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>
178 lines
3.9 KiB
Plaintext
178 lines
3.9 KiB
Plaintext
MOL_00001
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Mrv2115 01282214052D
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0 0 0 0 0 999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 77 88 0 0 0
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M V30 BEGIN ATOM
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M V30 1 Pd 0 0 0 0
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M V30 2 P 7.0156 0 0 0
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M V30 3 P 0 6.16 0 0
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M V30 4 P -7.3578 0 0 0
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M V30 5 P 0 -6.3311 0 0
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M V30 6 C 7.0156 -1.54 0 0
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M V30 7 C 8.5556 0 0 0
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M V30 8 C 7.0156 1.54 0 0
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M V30 9 C 0 7.7 0 0
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M V30 10 C 1.54 6.16 0 0
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M V30 11 C -1.54 6.16 0 0
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M V30 12 C -7.3578 1.54 0 0
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M V30 13 C -8.8978 0 0 0
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M V30 14 C -7.3578 -1.54 0 0
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M V30 15 C -1.54 -6.3311 0 0
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M V30 16 C 1.54 -6.3311 0 0
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M V30 17 C 0 -7.8711 0 0
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M V30 18 C 5.6467 -2.2244 0 0
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M V30 19 C 8.3844 -2.3956 0 0
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M V30 20 C 9.4111 -1.3689 0 0
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M V30 21 C 9.24 1.3689 0 0
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M V30 22 C 8.3844 2.3956 0 0
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M V30 23 C 5.6467 2.2244 0 0
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M V30 24 C 1.3689 8.5556 0 0
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M V30 25 C -1.3689 8.3844 0 0
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M V30 26 C 2.3956 4.7911 0 0
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M V30 27 C 2.2244 7.5289 0 0
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M V30 28 C -2.2244 7.5289 0 0
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M V30 29 C -2.2244 4.7911 0 0
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M V30 30 C -5.9889 2.2244 0 0
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M V30 31 C -8.7267 2.3956 0 0
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M V30 32 C -9.5822 1.3689 0 0
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M V30 33 C -9.5822 -1.3689 0 0
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M V30 34 C -8.7267 -2.2244 0 0
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M V30 35 C -5.9889 -2.3956 0 0
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M V30 36 C -2.3956 -4.9622 0 0
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M V30 37 C -2.2244 -7.7 0 0
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M V30 38 C 2.3956 -7.7 0 0
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M V30 39 C 2.2244 -4.9622 0 0
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M V30 40 C -1.3689 -8.5556 0 0
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M V30 41 C 1.3689 -8.7267 0 0
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M V30 42 C 5.6467 -3.7644 0 0
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M V30 43 C 8.3844 -3.9356 0 0
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M V30 44 C 10.9511 -1.3689 0 0
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M V30 45 C 10.78 1.3689 0 0
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M V30 46 C 8.3844 3.9356 0 0
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M V30 47 C 5.6467 3.7644 0 0
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M V30 48 C 1.3689 10.0956 0 0
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M V30 49 C -1.3689 9.9244 0 0
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M V30 50 C 3.9356 4.7911 0 0
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M V30 51 C 3.7644 7.5289 0 0
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M V30 52 C -3.7644 7.5289 0 0
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M V30 53 C -3.7644 4.7911 0 0
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M V30 54 C -5.9889 3.7644 0 0
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M V30 55 C -8.7267 3.9356 0 0
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M V30 56 C -11.1222 1.3689 0 0
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M V30 57 C -11.1222 -1.3689 0 0
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M V30 58 C -8.7267 -3.7644 0 0
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M V30 59 C -5.9889 -3.9356 0 0
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M V30 60 C -3.9356 -4.9622 0 0
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M V30 61 C -3.7644 -7.7 0 0
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M V30 62 C 3.9356 -7.7 0 0
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M V30 63 C 3.7644 -4.9622 0 0
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M V30 64 C -1.3689 -10.0956 0 0
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M V30 65 C 1.3689 -10.2667 0 0
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M V30 66 C 7.0156 -4.62 0 0
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M V30 67 C 11.8067 0 0 0
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M V30 68 C 7.0156 4.7911 0 0
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M V30 69 C 0 10.9511 0 0
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M V30 70 C 4.62 6.16 0 0
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M V30 71 C -4.62 6.16 0 0
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M V30 72 C -7.3578 4.62 0 0
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M V30 73 C -11.9778 0 0 0
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M V30 74 C -7.3578 -4.62 0 0
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M V30 75 C -4.7911 -6.3311 0 0
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M V30 76 C 4.7911 -6.3311 0 0
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M V30 77 C 0 -10.9511 0 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 6
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M V30 2 1 2 7
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M V30 3 1 2 8
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M V30 4 1 3 9
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M V30 5 1 3 10
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M V30 6 1 3 11
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M V30 7 1 4 12
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M V30 8 1 4 13
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M V30 9 1 4 14
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M V30 10 1 5 15
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M V30 11 1 5 16
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M V30 12 1 5 17
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M V30 13 2 6 18
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M V30 14 1 6 19
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M V30 15 2 7 20
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M V30 16 1 7 21
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M V30 17 2 8 22
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M V30 18 1 8 23
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M V30 19 2 9 24
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M V30 20 1 9 25
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M V30 21 2 10 26
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M V30 22 1 10 27
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M V30 23 2 11 28
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M V30 24 1 11 29
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M V30 25 2 12 30
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M V30 26 1 12 31
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M V30 27 2 13 32
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M V30 28 1 13 33
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M V30 29 2 14 34
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M V30 30 1 14 35
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M V30 31 2 15 36
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M V30 32 1 15 37
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M V30 33 2 16 38
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M V30 34 1 16 39
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M V30 35 2 17 40
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M V30 36 1 17 41
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M V30 37 1 18 42
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M V30 38 2 19 43
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M V30 39 1 20 44
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M V30 40 2 21 45
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M V30 41 1 22 46
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M V30 42 2 23 47
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M V30 43 1 24 48
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M V30 44 2 25 49
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M V30 45 1 26 50
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M V30 46 2 27 51
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M V30 47 1 28 52
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M V30 48 2 29 53
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M V30 49 1 30 54
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M V30 50 2 31 55
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M V30 51 1 32 56
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M V30 52 2 33 57
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M V30 53 1 34 58
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M V30 54 2 35 59
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M V30 55 1 36 60
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M V30 56 2 37 61
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M V30 57 1 38 62
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M V30 58 2 39 63
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M V30 59 1 40 64
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M V30 60 2 41 65
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M V30 61 2 42 66
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M V30 62 2 44 67
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M V30 63 2 46 68
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M V30 64 2 48 69
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M V30 65 2 50 70
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M V30 66 2 52 71
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M V30 67 2 54 72
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M V30 68 2 56 73
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M V30 69 2 58 74
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M V30 70 2 60 75
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M V30 71 2 62 76
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M V30 72 2 64 77
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M V30 73 1 43 66
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M V30 74 1 45 67
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M V30 75 1 47 68
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M V30 76 1 49 69
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M V30 77 1 51 70
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M V30 78 1 53 71
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M V30 79 1 55 72
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M V30 80 1 57 73
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M V30 81 1 59 74
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M V30 82 1 61 75
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M V30 83 1 63 76
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M V30 84 1 65 77
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M V30 85 9 4 1
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M V30 86 9 3 1
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M V30 87 9 2 1
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M V30 88 9 5 1
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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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