mirror of
https://github.com/rdkit/rdkit.git
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5fe20d270f
* First stab at disconnecting organometallics the Syngenta way. * Add support for Li and Na compounds, with tests. * Correct docstrings. * Add -1 valence to sodium. * Add changes from PR 5997. * Move declaration of disconnectOrganometallics. * Re-factor tests for disconnectOrganometallics to read V3000 files rather than hard-code in file. * Add optional options to constructor. * Python wrapping for disconnectOrganometallics. * Python tests. * Correct docString. * Test using in place overload of disconnect free function. * options_ should not be a reference. * Re-work the wrappers. * Added test MOL files. * Correct charge on iron atoms. * Fix tests for charged iron. * Added some more test complexes. * Port Marco's oxidation number Python to C++ Descriptor. * Rename functions. * Another test. * Python wrappers. * Comment in test. * Throws exception if atom-based function called with non-kekulized parent. * Fix typo. * Allow potassium as well. * Whole molecule calculations for oxidation number only. Rename prop to OxidationNumber. * Add OxidationNumber to common_properties. * Extra comment. * When deleting atom, update any ENDPTS props on bonds. Copied in from stale PR ExtraDoc. * Added hapticBondsToDative with python wrapper. * Extra test. * Re-factor endpts parsing. * Typo. * Add function for haptic end points inc. Python wrapper. * Add dative bonds in separate step. * C++ version of dativeBondstoHaptic. * Update test mols. * Python wrapper. * Fix indents in Python test script. * Corrected expected test result. * Only do non-metal to metal conversion of single bond to dative if the explicit valence of the non-metal allows it. * Fix test broken in a non-material way by previous change. * Export for DLL. * Remove redundant function declaration. * Dave hates Windows. * Move hapticBondEndpoints to Molops::details. * And take it out of the Python wrappers. * Run yapf on reformatted test script. * Get the DLL builds going. * addDativeBond -> addHapticBond. * Batch edits. * Position arithmetic. * setQuery. * Dummy positions for all confs. * Fix tests for dummy positions for all confs. * Move tests to catch_organometallics.cpp. * Modern docString. * Change member variable names. * sProp length, bonus batchEdit. * Add options object to disconnectOrganometallics. * Tidied license. Atom precondition. * GetIntProp. * Test opts aren't defaults. * Python wrapper for disconnectOrganometallics with options. * Minor edit. * Slightly random attempt to fix Java build. * Response to review. * Another stab at the doc strings. --------- Co-authored-by: David Cosgrove <david@cozchemix.co.uk> Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
109 lines
2.9 KiB
Plaintext
109 lines
2.9 KiB
Plaintext
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ChemDraw01202309422D
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0 0 0 0 0 0 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 44 52 0 0 0
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M V30 BEGIN ATOM
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M V30 1 Pd -0.795550 0.559801 0.000000 0 CHG=2
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M V30 2 P 1.443750 -0.736599 0.000000 0
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M V30 3 O -0.677650 -0.795599 0.000000 0 CHG=-1
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M V30 4 N -1.797349 -0.029499 0.000000 0
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M V30 5 C -0.795550 1.679401 0.000000 0 CHG=-1
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M V30 6 C 2.091950 -0.383099 0.000000 0
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M V30 7 C 3.270550 -3.270598 0.000000 0
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M V30 8 C 1.443750 -1.502699 0.000000 0
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M V30 9 S -1.325950 -1.149099 0.000000 0
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M V30 10 C -2.799150 0.559801 0.000000 0
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M V30 11 C -1.797349 2.268700 0.000000 0
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M V30 12 C 0.206250 2.268700 0.000000 0
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M V30 13 C 2.091950 -1.208099 0.000000 0
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M V30 14 C 1.679450 0.324100 0.000000 0
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M V30 15 C 2.916949 -0.383099 0.000000 0
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M V30 16 C 3.270550 -2.445598 0.000000 0
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M V30 17 C 2.858050 -3.977699 0.000000 0
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M V30 18 C 4.095549 -3.270598 0.000000 0
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M V30 19 C 0.795550 -1.856299 0.000000 0
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M V30 20 O -1.679449 -1.797299 0.000000 0
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M V30 21 O -0.913450 -1.797299 0.000000 0
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M V30 22 C -2.209849 -0.618799 0.000000 0
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M V30 23 C -2.799150 1.679401 0.000000 0
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M V30 24 C -3.800949 -0.029499 0.000000 0
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M V30 25 C -1.797349 3.388400 0.000000 0
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M V30 26 C 0.206250 3.388400 0.000000 0
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M V30 27 C 2.799049 -1.620598 0.000000 0
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M V30 28 C 2.386549 -0.088400 0.000000 0
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M V30 29 C 3.624049 -0.795599 0.000000 0
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M V30 30 C 3.977649 -2.033098 0.000000 0
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M V30 31 C 3.565149 -3.565199 0.000000 0
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M V30 32 C 4.802649 -2.858098 0.000000 0
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M V30 33 C 0.147350 -1.502699 0.000000 0
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M V30 34 C -3.800949 2.268700 0.000000 0
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M V30 35 C -4.802649 0.559801 0.000000 0
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M V30 36 C -0.795550 3.977699 0.000000 0
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M V30 37 C 2.386549 -0.913400 0.000000 0
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M V30 38 C 3.447349 -1.502699 0.000000 0
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M V30 39 C 3.211549 -0.088400 0.000000 0
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M V30 40 C 3.565149 -2.740199 0.000000 0
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M V30 41 C 4.625849 -2.150899 0.000000 0
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M V30 42 C 4.390149 -3.565199 0.000000 0
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M V30 43 C -0.500950 -1.856299 0.000000 0
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M V30 44 C -4.802649 1.679401 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 9 2 1
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M V30 2 9 3 1
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M V30 3 9 4 1
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M V30 4 9 5 1
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M V30 5 1 2 6
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M V30 6 1 2 7
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M V30 7 1 2 8
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M V30 8 1 3 9
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M V30 9 1 4 10
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M V30 10 1 5 11
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M V30 11 2 5 12
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M V30 12 1 6 13
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M V30 13 1 6 14
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M V30 14 1 6 15
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M V30 15 1 7 16
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M V30 16 1 7 17
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M V30 17 1 7 18
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M V30 18 1 8 19
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M V30 19 2 9 20
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M V30 20 2 9 21
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M V30 21 1 9 22
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M V30 22 2 10 23
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M V30 23 1 10 24
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M V30 24 2 11 25
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M V30 25 1 12 26
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M V30 26 1 13 27
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M V30 27 1 14 28
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M V30 28 1 15 29
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M V30 29 1 16 30
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M V30 30 1 17 31
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M V30 31 1 18 32
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M V30 32 1 19 33
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M V30 33 1 23 34
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M V30 34 2 24 35
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M V30 35 1 25 36
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M V30 36 1 27 37
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M V30 37 1 27 38
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M V30 38 1 28 39
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M V30 39 1 30 40
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M V30 40 1 30 41
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M V30 41 1 31 42
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M V30 42 1 33 43
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M V30 43 2 34 44
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M V30 44 1 11 23
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M V30 45 2 26 36
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M V30 46 1 28 37
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M V30 47 1 29 38
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M V30 48 1 29 39
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M V30 49 1 31 40
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M V30 50 1 32 41
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M V30 51 1 32 42
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M V30 52 1 35 44
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M V30 END BOND
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M V30 END CTAB
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M END
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