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S-groups: PARENT field should reference index #3175

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greglandrum opened this issue May 18, 2020 · 3 comments · Fixed by #3170
Closed

S-groups: PARENT field should reference index #3175

greglandrum opened this issue May 18, 2020 · 3 comments · Fixed by #3170
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2020_03_3

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@greglandrum
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greglandrum commented May 18, 2020 •
edited

Here's what index says in the docs:
image

and PARENT:
image

Since we can avoid altering the input data here, I think it makes sense to do so and to preserve the index and PARENT fields from SGroups in mol blocks. When we do that, the PARENT should reference an index property, not an index in the vector of SubstanceGroups.
@greglandrum greglandrum self-assigned this May 18, 2020
@greglandrum greglandrum added this to the 2020_03_3 milestone May 18, 2020
@ricrogz
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ricrogz commented May 18, 2020

This is a bit more clear after reading through #3170

(Had a bit of trouble understanding this without looking at your last comments there)

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@ricrogz : does the last paragraph I just added help?

greglandrum added a commit to greglandrum/rdkit that referenced this issue May 18, 2020
@greglandrum
Fixes rdkit#3175
eeafeea
@greglandrum greglandrum linked a pull request May 18, 2020 that will close this issue
Allow SubstanceGroups to survive molecule edits #3170
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@greglandrum greglandrum mentioned this issue May 18, 2020
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greglandrum added a commit that referenced this issue May 19, 2020
@greglandrum
Allow SubstanceGroups to survive molecule edits (#3170)
95613b6 
* Progress on #3168

* Fixes #3167

* Fixes #3169

* deal with CBONDS too

* test PATOMS

* Fixes #3175

* a bit of code simplification and test updates

still needs more testing

* more testing

* handle s-group hierarchy
also a couple of other changes in response to the review

* add forgotten test file

* changes in response to review
@ricrogz
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ricrogz commented May 19, 2020

@ricrogz : does the last paragraph I just added help?

Sorry, I missed this. Yeah, that helped. Somehow I missed that this was also about preserving the value of the "index" field on input.

greglandrum added a commit that referenced this issue Jun 9, 2020
@greglandrum
Allow SubstanceGroups to survive molecule edits (#3170)
73841c6 
* Progress on #3168

* Fixes #3167

* Fixes #3169

* deal with CBONDS too

* test PATOMS

* Fixes #3175

* a bit of code simplification and test updates

still needs more testing

* more testing

* handle s-group hierarchy
also a couple of other changes in response to the review

* add forgotten test file

* changes in response to review
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Allow SubstanceGroups to survive molecule edits greglandrum/rdkit
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