone has all labels present in the end groups and labels indicating the shortest path between end groups, and that each end group subgraph in each entry in the backbone tree is the top level of the corresponding end group tree.
specifically exempts Diels_alder_addition family from these requirements.
Groups were adapted to meet these requirements and pass all database tests.