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>
125 lines
3.4 KiB
Plaintext
125 lines
3.4 KiB
Plaintext
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ChemDraw01182316342D
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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 53 59 0 0 0
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M V30 BEGIN ATOM
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M V30 1 O 1.091394 1.424894 0.000000 0 CHG=-1
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M V30 2 Pd 0.376898 1.837392 0.000000 0 CHG=2
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M V30 3 P 0.376898 0.517397 0.000000 0
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M V30 4 C 1.201894 0.517397 0.000000 0
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M V30 5 C 1.614392 1.231795 0.000000 0
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M V30 6 C 2.439389 1.231795 0.000000 0
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M V30 7 C 2.851887 0.517397 0.000000 0
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M V30 8 C 2.439389 -0.197098 0.000000 0
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M V30 9 C 1.614392 -0.197098 0.000000 0
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M V30 10 C 0.491997 -0.797596 0.000000 0
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M V30 11 C 1.288794 -0.584098 0.000000 0
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M V30 12 C 1.872191 -1.167495 0.000000 0
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M V30 13 C 1.658692 -1.964291 0.000000 0
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M V30 14 C 0.861796 -2.177890 0.000000 0
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M V30 15 C 0.278399 -1.594493 0.000000 0
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M V30 16 C -0.304898 -2.177890 0.000000 0
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M V30 17 C -0.091400 -2.974787 0.000000 0
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M V30 18 C 0.705496 -3.188287 0.000000 0
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M V30 19 C 1.288794 -2.604888 0.000000 0
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M V30 20 C 0.918995 -3.985182 0.000000 0
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M V30 21 C -0.674798 -3.558084 0.000000 0
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M V30 22 C -1.471694 -3.344585 0.000000 0
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M V30 23 C -2.054992 -3.927982 0.000000 0
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M V30 24 C -2.851887 -3.714384 0.000000 0
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M V30 25 C -1.841493 -4.724879 0.000000 0
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M V30 26 C -1.685193 -2.547689 0.000000 0
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M V30 27 C -1.101795 -1.964291 0.000000 0
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M V30 28 C -1.450494 -1.216594 0.000000 0
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M V30 29 C -2.272291 -1.144696 0.000000 0
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M V30 30 C -0.977296 -0.540798 0.000000 0
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M V30 31 C -0.444998 0.589298 0.000000 0
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M V30 32 C -0.918196 -0.086500 0.000000 0
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M V30 33 C -1.739993 -0.014600 0.000000 0
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M V30 34 C -2.088692 0.733097 0.000000 0
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M V30 35 C -1.615493 1.408894 0.000000 0
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M V30 36 C -0.793597 1.336994 0.000000 0
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M V30 37 C -0.337599 2.249890 0.000000 0 CHG=-1
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M V30 38 C -1.051996 1.837392 0.000000 0
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M V30 39 C -1.766493 2.249890 0.000000 0
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M V30 40 C -1.766493 3.074887 0.000000 0
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M V30 41 C -1.051996 3.487385 0.000000 0
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M V30 42 C -0.337599 3.074887 0.000000 0
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M V30 43 C 0.376898 3.487385 0.000000 0
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M V30 44 C 0.376898 4.312382 0.000000 0
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M V30 45 C 1.091394 4.724879 0.000000 0
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M V30 46 C 1.805892 4.312382 0.000000 0
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M V30 47 C 1.805892 3.487385 0.000000 0
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M V30 48 C 1.091394 3.074887 0.000000 0
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M V30 49 N 1.091394 2.249890 0.000000 0
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M V30 50 S 1.853592 1.740593 0.000000 0
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M V30 51 C 2.671488 1.848292 0.000000 0
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M V30 52 O 1.853592 2.565588 0.000000 0
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M V30 53 O 2.508089 2.242790 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 1 2
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M V30 2 9 3 2
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M V30 3 1 3 4
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M V30 4 1 4 5
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M V30 5 1 5 6
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M V30 6 1 6 7
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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 4 9
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M V30 10 1 3 10
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M V30 11 2 10 11
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M V30 12 1 11 12
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M V30 13 2 12 13
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M V30 14 1 13 14
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M V30 15 2 14 15
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M V30 16 1 10 15
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M V30 17 1 15 16
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M V30 18 2 16 17
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M V30 19 1 17 18
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M V30 20 1 18 19
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M V30 21 1 18 20
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M V30 22 1 17 21
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M V30 23 2 21 22
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M V30 24 1 22 23
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M V30 25 1 23 24
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M V30 26 1 23 25
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M V30 27 1 22 26
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M V30 28 2 26 27
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M V30 29 1 16 27
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M V30 30 1 27 28
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M V30 31 1 28 29
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M V30 32 1 28 30
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M V30 33 1 3 31
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M V30 34 1 31 32
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M V30 35 1 32 33
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M V30 36 1 33 34
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M V30 37 1 34 35
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M V30 38 1 35 36
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M V30 39 1 31 36
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M V30 40 9 37 2
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M V30 41 1 37 38
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M V30 42 2 38 39
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M V30 43 1 39 40
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M V30 44 2 40 41
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M V30 45 2 37 42
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M V30 46 1 41 42
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M V30 47 1 42 43
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M V30 48 2 43 44
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M V30 49 1 44 45
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M V30 50 2 45 46
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M V30 51 1 46 47
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M V30 52 2 47 48
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M V30 53 1 43 48
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M V30 54 1 48 49
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M V30 55 9 49 2
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M V30 56 1 1 50
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M V30 57 1 50 51
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M V30 58 2 50 52
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M V30 59 2 50 53
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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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