Entry acessibility #128
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Entry acessibility #128
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Caught by fixing bug in parent/child database unit test. Moved them up a group from their original parents because their erroneous parents comment specifically said for noncyclic compounds, while the Lac and Lactum groups are all cyclic.
…ity test groups Cb-CbCbN3s - changed into Cb-N3s, as other Cb are redundant and moved in tree change and move Cs-(N3dN3d)CsCsH because invalid use of N3d, changed single bond to double bond based on examples of other groups change and move Cs-(N3dN3d)CsCsCs beause invalid use of N3d parent was Cs-N3dCsCsCs, changed single bond to double bond based on examples of other groups polycyclic s2_3_5_ene_side: made R to R!H because double bonded s2_3_5_ene_1_side made R to R!H because double bonded s2_3_5_ene - moved in tree to make its child s2_3_5_ene_side acessible s3_5_5_ene_side - made R to R!H because double bonded s3_5_5_ene - moved in tree to make its child s3_5_5_ene_side acessible
move bicyclo[1.1.1]pentane-C2 up a level in tree move bicyclo[1.1.0]butane-secondary lower in sibling list move cyclopentene-4 up in sibling list to make its child bicyclo[2.1.1]hex-2-ene-C5 acessible moved bicyclo[2.1.0]pent-2-ene-C5 from parent cyclopropane to another parent cyclopentene-4 move tricyclo[2.1.1.0(1,4)]hex-2-ene-C5 to be child of bicyclo[2.1.1]hex-2-ene-C5 move tricyclo[1.1.1.0(1,3)]pentane-C2 to be a child of bicyclo[1.1.1]pentane-C2 move tricyclo[2.1.1.0(1,4)]hexane-C2 up in sibling list move tricyclo[2.1.1.0(1,4)]hexane-C5 to be child of bicyclo[2.1.1]hexane-C5 move bicyclo[4.1.0]heptane-C6-2, bicyclo[4.1.0]heptane-C6-3, bicyclo[4.1.0]heptane-C6-3 up in sibling list above cycloheptane move bicyclo[3.1.1]heptane-C6 up sibling list above cyclobutane move bicyclo[3.1.1]heptane-C2 up sibling list above bicyclo[3.1.0]hexane-C5-2 to make its child tricyclo[3.1.1.0(1,5)]heptane-C2 acessibile move tricyclo[3.1.1.0(1,5)]heptane-C6 up sibling list above bicyclo[1.1.0]butane-secondary move tricyclo[2.2.1.0(1,4)]heptane-C2 up sibling list above cyclobutane move tricyclo[2.2.1.0(1,4)]heptane-C7 up siblig list above bicyclo[2.1.0]pentane-secondary-C3 move bicyclo[4.2.0]octane-C4-7 up sibling list above cyclobutane move bicyclo[2.2.2]octane-C2 up sibling list above cyclobutane for its child tricyclo[2.2.2.0(1,4)]octane-C2
In nonacentered.py: OxR3, OxR4, OxR5, OxR6 and OxR7, changed R to R!H because they have more than one bond SdOdOdN removed for now cause of multivalent sulfur moved N3sHCd(Od)N3sH up in sibling list In abraham.py: fix definition of Cb-notH, changing Cb to Cbf and R!H to Cbs and changing name to Cbf-notH moved Cbf-notH to be child of Cbf remove SdsOsOdOd because of multivalent sulfur, node was a child of S
Nitro - change atomtype from N to N5d and move up sibling list above Nitrites Nitrates - change atomtype from N to N5d
where changes made in database can fail RMG-Py unittests at least can alarm developers to be aware of data change is causing potential issues
also add an assertion test preventing child is same as parent
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This pull request fixes accessibility issues in the database.
For various reasons, sometimes an entry in a tree will not be descended to properly. I have created a unit test to make a sample molecule and attempt to descend the tree. All fixes from this commit was found with this unit test.