mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
0986d22c58
* Make kekulization deterministic * Add tautomer order-independence regression (python) * Adjust tautomer tests for deterministic kekulization * Update graphmol wedged-bond kekulization checks * SmilesParse: update aromatic bond index expectations * SmilesParse: refresh cxsmilesTest expected files * Depictor: update testDepictor expected MolBlocks * Depictor: update depictorCatch expectations * Depictor Wrap: update expected MolBlock for pyDepictor * MarvinParse: update testMrvToMol expected outputs * FileParsers: refresh testAtropisomers expected outputs * FileParsers: update tests for deterministic kekulization * MolDraw2D: refresh brittle bond assertions * RascalMCES: update expected cluster size * MinimalLib: make cffi wedging check order-independent * documentation fix * MinimalLib: update Kekulé bond table in aligned-coords test * Hoist duplicated lambdas to TEST_CASE scope * Remove unused originalWedges variable * Remove redundant bounds check; clarify wedge-end preference * Pre-sort allAtms by wedge-end + rank * Use mol.atomNeighbors() for neighbor iteration * Check inAllAtms before linear-scanning done * Drop redundant optsV/wedgedOptsV sorts * Remove unused Canon.h include * Add canonical parameter to Kekulize; skip ranking during sanitization * Test canonical re-kekulization preserves stereo across atom orderings * MinimalLib: update Kekulé bond orders in invertedWedges * Change Kekulize canonical default to false, expose in Python wrappers * keep rank order, push_back * Revert "RascalMCES: update expected cluster size" This reverts commita81bb39495. * docstring change * expose new flag to python wrapper * document changes in ReleaseNotes.md * revert minimallib test changes again * canonical = true defaults * Revert "revert minimallib test changes again" This reverts commit039e1d84da. * Reapply "RascalMCES: update expected cluster size" This reverts commit7b83a7a3e8. --------- Co-authored-by: greg landrum <greg.landrum@gmail.com>
167 lines
4.2 KiB
Plaintext
167 lines
4.2 KiB
Plaintext
$RXN V3000
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RDKit
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M V30 COUNTS 6 1
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M V30 BEGIN REACTANT
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M V30 BEGIN CTAB
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M V30 COUNTS 6 6 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -10.166760 2.269260 0.000000 0
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M V30 2 C -11.500307 1.499260 0.000000 0
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M V30 3 C -11.500307 -0.040927 0.000000 0
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M V30 4 C -10.166760 -0.810927 0.000000 0
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M V30 5 C -8.833027 -0.040927 0.000000 0
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M V30 6 C -8.833027 1.499260 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 2 2 3
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M V30 3 1 3 4
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M V30 4 2 4 5
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M V30 5 1 5 6
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M V30 6 2 6 1
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M V30 END BOND
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M V30 END CTAB
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M V30 BEGIN CTAB
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M V30 COUNTS 5 5 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -4.541667 2.247460 0.000000 0
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M V30 2 C -5.787480 1.342127 0.000000 0
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M V30 3 C -5.311667 -0.122460 0.000000 0
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M V30 4 C -3.771667 -0.122460 0.000000 0
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M V30 5 C -3.295853 1.342127 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 1 1 5
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M V30 3 1 2 3
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M V30 4 1 3 4
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M V30 5 1 4 5
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M V30 END BOND
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M V30 END CTAB
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M V30 BEGIN CTAB
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M V30 COUNTS 20 22 1 0 0
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M V30 BEGIN ATOM
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M V30 1 Pd -0.398423 -0.150500 0.000000 0 VAL=1
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M V30 2 P -0.398423 1.389500 0.000000 0
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M V30 3 C -1.732102 0.619500 0.000000 0
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M V30 4 C -3.065781 1.389500 0.000000 0
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M V30 5 C -4.399461 0.619500 0.000000 0
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M V30 6 C -4.399461 -0.920500 0.000000 0
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M V30 7 C -3.065781 -1.690500 0.000000 0
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M V30 8 C -1.732102 -0.920500 0.000000 0
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M V30 9 C 0.935256 0.619500 0.000000 0
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M V30 10 C 0.935256 -0.920500 0.000000 0
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M V30 11 C 2.268935 -1.690500 0.000000 0
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M V30 12 C 3.602615 -0.920500 0.000000 0
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M V30 13 C 3.602615 0.619500 0.000000 0
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M V30 14 C 2.268935 1.389500 0.000000 0
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M V30 15 C -0.398423 2.929500 0.000000 0
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M V30 16 C 0.935256 3.699500 0.000000 0
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M V30 17 C 0.935256 5.239500 0.000000 0
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M V30 18 C -0.398423 6.009500 0.000000 0
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M V30 19 C -1.732102 5.239500 0.000000 0
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M V30 20 C -1.732102 3.699500 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 2 19 20
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M V30 2 1 18 19
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M V30 3 2 17 18
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M V30 4 1 16 17
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M V30 5 2 15 16
