SKETCH-2375: Migrate to RDKit native attachment point handling - #360
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SKETCH-2375: Migrate to RDKit native attachment point handling#360cdvonbargen wants to merge 6 commits into
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Replace custom attachment point expand/collapse functions with RDKit's native MolOps::expandAttachmentPoints() and collapseAttachmentPoints(). Set _fromAttachPoint property on AP dummies for compatibility with the native API, while keeping atomLabel for molecule-level numbering. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…mentPoint Delegate is_attachment_point_dummy() to RDKit's MolOps::details::isAttachmentPoint() and replace make_new_attachment_point() with MolOps::details::addExplicitAttachmentPoint(). This requires all AP dummies to have _fromAttachPoint set, so label_expanded_attachment_points() now also marks CXSMILES-sourced APs that only have atomLabel. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…hmentPoint Remove the is_attachment_point_dummy wrapper from rdkit_extensions and replace all call sites with RDKit::MolOps::details::isAttachmentPoint(). Also simplify collapse_attachment_point_dummies to just call collapseAttachmentPoints without the redundant marking loop, since all AP creation and read paths now set _fromAttachPoint. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Inline the single collapseAttachmentPoints call at the write site and drop the unnecessary updatePropertyCache calls that bookended it. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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No "testing done" section. I assume this was tested?
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| if (atom.hasProp(RDKit::common_properties::_fromAttachPoint)) { | ||
| return true; | ||
| } | ||
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| std::string label; | ||
| return atom.getAtomicNum() == 0 && atom.getTotalDegree() == 1 && | ||
| atom.getPropIfPresent(RDKit::common_properties::atomLabel, label) && | ||
| label.find(ATTACHMENT_POINT_LABEL_PREFIX) == 0; | ||
| return atom.getPropIfPresent(RDKit::common_properties::atomLabel, label) && | ||
| label.starts_with(ATTACHMENT_POINT_LABEL_PREFIX); |
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Under what conditions would we see the attachment point prefix on the atom label, but we wouldn't see the _fromAttachPoint property?
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_fromAttachPoint is only set by RDKit when reading SD files or using the (relatively new) addExplicitAttachmentPoint/expandAttachmentPoints functions directly; so things like CXSMILES wouldn't have it.
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Understood, thanks. Is this well known, or would we benefit from adding a comment here to this effect?
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RDKit APIs used
MolOps::expandAttachmentPoints()replacesmolattachpt_property_to_attachment_point_dummies().MolOps::collapseAttachmentPoints()replacesattachment_point_dummies_to_molattachpt_property().MolOps::details::addExplicitAttachmentPoint()replacesmake_new_attachment_point().Functions kept for Sketcher behavior
is_attachment_point_dummy()cannot use RDKit'sisAttachmentPoint()because RDKit tests whether an AP can be collapsed and therefore rejects wedged APs. Sketcher must still recognize those as attachment points and support legacy_AP<n>labels.compute2DCoords()additionally handles HELM structures, frozen atoms, ring templates, and removal of stale molfile wedging.wedgeMolBonds()prevents RDKit from choosing attachment-point bonds for wedging by temporarily making those bonds ineligible._AP<n>UI numbering. RDKit's_fromAttachPointvalues only describe the first or second attachment on an individual parent atom.Testing Done
Added new tests; all existing tests pass