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>
92 lines
2.5 KiB
Plaintext
92 lines
2.5 KiB
Plaintext
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ChemDraw01202309472D
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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 39 40 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C 0.362289 1.072167 0.000000 0
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M V30 2 C 0.452886 -1.004770 0.000000 0
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M V30 3 P 1.192163 1.072167 0.000000 0
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M V30 4 P 1.273862 -1.004770 0.000000 0
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M V30 5 Pd 1.926941 0.065498 0.000000 0 CHG=2
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M V30 6 C 1.763647 1.675350 0.000000 0
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M V30 7 C 0.861074 -1.716948 0.000000 0
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M V30 8 C 1.845344 -1.580952 0.000000 0
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M V30 9 C 0.784076 1.820445 0.000000 0
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M V30 10 Cl 2.765817 -0.283791 0.000000 0 CHG=-1
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M V30 11 Cl 2.743217 0.437286 0.000000 0 CHG=-1
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M V30 12 C -0.045799 1.820445 0.000000 0
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M V30 13 C 0.035798 -1.716948 0.000000 0
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M V30 14 C 1.273862 -2.438027 0.000000 0
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M V30 15 C 1.654949 -2.370028 0.000000 0
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M V30 16 C 2.643421 -1.390458 0.000000 0
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M V30 17 C 2.561723 1.457655 0.000000 0
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M V30 18 C 1.573153 2.473426 0.000000 0
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M V30 19 C 1.192163 2.505225 0.000000 0
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M V30 20 C 2.265932 2.329830 0.000000 0
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M V30 21 C 0.371589 2.534923 0.000000 0
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M V30 22 C 2.428627 -2.164234 0.000000 0
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M V30 23 C -0.366190 1.459456 0.000000 0
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M V30 24 C -1.065769 1.022269 0.000000 0
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M V30 25 C -1.036969 0.197794 0.000000 0
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M V30 26 C -0.308591 -0.189495 0.000000 0
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M V30 27 C 0.391088 0.247693 0.000000 0
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M V30 28 C -0.043599 -0.345990 0.000000 0
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M V30 29 C -0.862374 -0.446486 0.000000 0
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M V30 30 C -1.184765 -1.206064 0.000000 0
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M V30 31 C -0.688280 -1.864744 0.000000 0
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M V30 32 C 0.753478 -2.534923 0.000000 0
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M V30 33 C 0.206594 -2.219133 0.000000 0
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M V30 34 N -1.861945 0.197794 0.000000 0
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M V30 35 N -2.003540 -1.306560 0.000000 0
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M V30 36 C -2.274432 -0.516685 0.000000 0
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M V30 37 C -2.274432 0.912173 0.000000 0
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M V30 38 C -2.325930 -2.066038 0.000000 0
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M V30 39 C -2.765817 -0.990870 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 3 1
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M V30 2 1 4 2
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M V30 3 1 6 3
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M V30 4 1 7 4
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M V30 5 1 8 4
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M V30 6 1 9 3
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M V30 7 9 10 5
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M V30 8 9 11 5
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M V30 9 1 12 9
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M V30 10 1 14 7
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M V30 11 1 15 8
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M V30 12 1 16 8
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M V30 13 1 17 6
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M V30 14 1 18 6
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M V30 15 1 19 9
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M V30 16 9 3 5
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M V30 17 9 4 5
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M V30 18 1 6 20
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M V30 19 1 9 21
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M V30 20 1 8 22
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M V30 21 1 23 24
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M V30 22 2 24 25
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M V30 23 1 25 26
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M V30 24 2 26 27
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M V30 25 1 27 1
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M V30 26 2 23 1
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M V30 27 1 28 29
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M V30 28 2 29 30
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M V30 29 1 30 31
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M V30 30 2 28 2
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M V30 31 2 31 13
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M V30 32 1 13 2
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M V30 33 1 7 32
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M V30 34 1 7 33
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M V30 35 1 25 34
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M V30 36 1 30 35
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M V30 37 1 34 36
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M V30 38 1 34 37
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M V30 39 1 35 38
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M V30 40 1 35 39
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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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