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M V30 6 1 15 20
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M V30 7 2 13 14
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M V30 8 1 12 13
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M V30 9 2 11 12
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M V30 10 1 10 11
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M V30 11 2 9 10
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M V30 12 1 9 14
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M V30 13 2 7 8
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M V30 14 1 6 7
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M V30 15 2 5 6
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M V30 16 1 4 5
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M V30 17 2 3 4
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M V30 18 1 3 8
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M V30 19 1 2 3
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M V30 20 1 2 9
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M V30 21 1 2 15
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M V30 22 1 1 2
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M V30 END BOND
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M V30 BEGIN SGROUP
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M V30 1 SUP 0 ATOMS=(20 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20) -
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M V30 LABEL=PdPPh3
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M V30 END SGROUP
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M V30 END CTAB
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M V30 BEGIN CTAB
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M V30 COUNTS 2 0 1 0 0
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M V30 BEGIN ATOM
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M V30 1 O 1.038244 -0.083333 0.000000 0 CHG=-1
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M V30 2 Na -0.501756 -0.083333 0.000000 0 CHG=1 VAL=-1
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M V30 END ATOM
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M V30 BEGIN SGROUP
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M V30 1 SUP 0 ATOMS=(2 1 2) LABEL=NaOH
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M V30 END SGROUP
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M V30 END CTAB
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M V30 BEGIN CTAB
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M V30 COUNTS 3 0 1 0 0
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M V30 BEGIN ATOM
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M V30 1 Cl 2.273270 -0.333333 0.000000 0 CHG=-1
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M V30 2 Cl 6.673190 -0.333333 0.000000 0 CHG=-1
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M V30 3 Pd 0.733270 -0.333333 0.000000 0 CHG=2 VAL=-1
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M V30 END ATOM
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M V30 BEGIN SGROUP
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M V30 1 SUP 0 ATOMS=(3 1 2 3) LABEL=PdCl2
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M V30 END SGROUP
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M V30 END CTAB
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M V30 BEGIN CTAB
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M V30 COUNTS 6 4 1 0 0
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M V30 BEGIN ATOM
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M V30 1 K 3.559910 -1.150000 0.000000 0 CHG=1 VAL=-1
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M V30 2 O 3.559910 0.390000 0.000000 0 CHG=-1
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M V30 3 Mn 3.559910 1.930000 0.000000 0 VAL=7
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M V30 4 O 3.559910 3.470000 0.000000 0
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M V30 5 O 5.099910 1.930000 0.000000 0
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M V30 6 O 2.019910 1.930000 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 2 3
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M V30 2 2 3 4
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M V30 3 2 3 5
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M V30 4 2 3 6
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M V30 END BOND
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M V30 BEGIN SGROUP
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M V30 1 SUP 0 ATOMS=(6 1 2 3 4 5 6) LABEL=KMnO4
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M V30 END SGROUP
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M V30 END CTAB
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M V30 END REACTANT
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M V30 BEGIN PRODUCT
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M V30 BEGIN CTAB
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M V30 COUNTS 9 10 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 8.583240 1.935927 0.000000 0
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M V30 2 C 7.249693 1.165927 0.000000 0
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M V30 3 C 7.249693 -0.374260 0.000000 0
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M V30 4 C 8.583240 -1.144260 0.000000 0
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M V30 5 C 9.916973 -0.374260 0.000000 0
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M V30 6 C 9.916973 1.165927 0.000000 0
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M V30 7 C 11.381476 -0.850252 0.000000 0
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M V30 8 C 12.286794 0.395540 0.000000 0
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M V30 9 C 11.381723 1.641437 0.000000 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 1 2
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M V30 2 2 2 3
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M V30 3 1 3 4
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M V30 4 2 4 5
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M V30 5 1 5 6
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M V30 6 2 6 1
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M V30 7 1 7 8
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M V30 8 1 8 9
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M V30 9 1 5 7
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M V30 10 1 6 9
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M V30 END BOND
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M V30 END CTAB
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M V30 END PRODUCT
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M END
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