Use `rdkit` for SSSR and RCs (bug fix + Python upgrade)#2796

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JacksonBurns wants to merge 84 commits intomainfrom

feat/rdkit_sssr

Commits on Dec 9, 2025

Use `rdkit` for SSSR and RCs (bug fix + Python upgrade)
JacksonBurns
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relax version constraint in setup
JacksonBurns
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move ring functions from graph to molecule

jonwzheng
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JacksonBurns
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update unit tests

jonwzheng
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JacksonBurns
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move all functions that previously called get_relevant_cycles or get_smallest_set_of_smallest_rings from Graph to Molecule

jonwzheng
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JacksonBurns
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update cython definition for graph

jonwzheng
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JacksonBurns
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update molecule cython file with new functions

jonwzheng
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JacksonBurns
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update molecule to make an Atom list rather than indices

jonwzheng
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JacksonBurns
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try remove_h in get_relevant_cycles

jonwzheng
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JacksonBurns
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call GetSymmSSSR on RDKit Mol object rather than Molecule

jonwzheng
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JacksonBurns
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Adjust ring matching logic to avoid SSSR on Graph

jonwzheng
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JacksonBurns
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add checks if species is electron

jonwzheng
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JacksonBurns
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remove some tests that appear backwards-incompatible with new RDKit adjacency list parsing rules

jonwzheng
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JacksonBurns
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get sample molecule instead of group for SSSR

jonwzheng
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JacksonBurns
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add vdW bond support for RDKit molecules

jonwzheng
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JacksonBurns
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remove RDKit mol sanitization

jonwzheng
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JacksonBurns
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move test_get_largest_ring from Graph to Molecule

jonwzheng
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JacksonBurns
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add electron check for loading from adj list

jonwzheng
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JacksonBurns
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try save order for ring perception

jonwzheng
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JacksonBurns
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try preserve atom order for ring perception

jonwzheng
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JacksonBurns
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only partially sanitize RDKit molecules

jonwzheng
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JacksonBurns
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make test_make_sample_molecule test logic more clear

jonwzheng
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JacksonBurns
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remove erroneously malformed sanitize arg

jonwzheng
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JacksonBurns
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Revert "remove some tests that appear backwards-incompatible with new RDKit adjacency list parsing rules"

jonwzheng
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JacksonBurns
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add support for RDKit fragment atom w/ dummy molecule

jonwzheng
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JacksonBurns
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fix pesky type error in rdkit mol creation due to type cython coercion

jonwzheng
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JacksonBurns
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update test_get_largest_ring

jonwzheng
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JacksonBurns
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fix error in test_Get_all_polycyclic_vertices

jonwzheng
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JacksonBurns
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make rdkit parsing more lenient with weird bond orders

jonwzheng
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JacksonBurns
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Modify sanitization to accommodate kekulization

jonwzheng
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JacksonBurns
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update scipy simps to sipmson

jonwzheng
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JacksonBurns
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remove python3.12 from CI for now

jonwzheng
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JacksonBurns
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make QM molecule partial sanitized with RDKit

jonwzheng
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JacksonBurns
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update setup.py to also exclude python 3.12

jonwzheng
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JacksonBurns
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added a test for drawing bidentates with charge separation

kirkbadger18
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JacksonBurns
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Make rdkit default for draw coordinate generation

jonwzheng
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JacksonBurns
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add ion test cases to drawTest

jonwzheng
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JacksonBurns
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remove pyrdl from conda recipe as well
JacksonBurns
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add more python versions to conda build
JacksonBurns
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Make fragment code compatible with RDKit changes

jonwzheng
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JacksonBurns
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Fix fragment error due to non-default return type

jonwzheng
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JacksonBurns
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add missing remove_h=False required flag to fragment to_rdkit_mol calls

jonwzheng
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JacksonBurns
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fix test_to_rdkit_mol because default args were changed

jonwzheng
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JacksonBurns
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update test expectted return type
JacksonBurns
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Revert "update test expectted return type"
JacksonBurns
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set default
JacksonBurns
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Double-check SSSR to_rdkit_mol for fragment compat

jonwzheng
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JacksonBurns
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Change debug level of RDKit-related warnings

jonwzheng
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JacksonBurns
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Fix ring unit test that was testing nothing.

rwest
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Add a unit test for identify_ring_membership for a big ring.

rwest
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Rewrite identfy_ring_membership() to use FastFindRings

rwest
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More extensive testing for test_ring_perception

rwest
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JacksonBurns
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Fix error in fragment exception handling.

rwest
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JacksonBurns
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Replace identify_ring_membership algorithm with existing is_vertex_in_cycle

rwest
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Renamed get_symmetrized_smallest_set_of_smallest_rings and related methods.

rwest
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JacksonBurns
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Temporary: add deprecation warnings and re-enable ring methods.

rwest
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JacksonBurns
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Revert "Temporary: add deprecation warnings and re-enable ring methods."

rwest
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JacksonBurns
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Use get_symmetrized_smallest_set_of_smallest_rings in many places.

rwest
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JacksonBurns
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Create unit test for get_symmetrized_smallest_set_of_smallest_rings()

rwest
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JacksonBurns
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Use get_symmetrized_smallest_set_of_smallest_rings in more places.

rwest
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JacksonBurns
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Change get_relevant_cycles test, now that it has been removed.

rwest
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JacksonBurns
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Using get_symmetrized_smallest_set_of_smallest_rings in more places.

rwest
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JacksonBurns
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Delete test_cycle_list_order_relevant_cycles test.

rwest
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JacksonBurns
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Fix sanitization issue in to_rdkit_mol

rwest
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JacksonBurns
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Make detect_cutting_label a static method.

rwest
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JacksonBurns
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Change to_rdkit_mol bond handling. Add ignore_bond_order option.

rwest
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JacksonBurns
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When doing ring detection, don't pass bond orders to RDKit.

rwest
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JacksonBurns
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Revert "Change debug level of RDKit-related warnings"

rwest
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JacksonBurns
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Possible simplification of to_rdkit_mol for cutting labels.

rwest
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Simplify and optimize cutting label lookup in to_rdkit_mol.

rwest
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Fragment.to_rdkit_mol now respects some kwargs instead of printing warnings.

rwest
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Ring finding code doesn't need to cope with unwanted mappings from to_rdkit_mol

rwest
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Tweak to MoleculeDrawer: don't bother making a Geometry object.

rwest
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JacksonBurns
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