Change IUPAC metal->non-metal single bonds to dative#6038
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DavidACosgrove
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February 1, 2023 15:48
Fix expected test results.
Explicitly exclude H, He, F, Ne from dative bonds. Fix tests.
greglandrum
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Feb 5, 2023
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greglandrum
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Some comments here, most of which are addressed by the PR I just did against your branch.
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| // Version 10 files can be read by 11, but not vice versa. | ||
| if (doc["rdkitjson"]["version"].GetInt() != currentRDKitJSONVersion) { | ||
| throw FileParseException("Bad Format: bad version in JSON"); | ||
| if (!(doc["rdkitjson"]["version"].GetInt() == 10 && | ||
| currentRDKitJSONVersion == 11)) { | ||
| throw FileParseException("Bad Format: bad version in JSON"); | ||
| } |
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I'd rather just commit to backwards compatibility here - we'll continue to read previous versions of the JSON format in the future. I don't think we want to do this for versions below 10 though, so how about making the check here:
if (int jsonVersion=doc["rdkitjson"]["version"].GetInt(); jsonVersion > currentRDKitJSONVersion || jsonVersion<10)
| // from the non-metal to the metal. | ||
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| auto isMetal = [](const Atom *a) -> bool { | ||
| // This is the list of not metal atoms from QueryOps.cpp |
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Not a request for a change, but I suspect that we're going to want to adjust this list to make it less permissive.
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ricrogz
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Feb 7, 2023
* Change atom to metal bonds from single to dative if appropriate. * Pedantic change whilst I was in the area. * Reinstate all tests, leave in debugging writes to see failing tests. * Re-did it. Failing tests now pass. * Move any positive charge from the non-metal to the metal. Fix expected test results. * Write dative bond to JSON. * Bump currentRDKitJSONVersion to 11, but allow parser to still read 10. * Only move 1 unit of charge at a time from non-metal to metal. * Greg's hack to not do it for O+ and N+ etc. Explicitly exclude H, He, F, Ne from dative bonds. Fix tests. * Update expected PostGres json version to 11. * suggestions for PR * Correct comment. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: greg landrum <greg.landrum@gmail.com>
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Reference Issue
Addresses #6019
What does this implement/fix? Explain your changes.
As suggested by @greglandrum, this changes surplus single bonds to metals to dative in MolOps.cc::cleanUp.
Any other comments?