Database test #33
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Database test #33
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Running the function EvaluateKinetics.py will use the new checkWellFormed database and make an output file called DatabaseWellFormedSummary.txt in the RMG-database folder
Another check that needs to be done is if each group is unique. I have added lines for output of that from checkWellFormed
Many of the adj lists in the rules did not match that of the groups. In this family, all the groups were always more general than the rules version, so I've changed the rule's adjList to be the same as the groups This error was found using the checkWellFormed function
Some children were labelled with a "C" atom when the parent had a "Cs" atom causing a discrepency. Probably harmless, but it's better to be consistent
Errors found by checkWellFormed (and a few stumbled while making manual corrections). In rules.py - O2_birad named wrong, should be O2b -XH_Rrad_birad has been updated to a logic Or at some point, but not in the top most node -Same with Y_rad_birad_trirad_quadrad In groups.py -Deleted group N3_atom_quartet, which was an accidental duplicate group -deleted N5dd/H_d_Rrad, which was an accidental duplicate group -Changed atom type on N5d/H_d_Rrad, which was a typo or mistake from recent merge -Moved C_rad/H/O2 and C_rad/H/CsO appear to be placed under the wrong parent. They have been moved from under C_rad/H/NonDeN to under C_rad/H/NonDeO. -Changed Y_rad adj list, it used to be defined R-R* for some reason, but now I've made it just R*. This clears up several children errors. -Added H_rad to LogicOr of Y_rad_birad_trirad_quadrad. That one seems important. -Made group XH_Rrad more general by allowing single or double bonds. So that XH_d_Rrad is a child -Many groups do not include an N atom as possible atoms, restricting descending down to certain children. An N atom has been added to the following groups: O_Rrad, COpri_Rrad, C/H/DeDe_Rrad, C_rad/H/OneDe, C/H2/Nd_Rrad, Cmethyl_Rrad, C/H/NdDe_Rrad, Cdpri_Rrad, C/H2/De_Rrad, C/H/NdNd_Rrad, Cpri_Rrad, Csec_Rrad -Changed Ct_rad/Ct atom one from C to Ct so it is proper child -Changed an monoradical atom type from R to R!H in NH_s_Rrad, which must be true by definition. Also made same change for all children -For groups N3s/H/NonDe_s_Rrad and N3s/H/Deloc_s_Rrad, changed an atom from N to R!H based on name and consulting the creator bbuessar
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Includes new test for database and some corrections to families I've been making using this new function.